BACKGROUND
fungal plant pathogens can be classified as biotrophic, necrotrophic or hemibiotrophic pathogens based on how they interact with their host.
biotrophic pathogens cause only minor responses from the plant, particularly at initial stages of the disease.
these biotrophic pathogens appear to evade plant defenses with stealthy methods  <cit> .
fungal biotrophs are often obligate pathogens, typically having narrow host ranges, possessing haustoria and secreting limited amounts of lytic enzymes  <cit> .
on the other hand, infection by necrotrophic pathogens causes rapid cell death in hosts and elicit major molecular responses from the plant.
necrotrophs appear to utilize brute force and overwhelm the plant defenses.
necrotrophs are typically non-obligate pathogens, have wide host ranges and secrete copious amounts of lytic enzymes and toxins  <cit> .
hemibiotrophs initiate infection with a period of biotrophy, followed by a necrotrophic phase, and they possess properties of both groups.
however, most of our understanding of how hemibiotrophs interact with their hosts is derived from these two extremes.
both biotrophic and necrotrophic fungi share common elements but these may have different purposes when causing disease.
during the host-interaction, the pathogens synthesize and secrete various peptides/proteins that block host responses  or kill the host cells .
among biotrophs, the rust fungus of flax, melampsora lini, excretes cysteine-rich avirulence elicitor proteins from the haustoria  <cit>  and the bean rust fungus uromyces fabae shows highly coordinated stage specific regulation of its secreted proteins  <cit> .
the necrotrophic fungus fusarium graminearum has  <dig> secreted cell wall degrading genes in its genome  <cit> , while alternaria species secrete non-host and host specific toxins that disrupt photosynthesis and kill plant cells  <cit> .
therefore, a detailed understanding of specific peptides/proteins secreted during the host-pathogen interaction is vital to elucidate the biotrophic and necrotrophic mechanisms.
moniliophthora roreri  h.c. evans, stalpers, samson & benny  <cit>  causes frosty pod rot , a devastating pod disease of theobroma cacao l. , the source of cocoa powder and cocoa butter.
phylogenetically, m. roreri is related to another fungal pathogen, moniliophthora perniciosa  aime and phillips-mora  <cit> , which causes witches’ broom disease , a disease that infects all cacao meristematic tissues including flowers, shoots, and pods  <cit> .
together, these pathogens cause two of the most economically important diseases of theobroma cacao in the western hemisphere  <cit> .
while both of these fungal species are pathogenic on the plant genera theobroma and herrania, m. roreri is not known to have any other hosts, whereas m. perniciosa has distinct biotypes that infect different host species  <cit> .
historically, these moniliophthora pathogens have spread independently to cacao producing areas across the western hemisphere and they have typically resulted in production losses of 75% or higher in nearly all the cacao growing regions in the americas  <cit> .
moniliophthora roreri and m. perniciosa are both hemibiotrophic pathogens, but have distinctive lifestyles and pathogenicity strategies.
unlike most other hemibiotrophic fungi, both moniliophthora species have protracted biotrophic stages or phases that last three to six weeks.
they also have distinctly different mycelial morphologies present at the beginning and the end of the disease process  <cit> .
in both moniliophthora diseases, the infected plant tissues are asymptomatic for  <dig> to  <dig> days.
after that period of time, these tissues typically begin to show some form of altered growth or swelling that continues for the remainder of the biotrophic phase, culminating with the necrosis of the host tissues, which marks the beginning of the necrotrophic phase.
in other hemibiotrophic fungi such as cladosporium fulvum, mycosphaerella graminicola, pyrenopeziza brassicae and septoria tritici, the biotrophic phase is asymptomatic with undifferentiated mycelia and lasts no more than two weeks  <cit> .
as with hemibiotrophic colletotrichum species, both m. roreri and m. perniciosa undergo distinct metabolic changes as they transition from the biotrophic phase to the necrotrophic phase of growth  <cit> .
these metabolic changes suggest significant shifts in gene expression and in enzymatic processes.
in this study we present the genome of m. roreri and compare it to the genome of the closely related cacao pathogen, m. perniciosa.
transcriptional analysis of the genome will focus on genes with putative signal peptides from the m. roreri genome and compare them with expressed genes, identified through rna sequencing of infected pods, to discover potential secreted proteins expressed during the disease process.
genes expressed in the early and late stages of fpr on pods were used to identify secreted genes that are potentially important during the biotrophic or necrotrophic phase of the disease cycle.
the results presented here are the first analyses of genes encoding secreted proteins derived from the m. roreri genome.
these new insights into the m. roreri genome, transcriptome and differential gene regulation provide a better understanding of the plant-pathogen interactions that occur during fpr.
RESULTS
genome structure
moniliophthora roreri has a genome size of  <dig>  mbp, which is  <dig>  mbp larger than the  <dig>  mbp found in the m. perniciosa genome .
despite the size difference, m. roreri had only  <dig> additional coding sequences  than m. perniciosa.
<dig>  coding sequences were detected in m. roreri.
the average gc% for the m. roreri genome  is lower than for the m. perniciosa genome ; however, the average g + c for the m. roreri cds is nearly identical to the value for m. perniciosa.
gene density for m. roreri was also found to be lower than for m. perniciosa.
m. roreri
and
m. perniciosa
*using trnascan default parameters yielded  <dig> contigs that have trna for a total of  <dig> trna’s.
#cds bases/total genome bases.
an analysis of the genomes of these pathogens has revealed that retro-transposons  contribute to about  <dig> %  of the m. roreri genome compared to about  <dig> %  in the m. perniciosa genome.
in m. perniciosa, transposable elements were reported to be active elements that may contribute to genetic variability of this pathogen  <cit> .
each genome was scanned for repetitive sequences and low complexity dna using the repeat modeler and repeatmasker programs.
m. roreri had  <dig> , <dig> bases associated with repeats and repetitive elements while m. perniciosa had  <dig> , <dig> bases associated with repeats and repetitive elements .
synteny
using a bi-directional blast with an e-value of e- <dig> as the cut-off value for two proteins being considered a match, a whole genome comparison of the predicted proteins between the m. roreri and m. perniciosa genomes was performed.
this analysis revealed that  <dig>  protein encoding genes  from m. roreri have sequence similarity to m. perniciosa protein encoding genes and  <dig>  protein encoding genes  from m. perniciosa have sequence similarity to m. roreri protein encoding genes.
at lower e-values, e- <dig> and e  <dig> , the m. roreri genome open reading frames  are 87% and 40% similar to the m. perniciosa genome orfs, respectively.
in m. roreri there are  <dig>  predicted genes or 49% that have no predicted function and are listed as hypothetical genes.
synteny between m. roreri and m. perniciosa was analyzed with the program mummer using the nucmer setting that compares the contigs from both genomes at the nucleotide level.
in this analysis, m. roreri contigs were queried using m. perniciosa contigs as the reference sequence.
contigs with high sequence identity resulted in a straight line graph, while translocations and inversions result in either a parallel shift in the line  or a line at a negative angle, respectively.
though both genomes are closely related at the nucleotide level, there are regions where inversions and translocations have potentially occurred.
this analysis confirms that these two genomes are very similar and most probably homologous, while it also shows that some regions in both genomes are unique.
due to the poor resolution of the mummer plot when all genome contigs were analyzed, we compared long intact regions of the genomes.
two hundred and fifty contigs from m. roreri and  <dig> contigs from m. perniciosa were compared that were at least 50 kb in length.
contigs with no corresponding sequence identity were eliminated, so that only contigs of high sequence identity between the two genomes were compared .
the results yielded a final comparison of  <dig> contigs from m. roreri and  <dig> contigs from m. perniciosa and showed highly similar sequences with slight shifts off the diagonal line, which indicate translocations in the contigs .
comparisons to other basidiomycete fungi
bidirectional blast analysis was conducted with m. roreri, m. perniciosa, laccaria bicolor, coprinopsis cinerea , and ustilago maydis.
these other genomes were selected because all are basidiomycetes but exhibit differing environmental adaptations representing a mushroom producing ectomycorrhizae a mushroom producing saprophyte and a pathogenic smut fungus, respectively.
figure  <dig> presents the venn-diagram of the analysis, and the tax plot is shown in table  <dig>  each of the five genomes is represented by an oval, and the numbers indicate how many genes are included within that intersect, at an e-value of e- <dig>  using this analysis, genes can be identified that are exclusive to a particular genome or to a particular group, which enables identification of putative similarities such as pathogenicity genes, and genus specific genes.
the number of predicted genes particular to a single genome is:  <dig>  for  m. roreri,  <dig>  for  m. perniciosa,  <dig>  for  l. bicolor,  <dig>  for  c. cinerea and  <dig>  for  u. maydis.
only seven of the  <dig>  m. roreri genes were detected by rna-seq analysis  and only  <dig> of the  <dig>  m. roreri genes have putative functions .
based on the annotation, several of these genes appear to have a role in genome integrity and function  while another set appears to be linked to retro elements .
the remaining genes have similarity to a mix of toxins ; heme binding ; cell adhesion ; pectin degradation ; possible oxidoreductases ; a putative cnvh-domain-containing protein and two capsule polysaccharide biosynthesis proteins.
the abcde intersection contains  <dig>  genes , which are common to all of these basidiomycetes, while there are  <dig> genes associated with abe and  <dig> with abc.
the moniliophthora intersect  has  <dig>  genes, of which only  <dig> or 8% have a putative function .
among the ab genes there are five antibiotic biosynthesis monooxygenases; five feruloyl esterases involved in hemicellulose degradation; four cellulose binding proteins; four cell wall glycosyl hydrolases, involved in cell wall sugar degradation; four chitin binding proteins; four het domain proteins associated with fungal vegetative incompatibility and mycelial cell death; three pectate lyases involved in pectin degradation; three family  <dig> carbohydrate esterases, a family that includes pectin acetylesterases, rhamnogalacturonan acetylesterases and acetyl xylan esterases; three biotrophy-associated secreted proteins that are putative effectors and  <dig> amidohydrolases, enzymes that act on amide bonds.
most of these ab intersect genes were constitutively expressed, but rna-seq data also showed differential gene expression for  <dig> genes, which are indicated in table  <dig> .
in the necrotrophic phase the following genes were upregulated: an antibiotic biosynthesis monooxygenase, two biotrophy-associated secreted proteins, a cellulose binding protein, a fad binding domain protein, an integral membrane protein, a lactam utilization protein, a lea domain-containing protein, a thaumatin-like protein, a transferase family protein and a urea hydro-lase cyanamide protein.
in the biotrophic phase a cell wall glycosyl hydrolase, a family  <dig> glycoside hydrolase and a nad binding phosphogluconate dehydrogenate-like protein were upregulated .
the pathogenic intersect  has  <dig> genes with known functions and these are shown in table  <dig>  the biotrophic intersect  has  <dig> genes with putative functions .
rna-seq data revealed that most of abc and abe intersect genes are constitutively expressed  at low to mid levels , with the exception of two genes from the abc intersect,  that were differentially expressed in the necrotrophic phase .
intersect
n indicates expression during the necrotrophic phase and b indicates expression during the biotrophic phase
identification of secreted proteins
because of the hemibiotrophic nature of m. roreri and the role that secreted proteins are expected to play in that interaction, we analyzed the genome for genes that express secreted proteins.
the first screening identified all of the putative proteins with signal peptides.
in m. roreri  <dig>  proteins  were found to have signal peptides, which is slightly lower than m. perniciosa which has  <dig>  proteins with signal peptides.
next the proteins with signal peptides were analyzed for transmembrane domains, to remove proteins that are expected to be incorporated into the membrane of the fungus.
ninety-two of the  <dig>  proteins have two or more transmembrane domains.
one hundred and twenty-five glycosylphosphatidylinositol  anchor proteins were also excluded from the list of secreted proteins .
while the gpi-anchored proteins are normally removed from secreted proteins, the posttranslational modification of glypiation is the only method of attachment to the membrane for these proteins, and because the bonds are subject to phospholipase cleavage, these proteins could still be released into the extracellular space via an enzymatic release process.
after removal of proteins with transmembrane and gpi moieties the total number of m. roreri secreted proteins was  <dig> , which is less than the  <dig>  secreted proteins predicted for m. perniciosa.
expression of the secretome
in this study we wanted to verify the expression of the predicted genes, including the secretome identified in the genome analysis.
we utilized a replicate set of infected pod tissues from a previous study to obtain transcriptomes representing the biotrophic and necrotrophic phases of the disease  <cit> .
while our present focus is on the secreted proteins, the complete fungal transcriptome, for fpr, in different resistant plant backgrounds will be addressed in a separate treatise.
the planting material used represents a segregating f <dig> population of progeny from highly susceptible clones .
briefly, the pods used in this study were derived from flowers hand-pollinated 60 days prior to infection with a spore suspension of 1×108m.
roreri spores ml- <dig>  the infected pods were frozen in liquid nitrogen and lyophilized at 30 days post infection  and at  <dig> dpi.
based on typical progression of fpr symptoms  <cit> , three malformed green pods were selected for rna-seq and rt-qpcr from  <dig> dpi pods  and three necrotic sporulating pods were selected for rna-seq and rt-qpcr from  <dig> dpi pods .
the  <dig> dpi pod samples yielded  <dig> ,927;  <dig> , <dig> and  <dig>   <dig>  reads and the number of fungal reads per sample were  <dig>  ,  <dig>   and  <dig>  , respectively.
for the  <dig> dpi pod samples  <dig> ,363;  <dig> , <dig> and  <dig> , <dig> reads were sequenced, with fungal reads accounting for  <dig>  ,  <dig>   and  <dig>  , respectively.
when all of the libraries were compared  <dig>  genes  from the m. roreri genome were found to be expressed in these infected pods.
the secreted proteins were then separated from the other expressed genes.
among the  <dig>  secreted protein genes identified  <dig>  or 88%, were expressed at some level under the tested conditions.
using a p-value of  <dig> , we found that  <dig> of the secreted protein genes were differentially expressed between the  <dig> dpi and  <dig> dpi pods.
all of the expressed secreted protein genes are listed in additional file  <dig>  the data revealed phase-dependent differential gene expression, where  <dig> of the genes were up-regulated in the  <dig> dpi pods while  <dig> were upregulated in the  <dig> dpi pods.
since the hypothetical genes can provided no information regarding their putative function they were eliminated from further consideration with regards to their role in the disease process.
genes expressed during the early stages of infection and disease development reflect gene products that function in the biotrophic phase of the disease development, which can be initially asymptomatic.
late-stage gene expression yields gene products that function in the necrotrophic phase, which is associated with pod chlorosis and necrosis, and possibly with sporulation of the fungus on pod tissue.
to validate the differential expression of genes encoding secreted proteins as suggested by the rna-seq analysis, rt-qpcr was conducted, with a selected number of genes comparing expression in a set of seven malformed green pods at  <dig> dpi and seven necrotic pods at  <dig> dpi.
at  <dig> dpi,  <dig> genes encoding secreted proteins with putative functions were expressed, with one being expressed only at this stage .
at  <dig> dpi,  <dig> genes encoding predicted secreted proteins with putative functions were expressed .
forty-one of the  <dig>  <dig> dpi genes were detected only in the necrotrophic phase.
rt-qpcr confirmed the up-regulation of the  <dig> dpi and  <dig> dpi genes .
although the gpi-anchored proteins were removed from the secretome we did find a number of them highly expressed in both the biotrophic and necrotrophic phases.
table  <dig> provides a list of the most highly expressed genes encoding gpi-anchored proteins in both phases since controlled release of these proteins from the fungal membrane is possible.
mean* is the normalized mean based on the size factor of the libraries.
mean* is the normalized mean based on the size factor of the libraries.
mean* is the normalized mean based on the size factor of the libraries.
several gene families of secreted proteins were prominently upregulated in the biotrophic phase.
in this phase the  <dig> genes with known functions were primarily associated with nutrient acquisition and with plant and fungal cell wall modification.
the largest single group identified was glycoside hydrolases .
eleven glycoside hydrolases genes were upregulated: two genes from gh family 5; five genes from gh family 18; and one gene each from the gh families  <dig>   <dig>   <dig>   <dig>  the gh family  <dig> genes are homologous to chitinase genes   <cit>  and gh family  <dig> genes are endo-enzymes that are capable of hydrolyzing both β-mannans and β-glucans  <cit>  and are homologous to beta- <dig> -glucanase, which includes endoglucanase, beta-mannanase, exo- <dig> -glucanase, endo- <dig> -glucanase, xylanase, and endoglycoceramidase.
the gh 16 s are homologous to endobeta  <dig> -glucanases  and xyloglucan:xylogluosyltransferase   <cit> , gh 28 s are homologous to polygalacturonases and includes pectin degrading enzymes like polygalacturonase , exopolygalacturonase , exo-poly-α-galacturonosidase   <cit> , gh 43 s are homologous to beta-xylosidases   <cit> , while the gh 92 s are alpha- <dig> –mannosidases  <cit>  .
in addition to the ghs, other enzymes were identified such as galactose-1-epimerase, a carbonic anhydrase, a family  <dig> carbohydrate esterase , and a tryptophan dimethylally transferase.
the plant cell wall-modifying enzymes identified in the biotrophic phase include an endo-polygalacturonase, a galactan  <dig> -beta-galactosidase, a cell wall glycosyl hydrolase, a catalase, an acetylxylan esterase and a xylanase a. additionally, three cerato-platanin genes, two hydrophobins, three pr-1-like proteins, and an immunomodulatory protein were all induced in the biotrophic phase that could be involved in the fungal host interaction .
based on rna-seq and verified by rt-qpcr analysis, the majority of the genes within the  <dig> genes expressed during the necrotrophic phase are associated with fungal growth/pathogenicity and nutrient acquisition.
several genes families were identified with multiple expressed genes such as hydrophobins , fad binding domain containing proteins , aryl-alcohol oxidases , laccases , extracellular triacylglycerol lipases  and cerato-platanins .
several of these highly upregulated genes are associated with lignin breakdown.
the aryl-alcohol oxidases  are fad containing extracellular enzymes in the glucose-methanol choline oxidase  family  <cit> .
aaos are involved in lignin degradation where the enzyme interacts with p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol polymers that make up the lignin, and o <dig> yielding aromatic aldehydes and hydrogen peroxide  <cit> .
laccases are polyphenol oxidases that reduce phenolic compounds in lignin  <cit> .
glyoxal oxidases are extracellular enzymes that form hydrogen peroxide during the breakdown of lignin  <cit> .
eight gh families were identified among the  <dig> gh genes .
the gh 35 s proteins are homologous to beta-galactosidases and gh 61 s proteins are homologous to endoglucanases.
the gh 3 s proteins are homologous to beta–glucosidases; gh 9 s proteins are endoglucanases or cellulases; and gh 10s proteins are xylanases  <cit> .
numerous other enzymes and pathogenicity-related genes were identified such as carboxypeptidases, carbohydrate esterases, tripeptidyl peptidase, a necrosis inducing protein, a fungal peroxidase, cytochrome p450s, and expansins.
the highest relative expressions were found for a dioxygenase, a fbox and fnip repeat-containing protein, a chitin synthase, a proline-rich antigen and one of the expansins .
several gene families were found to be differently regulated and had specific members upregulated in the biotrophic phase and others upregulated in the necrotrophic phase.
of the  <dig> hydrophobin genes found in the genome,  <dig> were differentially expressed;  <dig> were upregulated in the necrotrophic phase; two in the biotrophic phase.
among the eight cerato-platanin genes found in the genome six were differentially upregulated; three in each phase.
the expression of genes encoding fungal-derived pathogenesis-related proteins was detected in samples from the biotrophic phase, with mrpr-1n, mrpr-1 g and mrpr-1i <dig> being upregulated.
among the other nine genes encoding pr-1-like proteins found in the m. roreri genome, one mrpr-1d was upregulated in the necrotrophic phase and five were constitutively expressed under the tested conditions .
discussion
genome comparison
we have produced a high-quality draft genome of m. roreri using different next-generation sequencing technologies.
after sequence assembly using the whole genome shotgun  strategy, a total of  <dig>  contigs with a n <dig> value of  <dig>  kb was assembled with a total genome size calculated to be  <dig>  mbp.
although larger, the m. roreri genome is structurally and organizationally similar to m. perniciosa, a sister taxa with a draft genome consisting of  <dig>  contigs  and a genome size of  <dig>  mbp.
the majority of the size difference between the genomes is associated with repetitive dna.
the m. roreri genome size is larger than the genome of m. perniciosa, but the number of genes located in each genome is similar.
one factor for the size difference between m. roreri and m. perniciosa is highly correlated to the difference in the number of long terminal repeat–transposable elements  between the genomes.
about  <dig>  mbp or approximately 7% of the m. roreri genome is attributed to ltr-tes located in the genome, while only  <dig>  mbp or about 1% of the m. perniciosa genome is attributed to ltr-tes.
transposable elements  contribute no more than  <dig> to 15% in most fungal taxa  <cit> .
for example, the saccharomyces cereviseae genome contains  <dig> % tes  <cit> , the magnaporthe oryzae genome ranges from  <dig> -14%  <cit> , while 24% of the laccaria bicolor genome is transposon derived  <cit> .
within the m. perniciosa genome these repetitive elements are active and appear to contribute to the genetic variability of the species  <cit> .
another factor contributing to the size difference between the genomes is associated with repetitive elements and low complexity dna.
m. roreri genome has four times as many repetitive elements  as found in the m. perniciosa genome .
the classification and biological roles of these repetitive sequences and transposable elements in m. roreri are beyond the scope of this discussion but will be explored in depth in a separate treatise.
the high degree of similarity between m. roreri and m. perniciosa genomes supports their taxonomic relatedness, while distinctions have been identified that could contribute to their distinctive functional and morphologic differences.
bidirectional blast analysis of m. roreri with four other basidiomycetes revealed a set of  <dig>  genes specific to m. roreri.
the majority of these genes are hypothetical with only  <dig> genes having known homologies and most of these relate to tes.
expression analysis of the a gene set  revealed that only seven of these genes are expressed and all at low levels.
among the genes encoding hypothetical proteins that are specific to m. roreri,  <dig> were constitutively expressed and only three were differentially expressed in both the biotrophic and necrotrophic phases .
low to mid-level constitutive expression in genes from the abe and abc intersects  suggest that these genes are used in general functions common to the sampled basidiomycetes such as metabolism.
the differential expression of the  <dig> genes shared by m. roreri and m. perniciosa  in the biotrophic and necrotrophic phases, as expression of these genes suggests similarities in the hemibiotrophic life cycle of these species.
secretome targeting the plant cell
rna-seq, was used to validate the genome cds through transcriptome expression analysis of m. roreri infected cacao pods at  <dig> dpi and  <dig> dpi.
these two sampling points compare genes expressed in the early stage or biotrophic phase and the late stage or necrotrophic phase of the fpr disease cycle.
in silico analysis of genes with signal peptides, which have a high likelihood of being transported outside of the fungus, yielded  <dig>  genes expressed at some level in the  <dig> and  <dig> dpi samples, as detected by rna-seq.
only  <dig> of these genes were differentially expressed between the biotrophic and necrotrophic phases, using a p-value of  <dig> .
the similarities in gene expression between the two phases are greater than the dissimilarities.
for example, genes encoding plant cell wall-degrading cellulases were not upregulated in the biotrophic phase, but, their expression was detected.
although the functions of many of these genes are unknown their expression raises the potential that they serve critical roles in the m. roreri life cycle.
many of the known secreted protein encoding genes that were upregulated in the biotrophic phase encode for putative glycoside hydrolases  that act on oligosaccharides making up the plant cell wall.
of the  <dig> differentially expressed secreted protein genes associated with the biotrophic phase,  <dig> were glycoside hydrolases from six families of hydrolases, which enables m. roreri to interact with the different biochemical components of plant cell walls.
this diverse array of polysaccharide degrading enzymes could function together with other hemicelluloses-degrading enzymes, such as those that hydrolyze xylan.
all of these polysaccharide degrading enzymes appear to work in concert to loosen the connections between the plant cells, releasing nutrients that can be utilized by the fungus.
pectin is another major component of the intercellular matrix of the cacao pod husk  <cit> .
m. perniciosa, the causal agent of wbd on cacao, has been observed to express genes for pectin lyase and pectin methylesterases during infection of parthenocarpic pods  <cit> .
in fpr, pectin is also under attack during the biotrophic phase of m. roreri.
genes encoding pectin degrading enzymes are upregulated in this phase.
the biotrophic phase of m. roreri is a complex stage requiring controlled cell wall degradation and modification, allowing the invasion of the pod while the fungus remains substantially undetected by plant defenses.
all of the m. roreri genes encoding plant cell wall enzymes that are induced in the biotrophic phase are able to attack the matrix of the intercellular space.
this interaction likely facilitates penetration and spread of the fungus between cells without eliciting major responses from the plant.
in contrast, the expression pattern of genes encoding secreted proteins during the necrotrophic phase of m. roreri suggest a more aggressive breakdown of plant structures and the upregulation of aryl-alcohol oxidases, laccases, and a glyoxal oxidase gene during the necrotrophic phase suggests that m. roreri, targets lignin for breakdown during the necrotrophic phase.
this evidence is further supported by the fact that three of the four aryl alcohol oxidases and three of the four laccases genes are exclusively expressed during the necrotrophic phase   <cit> .
there are other upregulated enzymes that may also have a role in these ligninolytic reactions such as a fungal peroxidase, a copper amine oxidase and two dioxygenases.
fungal peroxidases were induced in m. perniciosa under nutrient limited conditions  <cit> , while intradiol dioxygenase was shown to be induced in m. roreri during necrotrophy in a prior study  <cit> .
similar to the biotrophic phase, eight glycoside hydrolase  families were also induced in the necrotrophic phase.
although the specific details concerning the exact function of these gh families of genes are lacking, it is interesting to note the differential expression patterns between the biotrophic and necrotrophic phases.
gh families shared with the biotrophic phase include families  <dig>   <dig> and  <dig>  gh families  <dig>   <dig> and  <dig> are unique to the biotrophic phase, whereas families  <dig>   <dig>   <dig>   <dig>  and  <dig> are unique to the necrotrophic phase.
the gh families unique to the necrotrophic phase include enzymes involved in the degradation of plant cell walls into compounds that the fungus can consume.
complex stage-specific regulation of genes targeting plant cell walls in association with the biotroph/necrotroph shift was also observed in hemibiotrophic colletotrichum species  <cit> .
the differential expression of genes with seemingly related functions provides the opportunity to fine tune aspects of growth and development to the changing conditions and requirements of the two phases of fpr.
other cell surface-modifying enzymes upregulated in the necrotrophic phase are triacylglycerol lipase precursors and a cutinase suggesting lipid breakdown and modification of the protective surfaces of the plant cells.
a necrosis inducing-like protein  that could be responsible for cell death and nutrient leakage was also found to be up-regulated  <cit> .
nlps have been identified in many pathogenic associations such as wbd and other biotrophic interactions  <cit> .
two genes from another class of virulence genes, biotrophy-associated secreted proteins bas  are highly expressed in the m. roreri necrotrophic phase.
these effector proteins have been shown to accumulate in the biotrophic interface region for the ascomycete magnaporthe grisea <cit> ; however, their roles in the necrotrophic phase of this interaction are yet to be determined.
at the same time in the necrotrophic phase, multiple extracellular peptidases are being upregulated possibly in response to the proteins and peptides that are now available from the necrotic plant cells  <cit> .
specific activities of m. roreri associated with the necrotrophic phase appear to target cell wall and membrane breakdown in associations with enzymes that are linked with the switch of this fungus from biotrophic to necrotrophic phase.
the differentially expressed secretome of the necrotroph suggests conditions for rapid growth of the fungus, where plant lignocellulosic cell walls are being degraded and multiple plant components are being released and are available to be used by the fungus as nutrients.
the need for stealth has been removed and nutrient acquisition is predominantly to support the rapid growth associated with the necrotrophic phase  <cit> .
secretome targeting modification of the fungal cell wall
there is no evidence that haustoria or other cell wall-penetrating structures are formed during the biotrophic phase of m. roreri.
the slow-growing m. roreri mycelia of the biotrophic phase are large pleomorphic cells that fill the spaces between the plant cells  <cit> .
this abnormal mycelial growth habit does have some similarity to haustoria-like structures, although they are outside the cell wall and, possibly provide the fungus with more surface area for cell-to-cell interactions and exchange of metabolites.
the necrotrophic mycelia are profuse and grow rapidly in necrotic tissues  <cit> .
these mycelia are thin and elongated.
the sporophores and resulting spores represent a second fungal morphology associated with the necrotrophic phase.
genes encoding proteins that are functional in and on the fungal cell wall were differentially expressed between the phases of fpr.
often unique members of the same gene family were differentially expressed.
chitin synthesis and modification
there were five differentially expressed family  <dig> glycoside hydrolases associated with the biotrophic phase and one associated with the necrotrophic phase.
these chitinolytic enzymes could be modifying the chitin structure and the surface of the mycelia.
these modifications could protect the mycelia from plant defenses such as plant chitinases  <cit> , thus allowing the fungus to grow intercellularly.
several chitinases are highly expressed in cacao pod tissues throughout development, and can be hyper-induced in response to m. roreri infection  <cit> .
another possibility is that the chitinases attack chitin oligosaccharides released from the fungus, after being attacked by plant chitinases.
additional extracellular chitinases could help eliminate these chitin oligosaccharides and prevent the elicitation of plant defense responses  <cit> .
a chitin deacetylase and a chitin synthase were highly upregulated in the necrotrophic phase.
the induction of chitin synthase is consistent with the rapid growth of the fungus initiated during the necrotrophic phase.
the chitin deacetylase and related enzymes like exo-beta-glucanases and family  <dig> carbohydrate esterases can modify chitin, either loosening the chitin polymer bonds or converting the chitin to chitosan.
like the rust fungus uromyces viciae-faba <cit> , m. roreri may use chitin deacetylase and other enzymes to modify its own cell wall reducing the effectiveness of the plant enzymes.
a resistant wall structure may be particularly important in the harsh environment created as plant tissues die.
although cacao defense genes were induced in the later stages of the biotrophic phase of fpr, their induction levels continued to increase once the necrotrophic phase has been initiated  <cit> .
pr- <dig> related proteins
pathogenesis–related  <dig> proteins  are a class of plant genes induced by pathogens during the infection stage and they are partially responsible for systemic acquired resistance responses in those plants.
it is of particular interest that plant-like defense proteins would be found in a pathogen and within two species of the same fungal genus.
of the  <dig> pr- <dig> related genes identified in the m. roreri genome,  <dig> have homology to pr- <dig> genes recently described in moniliophthora perniciosa <cit> .
three of these pr-1-like proteins are upregulated during the biotrophic phase, five are constitutively expressed and only mrpr-1d was upregulated in the necrotrophic phase.
all of the mrpr-1-like proteins have the scp/taps-like conserved domains .
the mrpr- <dig> g and mrpr-1a match the expression of their homologs in the biotrophic phase of m. perniciosa <cit> .
also of interest is the c-terminal extension of the mrpr-1g protein, which is found in both m. perniciosa and m. roreri and could have a specific protein–protein mediated function as purposed by teixeira et al.,  <cit> .
the mrpr-1b homolog was constitutively expressed in m. roreri, which differs from the case of m. perniciosa where it was upregulated in the necrotrophic phase.
while the exact function of these pr- <dig> proteins in fungi is unknown, these fungal-derived pr- <dig> like proteins may be masking the fungal cell wall from plant defense mechanisms, or they may bind to them preventing their activity.
riviere et al.,  <cit>  demonstrated that pr-1a proteins in tobacco plants regulate the extracellular enzyme activity of β--glucanase activity and plants with pr- <dig> silenced genes had higher enzyme levels along with a decrease in the deposition of β- glucans and callose.
callose deposition in the cell-wall sheath around the plasmodesmata openings is a dynamic regulator mechanism that appears to alter the size of the plasmodesmata orifice, which in turn can modify cell to cell transport by restricting the size of transport molecules  <cit> .
previous work has shown that m. roreri infected cacao pods at  <dig> dpi have a  <dig>  to  <dig> fold reduction in glucose, phenylalanine and asparagine levels  <cit> , which suggests the fungus has access to these plant metabolites, despite being limited to the intercellular spaces.
during the necrotrophic phase  most pod metabolites are severely depleted.
the m. roreri mycelia, which grow between plant cells, may have access to the plasmodesmata passages and the nutrients that pass through them.
the pr- <dig> like proteins appear to be important to virulence, and it has been suggested that they support systemic spread of the fungus, possibly by limiting susceptibility to host defenses, or they may act as effectors suppressing host defenses  <cit> .
the phase specific expression of the different pr- <dig> encoding genes is interesting, particularly because of the difference in the host interactions of the biotroph and necrotroph.
the pr- <dig> proteins expressed by m. roreri in the different phases could be acting to alter the plant cell walls or as competitive inhibitors of plant pr- <dig> proteins, thus minimizing the plant defense response, or they could have antimicrobial activity, which would function to prevent subsequent infection and development of competing microorganisms.
hydrophobins
of the  <dig> hydrophobins found in the genome, three members of the hydrophobin gene family are up-regulated in the biotrophic phase and  <dig> members are up regulated in the necrotrophic phase.
the hydrophobins interact at the fungal cell surface creating a hydrophobic surface layer and are important in many morphogenetic processes such as sporulation, fruiting body formation and infection structures  <cit> .
hydrophobins are grouped into three classes ia, ib, and ii, with ia and ii occurring in ascomycetes and ib in basidiomycetes  <cit> .
these proteins have the unique ability to self assemble once secreted and they function at the fungal wall-air interface, limiting desiccation and providing protection against both chemical and enzymatic attack  <cit> .
it is easy to postulate the need for different hydrophobins between the two phases of fpr, considering the need to limit detection in the biotrophic phase and the need to protect the surface from enzymatic and chemical attack in the necrotrophic phase.
in animal systems at least, hydrophobins are known to prevent host recognition of pathogen-associated molecular patterns, thus preventing the activation of host immune response  <cit> .
hydrophobins are also of interest because of their potential uses in industrial processes  <cit> .
cerato-platanins and related proteins
three cerato-platanin  genes are up-regulated in the biotroph and four are upregulated in the necrotroph.
cerato-platanin domain-containing proteins such as epl , snodprot, swollenins and expansins have a double ψβ-barrel fold and a carbohydrate binding site that have been shown to induce plant defense response  <cit> .
cerato-platanins can cause nutrient leakage and cell death in cacao  <cit> .
ectopic expression of the magnaporthe grisea cp gene, mgsm <dig>  upregulates the expression of plant defense genes such as pr- <dig>  pr- <dig> and pdf <dig>  and induces local hyper-sensitivity reactions   <cit> .
this class of fungal proteins is called elicitors or effector proteins.
a fungal effector protein found in colletotrichum truncatum  is expressed during the infection stage  <cit> .
unlike the mgms <dig> protein, ctcp <dig> does not cause hr or elicit a plant defense response,  <cit>  demonstrating that the activity of cerato-platanins can be both host and protein specific.
an epl gene from trichoderma species produces a protein that binds to chitin and self assembles at the air/water interface like a hydrophobin  <cit> .
when msp <dig>  a snodprot <dig> homolog protein, was knocked out in magnaporthe oryzae, the fungus was unable to grow within the plant after normal infection suggesting this protein has a key function during the intercellular growth of this fungus  <cit> .
other cp-family proteins such as snodprot <dig> homologs are expressed in ecotomycorrhizal fungi pisolithus microcarpus and laccaria bicolor <cit> , suggesting a role for this family of genes during the plant fungal interaction.
two expansins were upregulated in the necrotrophic phase of this study.
expansins were first discovered in plants, due to their role in developmental processes involving cell wall modifications, including cell enlargement, by “loosening” plant cell walls  <cit> .
a functional expansin family protein was reported in the basidiomycete bjerkandera adusta <cit> , and expansin-like proteins have been reported in other fungi, including plant pathogens.
brotman et al.
<cit>  reported swollenin, an expansin family protein, in trichoderma that is involved in colonization of plant roots and apparently elicits plant-defense responses.
the expansin-like and cerato-platanin proteins may be involved in invasion and pathogenesis of plant tissues by phytopathogens that employ penetration of host/susceptible tissues.
since members of the cerato-platanin family are highly expressed in both phases of fpr, it further supports scenarios in which the fungus uses unique members of complex gene families to facilitate growth and spreading under the conditions unique to each phase.
another indicator of the biotrophic/necrotrophic switch is the upregulation of several genes in the necrotrophic phase that are associated with fungal reproduction such as the heterokaryon incompatibility protein, a fruiting body-specific gene and a riboflavin aldehyde-forming enzyme.
the reproductive stage of the fungus occurs after the necrotrophic phase and is a nutrient intensive process  <cit> .
cytochrome p450s and hydrophobins have been previously found in necrotic cacao pods infected with fpr  <cit>  and have been shown to be expressed during fungal reproduction, specifically in the fruiting body development  <cit> .
however, unlike most basidiomycetes, m. roreri has lost the ability to form a basdiocarp or mushroom and sporulates directly from the mycelial mat that it forms on the diseased pod  <cit> .
CONCLUSIONS
the m. roreri genome and expression analyses provide insight into the molecular mechanisms of the biotrophic and necrotrophic phases of this important hemibiotrophic pathogen.
rna-seq analysis revealed differential gene expression during the biotrophic and necrotrophic phases of m. roreri during the development of fpr disease of cacao.
focusing on the secreted proteins found in this genome, we observed specific secreted proteins putatively involved in plant cell wall degradation in the biotrophic phase, which seem to degrade and utilize the intercellular spaces.
at the same time, they appear to be masking or modifying the fungal cell surface to avoid plant defenses, allowing the fungus to colonize the pod.
in contrast, other secreted proteins upregulated in the necrotrophic phase suggest that the fungus continues to protect its mycelia from plant defenses, while actively releasing enzymes and toxins that have been reported to attack the plant cell wall components and utilizing plant nutrients that are released during plant cell death.
these findings support the existing pathogenesis model for fpr while giving greater details regarding the identity of putative secreted proteins involved in the different stages, and information regarding the differential use of unique members of complex gene families.
due to the high number of genes that encode hypothetical proteins in this genome and that are expressed during the disease process more research is needed to fully understand the various phases of this hemibiotrophic fungus.

 fungal plant pathogens can be classified as biotrophic, necrotrophic or hemibiotrophic pathogens based on how they interact with their host. biotrophic pathogens cause only minor responses from the plant, particularly at initial stages of the disease. these biotrophic pathogens appear to evade plant defenses with stealthy methods. fungal biotrophs are often obligate pathogens, typically having narrow host ranges, possessing haustoria and secreting limited amounts of lytic enzymes. on the other hand, infection by necrotrophic pathogens causes rapid cell death in hosts and elicit major molecular responses from the plant. necrotrophs appear to utilize brute force and overwhelm the plant defenses. necrotrophs are typically non-obligate pathogens, have wide host ranges and secrete copious amounts of lytic enzymes and toxins. hemibiotrophs initiate infection with a period of biotrophy, followed by a necrotrophic phase, and they possess properties of both groups. however, most of our understanding of how hemibiotrophs interact with their hosts is derived from these two extremes. both biotrophic and necrotrophic fungi share common elements but these may have different purposes when causing disease. during the host-interaction, the pathogens synthesize and secrete various peptides/proteins that block host responses or kill the host cells. among biotrophs, the rust fungus of flax, melampsora lini, excretes cysteine-rich avirulence elicitor proteins from the haustoria and the bean rust fungus uromyces fabae shows highly coordinated stage specific regulation of its secreted proteins. the necrotrophic fungus fusarium graminearum has secreted cell wall degrading genes in its genome, while alternaria species secrete non-host and host specific toxins that disrupt photosynthesis and kill plant cells. therefore, a detailed understanding of specific peptides/proteins secreted during the host-pathogen interaction is vital to elucidate the biotrophic and necrotrophic mechanisms. moniliophthora roreri h.c. evans, stalpers, samson & benny causes frosty pod rot, a devastating pod disease of theobroma cacao l., the source of cocoa powder and cocoa butter. phylogenetically, m. roreri is related to another fungal pathogen, moniliophthora perniciosa aime and phillips-mora, which causes witches’ broom disease, a disease that infects all cacao meristematic tissues including flowers, shoots, and pods. together, these pathogens cause two of the most economically important diseases of theobroma cacao in the western hemisphere. while both of these fungal species are pathogenic on the plant genera theobroma and herrania, m. roreri is not known to have any other hosts, whereas m. perniciosa has distinct biotypes that infect different host species. historically, these moniliophthora pathogens have spread independently to cacao producing areas across the western hemisphere and they have typically resulted in production losses of 75% or higher in nearly all the cacao growing regions in the americas. moniliophthora roreri and m. perniciosa are both hemibiotrophic pathogens, but have distinctive lifestyles and pathogenicity strategies. unlike most other hemibiotrophic fungi, both moniliophthora species have protracted biotrophic stages or phases that last three to six weeks. they also have distinctly different mycelial morphologies present at the beginning and the end of the disease process. in both moniliophthora diseases, the infected plant tissues are asymptomatic for to days. after that period of time, these tissues typically begin to show some form of altered growth or swelling that continues for the remainder of the biotrophic phase, culminating with the necrosis of the host tissues, which marks the beginning of the necrotrophic phase. in other hemibiotrophic fungi such as cladosporium fulvum, mycosphaerella graminicola, pyrenopeziza brassicae and septoria tritici, the biotrophic phase is asymptomatic with undifferentiated mycelia and lasts no more than two weeks. as with hemibiotrophic colletotrichum species, both m. roreri and m. perniciosa undergo distinct metabolic changes as they transition from the biotrophic phase to the necrotrophic phase of growth. these metabolic changes suggest significant shifts in gene expression and in enzymatic processes. in this study we present the genome of m. roreri and compare it to the genome of the closely related cacao pathogen, m. perniciosa. transcriptional analysis of the genome will focus on genes with putative signal peptides from the m. roreri genome and compare them with expressed genes, identified through rna sequencing of infected pods, to discover potential secreted proteins expressed during the disease process. genes expressed in the early and late stages of fpr on pods were used to identify secreted genes that are potentially important during the biotrophic or necrotrophic phase of the disease cycle. the results presented here are the first analyses of genes encoding secreted proteins derived from the m. roreri genome. these new insights into the m. roreri genome, transcriptome and differential gene regulation provide a better understanding of the plant-pathogen interactions that occur during fpr.  genome structure moniliophthora roreri has a genome size of mbp, which is mbp larger than the mbp found in the m. perniciosa genome. despite the size difference, m. roreri had only additional coding sequences than m. perniciosa. coding sequences were detected in m. roreri. the average gc% for the m. roreri genome is lower than for the m. perniciosa genome; however, the average g + c for the m. roreri cds is nearly identical to the value for m. perniciosa. gene density for m. roreri was also found to be lower than for m. perniciosa. m. roreri and m. perniciosa *using trnascan default parameters yielded contigs that have trna for a total of trna’s. #cds bases/total genome bases. an analysis of the genomes of these pathogens has revealed that retro-transposons contribute to about % of the m. roreri genome compared to about % in the m. perniciosa genome. in m. perniciosa, transposable elements were reported to be active elements that may contribute to genetic variability of this pathogen. each genome was scanned for repetitive sequences and low complexity dna using the repeat modeler and repeatmasker programs. m. roreri had, bases associated with repeats and repetitive elements while m. perniciosa had, bases associated with repeats and repetitive elements. synteny using a bi-directional blast with an e-value of e- as the cut-off value for two proteins being considered a match, a whole genome comparison of the predicted proteins between the m. roreri and m. perniciosa genomes was performed. this analysis revealed that protein encoding genes from m. roreri have sequence similarity to m. perniciosa protein encoding genes and protein encoding genes from m. perniciosa have sequence similarity to m. roreri protein encoding genes. at lower e-values, e- and e, the m. roreri genome open reading frames are 87% and 40% similar to the m. perniciosa genome orfs, respectively. in m. roreri there are predicted genes or 49% that have no predicted function and are listed as hypothetical genes. synteny between m. roreri and m. perniciosa was analyzed with the program mummer using the nucmer setting that compares the contigs from both genomes at the nucleotide level. in this analysis, m. roreri contigs were queried using m. perniciosa contigs as the reference sequence. contigs with high sequence identity resulted in a straight line graph, while translocations and inversions result in either a parallel shift in the line or a line at a negative angle, respectively. though both genomes are closely related at the nucleotide level, there are regions where inversions and translocations have potentially occurred. this analysis confirms that these two genomes are very similar and most probably homologous, while it also shows that some regions in both genomes are unique. due to the poor resolution of the mummer plot when all genome contigs were analyzed, we compared long intact regions of the genomes. two hundred and fifty contigs from m. roreri and contigs from m. perniciosa were compared that were at least 50 kb in length. contigs with no corresponding sequence identity were eliminated, so that only contigs of high sequence identity between the two genomes were compared. the results yielded a final comparison of contigs from m. roreri and contigs from m. perniciosa and showed highly similar sequences with slight shifts off the diagonal line, which indicate translocations in the contigs. comparisons to other basidiomycete fungi bidirectional blast analysis was conducted with m. roreri, m. perniciosa, laccaria bicolor, coprinopsis cinerea, and ustilago maydis. these other genomes were selected because all are basidiomycetes but exhibit differing environmental adaptations representing a mushroom producing ectomycorrhizae a mushroom producing saprophyte and a pathogenic smut fungus, respectively. figure  presents the venn-diagram of the analysis, and the tax plot is shown in table  each of the five genomes is represented by an oval, and the numbers indicate how many genes are included within that intersect, at an e-value of e- using this analysis, genes can be identified that are exclusive to a particular genome or to a particular group, which enables identification of putative similarities such as pathogenicity genes, and genus specific genes. the number of predicted genes particular to a single genome is: for m. roreri, for m. perniciosa, for l. bicolor, for c. cinerea and for u. maydis. only seven of the  m. roreri genes were detected by rna-seq analysis and only of the  m. roreri genes have putative functions. based on the annotation, several of these genes appear to have a role in genome integrity and function while another set appears to be linked to retro elements. the remaining genes have similarity to a mix of toxins; heme binding; cell adhesion; pectin degradation; possible oxidoreductases; a putative cnvh-domain-containing protein and two capsule polysaccharide biosynthesis proteins. the abcde intersection contains genes, which are common to all of these basidiomycetes, while there are genes associated with abe and with abc. the moniliophthora intersect has genes, of which only or 8% have a putative function. among the ab genes there are five antibiotic biosynthesis monooxygenases; five feruloyl esterases involved in hemicellulose degradation; four cellulose binding proteins; four cell wall glycosyl hydrolases, involved in cell wall sugar degradation; four chitin binding proteins; four het domain proteins associated with fungal vegetative incompatibility and mycelial cell death; three pectate lyases involved in pectin degradation; three family carbohydrate esterases, a family that includes pectin acetylesterases, rhamnogalacturonan acetylesterases and acetyl xylan esterases; three biotrophy-associated secreted proteins that are putative effectors and amidohydrolases, enzymes that act on amide bonds. most of these ab intersect genes were constitutively expressed, but rna-seq data also showed differential gene expression for genes, which are indicated in table . in the necrotrophic phase the following genes were upregulated: an antibiotic biosynthesis monooxygenase, two biotrophy-associated secreted proteins, a cellulose binding protein, a fad binding domain protein, an integral membrane protein, a lactam utilization protein, a lea domain-containing protein, a thaumatin-like protein, a transferase family protein and a urea hydro-lase cyanamide protein. in the biotrophic phase a cell wall glycosyl hydrolase, a family glycoside hydrolase and a nad binding phosphogluconate dehydrogenate-like protein were upregulated. the pathogenic intersect has genes with known functions and these are shown in table  the biotrophic intersect has genes with putative functions. rna-seq data revealed that most of abc and abe intersect genes are constitutively expressed at low to mid levels, with the exception of two genes from the abc intersect, that were differentially expressed in the necrotrophic phase. intersect n indicates expression during the necrotrophic phase and b indicates expression during the biotrophic phase identification of secreted proteins because of the hemibiotrophic nature of m. roreri and the role that secreted proteins are expected to play in that interaction, we analyzed the genome for genes that express secreted proteins. the first screening identified all of the putative proteins with signal peptides. in m. roreri proteins were found to have signal peptides, which is slightly lower than m. perniciosa which has proteins with signal peptides. next the proteins with signal peptides were analyzed for transmembrane domains, to remove proteins that are expected to be incorporated into the membrane of the fungus. ninety-two of the proteins have two or more transmembrane domains. one hundred and twenty-five glycosylphosphatidylinositol anchor proteins were also excluded from the list of secreted proteins. while the gpi-anchored proteins are normally removed from secreted proteins, the posttranslational modification of glypiation is the only method of attachment to the membrane for these proteins, and because the bonds are subject to phospholipase cleavage, these proteins could still be released into the extracellular space via an enzymatic release process. after removal of proteins with transmembrane and gpi moieties the total number of m. roreri secreted proteins was, which is less than the secreted proteins predicted for m. perniciosa. expression of the secretome in this study we wanted to verify the expression of the predicted genes, including the secretome identified in the genome analysis. we utilized a replicate set of infected pod tissues from a previous study to obtain transcriptomes representing the biotrophic and necrotrophic phases of the disease. while our present focus is on the secreted proteins, the complete fungal transcriptome, for fpr, in different resistant plant backgrounds will be addressed in a separate treatise. the planting material used represents a segregating f population of progeny from highly susceptible clones. briefly, the pods used in this study were derived from flowers hand-pollinated 60 days prior to infection with a spore suspension of 1×108m. roreri spores ml- the infected pods were frozen in liquid nitrogen and lyophilized at 30 days post infection and at dpi. based on typical progression of fpr symptoms, three malformed green pods were selected for rna-seq and rt-qpcr from dpi pods and three necrotic sporulating pods were selected for rna-seq and rt-qpcr from dpi pods. the dpi pod samples yielded,927;, and reads and the number of fungal reads per sample were, and, respectively. for the dpi pod samples,363;, and, reads were sequenced, with fungal reads accounting for, and, respectively. when all of the libraries were compared genes from the m. roreri genome were found to be expressed in these infected pods. the secreted proteins were then separated from the other expressed genes. among the secreted protein genes identified or 88%, were expressed at some level under the tested conditions. using a p-value of, we found that of the secreted protein genes were differentially expressed between the dpi and dpi pods. all of the expressed secreted protein genes are listed in additional file the data revealed phase-dependent differential gene expression, where of the genes were up-regulated in the dpi pods while were upregulated in the dpi pods. since the hypothetical genes can provided no information regarding their putative function they were eliminated from further consideration with regards to their role in the disease process. genes expressed during the early stages of infection and disease development reflect gene products that function in the biotrophic phase of the disease development, which can be initially asymptomatic. late-stage gene expression yields gene products that function in the necrotrophic phase, which is associated with pod chlorosis and necrosis, and possibly with sporulation of the fungus on pod tissue. to validate the differential expression of genes encoding secreted proteins as suggested by the rna-seq analysis, rt-qpcr was conducted, with a selected number of genes comparing expression in a set of seven malformed green pods at dpi and seven necrotic pods at dpi. at dpi, genes encoding secreted proteins with putative functions were expressed, with one being expressed only at this stage. at dpi, genes encoding predicted secreted proteins with putative functions were expressed. forty-one of the dpi genes were detected only in the necrotrophic phase. rt-qpcr confirmed the up-regulation of the dpi and dpi genes. although the gpi-anchored proteins were removed from the secretome we did find a number of them highly expressed in both the biotrophic and necrotrophic phases. table  provides a list of the most highly expressed genes encoding gpi-anchored proteins in both phases since controlled release of these proteins from the fungal membrane is possible. mean* is the normalized mean based on the size factor of the libraries. mean* is the normalized mean based on the size factor of the libraries. mean* is the normalized mean based on the size factor of the libraries. several gene families of secreted proteins were prominently upregulated in the biotrophic phase. in this phase the genes with known functions were primarily associated with nutrient acquisition and with plant and fungal cell wall modification. the largest single group identified was glycoside hydrolases. eleven glycoside hydrolases genes were upregulated: two genes from gh family 5; five genes from gh family 18; and one gene each from the gh families the gh family genes are homologous to chitinase genes and gh family genes are endo-enzymes that are capable of hydrolyzing both β-mannans and β-glucans and are homologous to beta- -glucanase, which includes endoglucanase, beta-mannanase, exo- -glucanase, endo- -glucanase, xylanase, and endoglycoceramidase. the gh 16 s are homologous to endobeta -glucanases and xyloglucan:xylogluosyltransferase, gh 28 s are homologous to polygalacturonases and includes pectin degrading enzymes like polygalacturonase, exopolygalacturonase, exo-poly-α-galacturonosidase, gh 43 s are homologous to beta-xylosidases, while the gh 92 s are alpha- –mannosidases. in addition to the ghs, other enzymes were identified such as galactose-1-epimerase, a carbonic anhydrase, a family carbohydrate esterase, and a tryptophan dimethylally transferase. the plant cell wall-modifying enzymes identified in the biotrophic phase include an endo-polygalacturonase, a galactan -beta-galactosidase, a cell wall glycosyl hydrolase, a catalase, an acetylxylan esterase and a xylanase a. additionally, three cerato-platanin genes, two hydrophobins, three pr-1-like proteins, and an immunomodulatory protein were all induced in the biotrophic phase that could be involved in the fungal host interaction. based on rna-seq and verified by rt-qpcr analysis, the majority of the genes within the genes expressed during the necrotrophic phase are associated with fungal growth/pathogenicity and nutrient acquisition. several genes families were identified with multiple expressed genes such as hydrophobins, fad binding domain containing proteins, aryl-alcohol oxidases, laccases, extracellular triacylglycerol lipases and cerato-platanins. several of these highly upregulated genes are associated with lignin breakdown. the aryl-alcohol oxidases are fad containing extracellular enzymes in the glucose-methanol choline oxidase family. aaos are involved in lignin degradation where the enzyme interacts with p-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol polymers that make up the lignin, and o yielding aromatic aldehydes and hydrogen peroxide. laccases are polyphenol oxidases that reduce phenolic compounds in lignin. glyoxal oxidases are extracellular enzymes that form hydrogen peroxide during the breakdown of lignin. eight gh families were identified among the gh genes. the gh 35 s proteins are homologous to beta-galactosidases and gh 61 s proteins are homologous to endoglucanases. the gh 3 s proteins are homologous to beta–glucosidases; gh 9 s proteins are endoglucanases or cellulases; and gh 10s proteins are xylanases. numerous other enzymes and pathogenicity-related genes were identified such as carboxypeptidases, carbohydrate esterases, tripeptidyl peptidase, a necrosis inducing protein, a fungal peroxidase, cytochrome p450s, and expansins. the highest relative expressions were found for a dioxygenase, a fbox and fnip repeat-containing protein, a chitin synthase, a proline-rich antigen and one of the expansins. several gene families were found to be differently regulated and had specific members upregulated in the biotrophic phase and others upregulated in the necrotrophic phase. of the hydrophobin genes found in the genome, were differentially expressed; were upregulated in the necrotrophic phase; two in the biotrophic phase. among the eight cerato-platanin genes found in the genome six were differentially upregulated; three in each phase. the expression of genes encoding fungal-derived pathogenesis-related proteins was detected in samples from the biotrophic phase, with mrpr-1n, mrpr-1 g and mrpr-1i being upregulated. among the other nine genes encoding pr-1-like proteins found in the m. roreri genome, one mrpr-1d was upregulated in the necrotrophic phase and five were constitutively expressed under the tested conditions. discussion genome comparison we have produced a high-quality draft genome of m. roreri using different next-generation sequencing technologies. after sequence assembly using the whole genome shotgun strategy, a total of contigs with a n value of  kb was assembled with a total genome size calculated to be mbp. although larger, the m. roreri genome is structurally and organizationally similar to m. perniciosa, a sister taxa with a draft genome consisting of contigs and a genome size of mbp. the majority of the size difference between the genomes is associated with repetitive dna. the m. roreri genome size is larger than the genome of m. perniciosa, but the number of genes located in each genome is similar. one factor for the size difference between m. roreri and m. perniciosa is highly correlated to the difference in the number of long terminal repeat–transposable elements between the genomes. about mbp or approximately 7% of the m. roreri genome is attributed to ltr-tes located in the genome, while only mbp or about 1% of the m. perniciosa genome is attributed to ltr-tes. transposable elements contribute no more than to 15% in most fungal taxa. for example, the saccharomyces cereviseae genome contains % tes, the magnaporthe oryzae genome ranges from -14%, while 24% of the laccaria bicolor genome is transposon derived. within the m. perniciosa genome these repetitive elements are active and appear to contribute to the genetic variability of the species. another factor contributing to the size difference between the genomes is associated with repetitive elements and low complexity dna. m. roreri genome has four times as many repetitive elements as found in the m. perniciosa genome. the classification and biological roles of these repetitive sequences and transposable elements in m. roreri are beyond the scope of this discussion but will be explored in depth in a separate treatise. the high degree of similarity between m. roreri and m. perniciosa genomes supports their taxonomic relatedness, while distinctions have been identified that could contribute to their distinctive functional and morphologic differences. bidirectional blast analysis of m. roreri with four other basidiomycetes revealed a set of genes specific to m. roreri. the majority of these genes are hypothetical with only genes having known homologies and most of these relate to tes. expression analysis of the a gene set revealed that only seven of these genes are expressed and all at low levels. among the genes encoding hypothetical proteins that are specific to m. roreri, were constitutively expressed and only three were differentially expressed in both the biotrophic and necrotrophic phases. low to mid-level constitutive expression in genes from the abe and abc intersects suggest that these genes are used in general functions common to the sampled basidiomycetes such as metabolism. the differential expression of the genes shared by m. roreri and m. perniciosa in the biotrophic and necrotrophic phases, as expression of these genes suggests similarities in the hemibiotrophic life cycle of these species. secretome targeting the plant cell rna-seq, was used to validate the genome cds through transcriptome expression analysis of m. roreri infected cacao pods at dpi and dpi. these two sampling points compare genes expressed in the early stage or biotrophic phase and the late stage or necrotrophic phase of the fpr disease cycle. in silico analysis of genes with signal peptides, which have a high likelihood of being transported outside of the fungus, yielded genes expressed at some level in the and dpi samples, as detected by rna-seq. only of these genes were differentially expressed between the biotrophic and necrotrophic phases, using a p-value of. the similarities in gene expression between the two phases are greater than the dissimilarities. for example, genes encoding plant cell wall-degrading cellulases were not upregulated in the biotrophic phase, but, their expression was detected. although the functions of many of these genes are unknown their expression raises the potential that they serve critical roles in the m. roreri life cycle. many of the known secreted protein encoding genes that were upregulated in the biotrophic phase encode for putative glycoside hydrolases that act on oligosaccharides making up the plant cell wall. of the differentially expressed secreted protein genes associated with the biotrophic phase, were glycoside hydrolases from six families of hydrolases, which enables m. roreri to interact with the different biochemical components of plant cell walls. this diverse array of polysaccharide degrading enzymes could function together with other hemicelluloses-degrading enzymes, such as those that hydrolyze xylan. all of these polysaccharide degrading enzymes appear to work in concert to loosen the connections between the plant cells, releasing nutrients that can be utilized by the fungus. pectin is another major component of the intercellular matrix of the cacao pod husk. m. perniciosa, the causal agent of wbd on cacao, has been observed to express genes for pectin lyase and pectin methylesterases during infection of parthenocarpic pods. in fpr, pectin is also under attack during the biotrophic phase of m. roreri. genes encoding pectin degrading enzymes are upregulated in this phase. the biotrophic phase of m. roreri is a complex stage requiring controlled cell wall degradation and modification, allowing the invasion of the pod while the fungus remains substantially undetected by plant defenses. all of the m. roreri genes encoding plant cell wall enzymes that are induced in the biotrophic phase are able to attack the matrix of the intercellular space. this interaction likely facilitates penetration and spread of the fungus between cells without eliciting major responses from the plant. in contrast, the expression pattern of genes encoding secreted proteins during the necrotrophic phase of m. roreri suggest a more aggressive breakdown of plant structures and the upregulation of aryl-alcohol oxidases, laccases, and a glyoxal oxidase gene during the necrotrophic phase suggests that m. roreri, targets lignin for breakdown during the necrotrophic phase. this evidence is further supported by the fact that three of the four aryl alcohol oxidases and three of the four laccases genes are exclusively expressed during the necrotrophic phase. there are other upregulated enzymes that may also have a role in these ligninolytic reactions such as a fungal peroxidase, a copper amine oxidase and two dioxygenases. fungal peroxidases were induced in m. perniciosa under nutrient limited conditions, while intradiol dioxygenase was shown to be induced in m. roreri during necrotrophy in a prior study. similar to the biotrophic phase, eight glycoside hydrolase families were also induced in the necrotrophic phase. although the specific details concerning the exact function of these gh families of genes are lacking, it is interesting to note the differential expression patterns between the biotrophic and necrotrophic phases. gh families shared with the biotrophic phase include families and gh families and are unique to the biotrophic phase, whereas families and are unique to the necrotrophic phase. the gh families unique to the necrotrophic phase include enzymes involved in the degradation of plant cell walls into compounds that the fungus can consume. complex stage-specific regulation of genes targeting plant cell walls in association with the biotroph/necrotroph shift was also observed in hemibiotrophic colletotrichum species. the differential expression of genes with seemingly related functions provides the opportunity to fine tune aspects of growth and development to the changing conditions and requirements of the two phases of fpr. other cell surface-modifying enzymes upregulated in the necrotrophic phase are triacylglycerol lipase precursors and a cutinase suggesting lipid breakdown and modification of the protective surfaces of the plant cells. a necrosis inducing-like protein that could be responsible for cell death and nutrient leakage was also found to be up-regulated. nlps have been identified in many pathogenic associations such as wbd and other biotrophic interactions. two genes from another class of virulence genes, biotrophy-associated secreted proteins bas are highly expressed in the m. roreri necrotrophic phase. these effector proteins have been shown to accumulate in the biotrophic interface region for the ascomycete magnaporthe grisea; however, their roles in the necrotrophic phase of this interaction are yet to be determined. at the same time in the necrotrophic phase, multiple extracellular peptidases are being upregulated possibly in response to the proteins and peptides that are now available from the necrotic plant cells. specific activities of m. roreri associated with the necrotrophic phase appear to target cell wall and membrane breakdown in associations with enzymes that are linked with the switch of this fungus from biotrophic to necrotrophic phase. the differentially expressed secretome of the necrotroph suggests conditions for rapid growth of the fungus, where plant lignocellulosic cell walls are being degraded and multiple plant components are being released and are available to be used by the fungus as nutrients. the need for stealth has been removed and nutrient acquisition is predominantly to support the rapid growth associated with the necrotrophic phase. secretome targeting modification of the fungal cell wall there is no evidence that haustoria or other cell wall-penetrating structures are formed during the biotrophic phase of m. roreri. the slow-growing m. roreri mycelia of the biotrophic phase are large pleomorphic cells that fill the spaces between the plant cells. this abnormal mycelial growth habit does have some similarity to haustoria-like structures, although they are outside the cell wall and, possibly provide the fungus with more surface area for cell-to-cell interactions and exchange of metabolites. the necrotrophic mycelia are profuse and grow rapidly in necrotic tissues. these mycelia are thin and elongated. the sporophores and resulting spores represent a second fungal morphology associated with the necrotrophic phase. genes encoding proteins that are functional in and on the fungal cell wall were differentially expressed between the phases of fpr. often unique members of the same gene family were differentially expressed. chitin synthesis and modification there were five differentially expressed family glycoside hydrolases associated with the biotrophic phase and one associated with the necrotrophic phase. these chitinolytic enzymes could be modifying the chitin structure and the surface of the mycelia. these modifications could protect the mycelia from plant defenses such as plant chitinases, thus allowing the fungus to grow intercellularly. several chitinases are highly expressed in cacao pod tissues throughout development, and can be hyper-induced in response to m. roreri infection. another possibility is that the chitinases attack chitin oligosaccharides released from the fungus, after being attacked by plant chitinases. additional extracellular chitinases could help eliminate these chitin oligosaccharides and prevent the elicitation of plant defense responses. a chitin deacetylase and a chitin synthase were highly upregulated in the necrotrophic phase. the induction of chitin synthase is consistent with the rapid growth of the fungus initiated during the necrotrophic phase. the chitin deacetylase and related enzymes like exo-beta-glucanases and family carbohydrate esterases can modify chitin, either loosening the chitin polymer bonds or converting the chitin to chitosan. like the rust fungus uromyces viciae-faba, m. roreri may use chitin deacetylase and other enzymes to modify its own cell wall reducing the effectiveness of the plant enzymes. a resistant wall structure may be particularly important in the harsh environment created as plant tissues die. although cacao defense genes were induced in the later stages of the biotrophic phase of fpr, their induction levels continued to increase once the necrotrophic phase has been initiated. pr- related proteins pathogenesis–related proteins are a class of plant genes induced by pathogens during the infection stage and they are partially responsible for systemic acquired resistance responses in those plants. it is of particular interest that plant-like defense proteins would be found in a pathogen and within two species of the same fungal genus. of the pr- related genes identified in the m. roreri genome, have homology to pr- genes recently described in moniliophthora perniciosa. three of these pr-1-like proteins are upregulated during the biotrophic phase, five are constitutively expressed and only mrpr-1d was upregulated in the necrotrophic phase. all of the mrpr-1-like proteins have the scp/taps-like conserved domains. the mrpr- g and mrpr-1a match the expression of their homologs in the biotrophic phase of m. perniciosa. also of interest is the c-terminal extension of the mrpr-1g protein, which is found in both m. perniciosa and m. roreri and could have a specific protein–protein mediated function as purposed by teixeira et al.,. the mrpr-1b homolog was constitutively expressed in m. roreri, which differs from the case of m. perniciosa where it was upregulated in the necrotrophic phase. while the exact function of these pr- proteins in fungi is unknown, these fungal-derived pr- like proteins may be masking the fungal cell wall from plant defense mechanisms, or they may bind to them preventing their activity. riviere et al., demonstrated that pr-1a proteins in tobacco plants regulate the extracellular enzyme activity of β--glucanase activity and plants with pr- silenced genes had higher enzyme levels along with a decrease in the deposition of β- glucans and callose. callose deposition in the cell-wall sheath around the plasmodesmata openings is a dynamic regulator mechanism that appears to alter the size of the plasmodesmata orifice, which in turn can modify cell to cell transport by restricting the size of transport molecules. previous work has shown that m. roreri infected cacao pods at dpi have a to fold reduction in glucose, phenylalanine and asparagine levels, which suggests the fungus has access to these plant metabolites, despite being limited to the intercellular spaces. during the necrotrophic phase most pod metabolites are severely depleted. the m. roreri mycelia, which grow between plant cells, may have access to the plasmodesmata passages and the nutrients that pass through them. the pr- like proteins appear to be important to virulence, and it has been suggested that they support systemic spread of the fungus, possibly by limiting susceptibility to host defenses, or they may act as effectors suppressing host defenses. the phase specific expression of the different pr- encoding genes is interesting, particularly because of the difference in the host interactions of the biotroph and necrotroph. the pr- proteins expressed by m. roreri in the different phases could be acting to alter the plant cell walls or as competitive inhibitors of plant pr- proteins, thus minimizing the plant defense response, or they could have antimicrobial activity, which would function to prevent subsequent infection and development of competing microorganisms. hydrophobins of the hydrophobins found in the genome, three members of the hydrophobin gene family are up-regulated in the biotrophic phase and members are up regulated in the necrotrophic phase. the hydrophobins interact at the fungal cell surface creating a hydrophobic surface layer and are important in many morphogenetic processes such as sporulation, fruiting body formation and infection structures. hydrophobins are grouped into three classes ia, ib, and ii, with ia and ii occurring in ascomycetes and ib in basidiomycetes. these proteins have the unique ability to self assemble once secreted and they function at the fungal wall-air interface, limiting desiccation and providing protection against both chemical and enzymatic attack. it is easy to postulate the need for different hydrophobins between the two phases of fpr, considering the need to limit detection in the biotrophic phase and the need to protect the surface from enzymatic and chemical attack in the necrotrophic phase. in animal systems at least, hydrophobins are known to prevent host recognition of pathogen-associated molecular patterns, thus preventing the activation of host immune response. hydrophobins are also of interest because of their potential uses in industrial processes. cerato-platanins and related proteins three cerato-platanin genes are up-regulated in the biotroph and four are upregulated in the necrotroph. cerato-platanin domain-containing proteins such as epl, snodprot, swollenins and expansins have a double ψβ-barrel fold and a carbohydrate binding site that have been shown to induce plant defense response. cerato-platanins can cause nutrient leakage and cell death in cacao. ectopic expression of the magnaporthe grisea cp gene, mgsm upregulates the expression of plant defense genes such as pr- pr- and pdf and induces local hyper-sensitivity reactions. this class of fungal proteins is called elicitors or effector proteins. a fungal effector protein found in colletotrichum truncatum is expressed during the infection stage. unlike the mgms protein, ctcp does not cause hr or elicit a plant defense response, demonstrating that the activity of cerato-platanins can be both host and protein specific. an epl gene from trichoderma species produces a protein that binds to chitin and self assembles at the air/water interface like a hydrophobin. when msp a snodprot homolog protein, was knocked out in magnaporthe oryzae, the fungus was unable to grow within the plant after normal infection suggesting this protein has a key function during the intercellular growth of this fungus. other cp-family proteins such as snodprot homologs are expressed in ecotomycorrhizal fungi pisolithus microcarpus and laccaria bicolor, suggesting a role for this family of genes during the plant fungal interaction. two expansins were upregulated in the necrotrophic phase of this study. expansins were first discovered in plants, due to their role in developmental processes involving cell wall modifications, including cell enlargement, by “loosening” plant cell walls. a functional expansin family protein was reported in the basidiomycete bjerkandera adusta, and expansin-like proteins have been reported in other fungi, including plant pathogens. brotman et al. reported swollenin, an expansin family protein, in trichoderma that is involved in colonization of plant roots and apparently elicits plant-defense responses. the expansin-like and cerato-platanin proteins may be involved in invasion and pathogenesis of plant tissues by phytopathogens that employ penetration of host/susceptible tissues. since members of the cerato-platanin family are highly expressed in both phases of fpr, it further supports scenarios in which the fungus uses unique members of complex gene families to facilitate growth and spreading under the conditions unique to each phase. another indicator of the biotrophic/necrotrophic switch is the upregulation of several genes in the necrotrophic phase that are associated with fungal reproduction such as the heterokaryon incompatibility protein, a fruiting body-specific gene and a riboflavin aldehyde-forming enzyme. the reproductive stage of the fungus occurs after the necrotrophic phase and is a nutrient intensive process. cytochrome p450s and hydrophobins have been previously found in necrotic cacao pods infected with fpr and have been shown to be expressed during fungal reproduction, specifically in the fruiting body development. however, unlike most basidiomycetes, m. roreri has lost the ability to form a basdiocarp or mushroom and sporulates directly from the mycelial mat that it forms on the diseased pod.  the m. roreri genome and expression analyses provide insight into the molecular mechanisms of the biotrophic and necrotrophic phases of this important hemibiotrophic pathogen. rna-seq analysis revealed differential gene expression during the biotrophic and necrotrophic phases of m. roreri during the development of fpr disease of cacao. focusing on the secreted proteins found in this genome, we observed specific secreted proteins putatively involved in plant cell wall degradation in the biotrophic phase, which seem to degrade and utilize the intercellular spaces. at the same time, they appear to be masking or modifying the fungal cell surface to avoid plant defenses, allowing the fungus to colonize the pod. in contrast, other secreted proteins upregulated in the necrotrophic phase suggest that the fungus continues to protect its mycelia from plant defenses, while actively releasing enzymes and toxins that have been reported to attack the plant cell wall components and utilizing plant nutrients that are released during plant cell death. these findings support the existing pathogenesis model for fpr while giving greater details regarding the identity of putative secreted proteins involved in the different stages, and information regarding the differential use of unique members of complex gene families. due to the high number of genes that encode hypothetical proteins in this genome and that are expressed during the disease process more research is needed to fully understand the various phases of this hemibiotrophic fungus. 
we sequenced and assembled mb into contigs that represent the m. roreri genome. of the predicted open reading frames, were validated by rna-seq. analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase. analysis of rna-seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. this hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp. using read count data from rna sequencing of cacao pods at and days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. the secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. of the genes encoding putative secreted proteins, were expressed in the biotrophic and necrotrophic phases. based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. the basidiomycete moniliophthora roreri is the causal agent of frosty pod rot disease of cacao, the source of chocolate, and fpr is one of the most destructive diseases of this important perennial crop in the americas. high sequence identity between moniliophthora roreri genes and moniliophthora perniciosa genes supports the taxonomic relationship with moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes.
 the basidiomycete moniliophthora roreri is the causal agent of frosty pod rot disease of cacao, the source of chocolate, and fpr is one of the most destructive diseases of this important perennial crop in the americas. this hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.  we sequenced and assembled mb into contigs that represent the m. roreri genome. of the predicted open reading frames, were validated by rna-seq. using read count data from rna sequencing of cacao pods at and days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. the sequencing data were used to develop a genome based secretome for the infected pods. of the genes encoding putative secreted proteins, were expressed in the biotrophic and necrotrophic phases. analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.  genome sequencing and rna-seq was used to determine and validate the moniliophthora roreri genome and secretome. high sequence identity between moniliophthora roreri genes and moniliophthora perniciosa genes supports the taxonomic relationship with moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. analysis of rna-seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. the secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. these genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease. 