BACKGROUND
the fungal genus sporothrix includes about  <dig> species found on all inhabited continents mainly occurring as environmental saprobes, living in association with plants or decaying matter.
one lineage within the genus is composed of at least four pathogenic species associated with human and animal sporotrichosis: sporothrix schenckii sensu stricto, s. brasiliensis, s. globosa, and s. luriei
.
subcutaneous infections caused by s. schenckii are globally endemic  <cit> .
additionally, outbreaks have been described from south africa, australia, china and india .
during the last two decades, an ongoing zoonotic outbreak of sporotrichosis has been observed in brazil.
initially thought to be caused by sporothrix schenckii, detailed studies demonstrated that most outbreak isolates were actually s. brasiliensis
<cit> .
sporothricosis is classically associated with rural activities such as agriculture, floriculture or hunting, but more recently felines have emerged as source of human infection.
the most common clinical form is a chronic subcutaneous/lymphocutaneous disease acquired after inoculation of fungal material into the skin.
extracutaneous and disseminated forms secondary to cutaneous infection have been described in patients who are immunocompromised as a result of aids, chronic alcoholism and diabetes  <cit> .
rarely, severe cases involving pulmonary infection are noted  <cit> .
the pathogens of the genus sporothrix exhibit a thermo-dimorphic phenotype: in its saprophytic stage or in in vitro culture at 25°c the fungus grows with its filamentous form characterized by hyaline, septate hyphae with sympodial conidiogenous cells that produce two types of spores: hyaline conidia that form clusters and brown, thick-walled spores that are distributed perpendicularly alongside the hyphae.
during the parasitic stage, the fungus is found as cigar-shaped yeast cells that can also be obtained in vitro by switching the temperature to 37°c  <cit> .
this dimorphism is essential for virulence in the mammalian host  <cit>  and is also found in other human pathogenic fungi such as blastomyces dermatitidis, b. gilchristii, histoplasma capsulatum, paracoccidioides brasiliensis, p. lutzii, coccidioides immitis and c. posadasi.
however, all of these other dimorphic fungi are members of the order onygenales, phylogenetically distant from sporothrix in the ophiostomatales  <cit> .
the long genetic distance between these two orders suggests that thermo-dimorphism is a convergent phenotype shared by only a few members of these two orders.
genes such as histidine kinase  regulates the transition of mycelium to yeast and consequently the maintenance of virulence in b. dermatitidis and h. capsulatum
<cit> .
this gene, also identified in s. schenckii, shows 65% of identity with its ortholog in b.dermatitidis and seems to be highly expressed during the yeast stage  <cit> .
besides dimorphism and thermo-tolerance, current knowledge about virulence factors of sporothrix remains scant.
the cell surface of pathogenic fungi plays a key role in the host-fungus interplay, mediating various processes associated with pathogenesis.
the fungal cell wall is mainly composed of glycoconjugates: structural polysaccharides such as chitin and β-glucans, and cell wall glycoproteins  <cit> .
few proteins and glycoconjugates have been identified so far in the s. schenckii cell wall and their relevance for the host-fungus interaction and stimulation of the host immune system was reinforced by recent studies  <cit> .
however, the identity of the enzymes involved in biosynthetic pathways of cell wall components is still lacking.
another cell wall virulence factor, melanin, was found in s. schenckii conidia and yeast cells being produced in vitro or in vivo during infection  <cit> .
melanin pigments protect the fungus from the mammalian host’s innate immune responses providing resistance to oxidizing agents and fungal cell death during phagocytosis  <cit> .
members of the pathogenic lineage in sporothrix seem to behave in the host remarkably different from ophiostoma species, suggesting a fundamental habitat shift from a plant- to a mammal-associated life style  <cit> .
remarkably, most fungi from the order ophiostomatales live in association with bark beetles in woody plants, displaying adaptation strategies for insect transmission that are very different from those of s. schenckii and their relatives  <cit> .
the main biological questions of this work revolve around the dimorphic and pathogenic status of the two sporothrix species, which are phenotypically similar to human/animal pathogenic onygenales but philogenetically closely related to plant-associated sordariomycetes.
to address these questions, we performed a comparative genomic analysis of the pathogens with  <dig> other fungi, either dimorphic pathogens or plant-associated sordariomycetes.
of these, we chose the closest relative to the sporothrix lineage, grosmannia clavigera, for more detailed comparison.
g. clavigera is a tree-pathogenic and insect-associated fungus from a related genus from the ophiostomatales order  <cit> .
it is a haploid filamentous ascomycete and a symbiont of the bark beetle dendroctonus ponderosae, which affects commercial conifer forests, parks, protected areas and urban forests across north america  <cit> .
these genomic analyses allowed us to identify the core genes for general and secondary metabolism as well genes related to autophagy, adhesion, cell wall assembly and melanin biosynthetic processes.
we have also shown that genomic adaptation in the sporothrix lineage has led to expansion of some protein domains and lack of genes associated with plant biomass decay when compared to other sordariomycetes, which can be interpreted as an adaptation from plant to an animal associated life style.
RESULTS
genomes features, assemblies and synteny
the s. schenckii and s. brasiliensis genomes were each pyrosequenced to ~20x coverage.
the s. schenckii genome  yielded  <dig> scaffolds with n <dig> of  <dig>  mb, containing  <dig> contigs comprising a total size of  <dig>  mb.
the s. brasiliensis genome  yielded  <dig> scaffolds with n <dig> of  <dig>  mb, containing  <dig> contigs, had a total genome size of  <dig>  mb, and shared similar genomic characteristics with g. clavigera
<cit>  .
telomeric repeats n were found at 5’ or 3’ terminal ends of  <dig> out of  <dig> scaffolds in the s. schenckii and  <dig> out of  <dig> scaffolds in the s. brasiliensis genome.
terminal repeats were found in both ends of  <dig> and  <dig> scaffolds of s. schenckii and s. brasiliensis respectively, revealing the presence of complete linear chromosomes.
pair-wise genome alignments showed that both sporothrix species are highly syntenic sharing  <dig> % average sequence identity .
according to the genomic alignments long inverted segments were found in the two sporothrix genomes .
s. schenckii and s. brasiliensis were predicted to have  <dig>  and  <dig>  protein coding genes respectively, similar to other eurotiomycetes and sordariomycetes, and slightly higher than g. clavigera .
the g + c content in s. schenckii and s. brasiliensis genomes is one of the highest in ascomycota.
s. schenckii and s. brasiliensis genomes display 62% of g + c contents in both species, which is considerably higher than g. clavigera   <cit>  and 50–52% in most other fungi in pezizomycotina  <cit> .
we detected similar distributions of transcript lengths, but we found less introns per gene in sporothrix genomes than in those of g. clavigera.
the trna contents revealed a great discrepancy among the analyzed fungi; g. clavigera harbors at least 2-fold more trnas than sporothrix genomes .
we analyzed the homology relationships among fungi from the ophiostomataceae family, comparing the gene content of s. schenckii, s. brasiliensis and g. clavigera by bidirectional-best blast hits .
a total of  <dig>  genes were found in all three genomes and  <dig>  were found to be sporothrix-restricted genes, indicating a high content of specific genes in the sporothrix lineage.
a total of  <dig>  and  <dig> genes were considered orphan sequences in s. schenckii and s. brasiliensis, respectively .
we have performed the comparative analysis of core genes involved in general and secondary metabolism, as well genes involved in transport and catabolism showing a high degree of conservation when compared to those present in other ascomycetes .
genomes from s. schenckii and s. brasiliensis were deposited in the genbank under respectively accession numbers: axcr <dig> and awtv <dig> table  <dig>
sporothrix
genome characteristics
s. schenckii
s. brasiliensis
g. clavigera*
*genomic information collected according previously published g. clavirera genome  <cit> .
genomic alignments, synteny and homology of
s. schenckii
and
s. brasiliensis
.
a) dot-plot of s. schenckii and s. brasiliensis using ordered scaffold sequences.
b) predicted proteins in s. schenckii and s. brasiliensis were compared with the predicted proteins of g. clavigera.
the venn diagram was built using minimum query/subject coverage of 50% and e-value of e ≤ 1×10− <dig>  c) genomic alignments of s. schenckii  and s. brasiliensis  showing chromosomal inversions in the genomes of these pathogens.
phylogenomic analysis
a total of  <dig> orthologous protein clusters were identified by bbh after searching  <dig> fungal genomes, including ascomycetes, basidiomycetes and chytridiomycetes .
a maximum likelihood phylogenomic tree was generated using a  <dig>  amino acids position alignment and calibrated with the origin of ascomycota clade around 500– <dig> mya.
the phylogenomic tree, as expected, placed s. schenckii and s. brasiliensis in a monophyletic clade closest to g. clavigera being apart from other sordariomycetes .
according to the phylogenomic tree, s. schenckii and s. brasiliensis diverged about  <dig> - <dig>  mya suggesting a recent event of speciation in the genus sporothrix.
additionally, evolutionary origin of the ophiostomatoid fungi was dated to  <dig> - <dig>  mya, being highly divergent from the plant pathogen g. clavigera .
the divergence time varied across sister species of fungal pathogens along the ascomycota phylum, such as c. immitis vs. c. posadasii diverged about  <dig>  mya  <cit>  and p. brasiliensis vs. p. lutzii about  <dig> to  <dig> mya  <cit> .figure  <dig>
phylogenomic relationships of
sporothrix
species and other thermodimorphic fungal pathogens.
the phylogenetic tree was constructed from an alignment of  <dig>  amino acids of  <dig> orthologous protein clusters.
the tree was inferred by maximum likelihood method implemented in raxml and dayhoff amino acid substitution was used as the best protein substitution model.
the tree was calibrated with the origin of the ascomycota clade around 500– <dig> mya.
mitochondrial genomic comparisons
the mitochondrial genome assembly of s. schenckii strain 1099– <dig> is  <dig>  kb in size and shares 99-100% average sequence identity and 97-100% coverage in comparison to that of previously published s. schenckii strains atcc  <dig>  and kmu <dig>  .
the mitochondrial genome assembly of s. brasiliensis strain  <dig> spans  <dig> kb but covers only 71-75% of the three s. schenckii mentioned genomes before.
despite the high similarity between the two analyzed mitochondrial genomes , s. brasiliensis harbors parasitic group-i intron encoding homing endonucleases  which is responsible for the higher mitochondrial genome size in this species.
those elements were detected in the cytochrome c oxidase  <dig>  atp synthase subunit  <dig> and between nadh dehydrogenase subunits  <dig> and  <dig> orf’s .
these he’s found in the s. brasiliensis mitochondrial genome were classified into two families according interpro domain screening: laglidadg and giy-yig.
mitochondrial laglidadg he’s from s. brasiliensis  shared 75%, 84% and 78% of identity to madurella mycetomatis , fusarium graminearum  and f. solani , respectively.
the s. brasiliensis mitochondrial giy-yig he  is highly conserved among other sordarimycetes, sharing 72% and 77% of identity to podospora anserina  and ceratocystis cacofunesta , respectively .
c. cacofunesta contains  <dig> intronic orfs, thus being responsible for one of the largest mitochondrial genomes among sordariomycetes  <cit> .
fungal mitochondrial genomes present a constant genetic mobility, probably due to the activity of group-i intron encoding homing endonucleases.
mitochondrial introns and their orfs have been associated with mitochondrial parasitism and genomic size changes thus causing genomic instability, which was reported before in s. cereviseae, p. anserina, neurospora crassa, ophiostoma and aspergillus
.
according to the phylogenetic tree, no common ancestor was found in sordariomycetes class, suggesting an independent or convergent evolution of group-i intron encoding laglidadg and giy-yig elements in ascomycota .figure  <dig>
comparative analysis of mitochondrial genomes of
s. schenckii
and
s. brasiliensis
.
gene content and order in mitochondrial genomes of s. schenckii vs. s. brasiliensis showing high synteny despite the considerable difference in size.
insertions of laglidadg and giy-yig intron i type homing endonucleases in s. brasiliensis are present inside cytochrome c oxidase  <dig>  atp synthase subunit  <dig> and nadh dehydrogenase subunits  <dig> and  <dig> genes.
phylogenetic analysis was performed using the five laglidadg or giy-yig elements found in s. brasiliensis showing no pattern of ancestry with other close related species.
transposable elements expansions in s. brasiliensisgenome
transposable elements  comprise  <dig> % and  <dig> % of the s. schenckii and s. brasiliensis genomes, respectively .
fungal genomes contain substantially different amounts of repetitive dna sequences.
the assembled genome of magnaporthe oryzae contains  <dig> % of repetitive dna sequences, in m. grisea it is  <dig> %, in n. crassa is 10% and in s. cerevisiae almost 6% .
differences in the te contents are observed even between closely related species, e.g.
in the genus paracoccidioides.
in p. brasiliensis tes correspond to 8-9% of the genome and twice this amount in p. lutzii   <cit> .
although less common, lower te contents have been described in other fungi, for example  <dig> % of trichoderma and  <dig> % of fusarium graminearum genomes assemblies  <cit> .table  <dig>
transposable element composition in
sporothrix
genomes
s. schenckii
s. brasiliensis
athe number of potentially functional elements is shown in parentheses.
despite their lower content in sporothrix genome, all classes of tes have been detected with large variation in number and diversity between s. schenckii and s. brasiliensis.
two major types of retrotransposons, lines and ltrs, were found in s. schenckii and s. brasiliensis, but no sine elements were found .
in s. brasiliensis, a five-fold expansion of gypsy-like elements was observed compared to s. schenckii and both genomes contain more gypsy-like elements than copia-like elements.
we have observed a  <dig> and  <dig> fold-change between gypsy-like and copia-like elements for s. schenckii and s. brasiliensis respectively, as usual for fungal genomes  <cit> .
the overall 2-fold expansion of repetitive sequence content between sporothrix species may reflect an expansion of retrotransposons in the s. brasiliensis genome or either a contraction in that of s. schenckii .
according to population genomics studies and mating type distribution, the s. brasiliensis population appears to be clonal and no recombination events were detected  <cit> .
we observed a predominance of a single mating clone in epidemics of sporotrichosis and no or limiting sex could favor the accumulation of repetitive elements in microorganisms genomes  <cit> .
assexual propagation could lead extinction due inability to control proliferation of vertically transmitted tes, as accumulation occurs due to the inefficiency of purifying selection in clonal species  <cit> .figure  <dig>
transposable element content in
sporothrix schenckii
and
s. brasiliensis
genomes.
the number of potentially functional elements is shown in parentheses.
equivalent numbers of dna transposons were found in s. schenckii and s. brasiliensis genomes.
hat-like elements were the most prevalent in both species .
transposons from tc1/mariner and mutator superfamilies were also found in both genomes.
four copies of helitrons were identified in s. brasiliensis while a piggybac-like element was detected only in s. schenckii.
almost all tes identified in sporothrix genomes corresponded to defective and truncated copies, with exception of one line-like element found in s. schenckii, suggesting that sporothrix species are able to control their proliferation.
this finding suggests that tes are present in sporothrix but with low transposition activity.
we discuss why this could be below.
protein family expansion and contraction in the sporothrixlineages
gene duplications are an important source of evolutionary innovation and new gene copies can evolve new adaptive functions shaping an organism’s gene content.
the differences among gene families have been related to emerging processes due to differential degrees of genetic drift, and thus the effectiveness of selection, acting on genomes  <cit> .
the pathogenic phenotypes of s. schenckii and s. brasiliensis could result of expansion in specific gene families that confer advantages in the interaction with human/animal hosts.
on the other hand, gene families that ate necessary for the plant-associated lifestyles of other sordariomycetes could be contracted.
to test these hypotheses, we have compared the genomes from closely related sordariomycetes and dimorphic fungal pathogens.
changes in s. schenckii and s. brasiliensis gene families were inferred based on domain expansions or contractions assigned by interpro, pfam and smart databases and statistically tested by hypergeometric comparisons  and the reported p-values were used for multiple testing using q-value.figure  <dig>
interpro domains most enriched  or depleted  in
sporothrix
lineages compared to other thermo dimorphic fungi and close related sordariomycetes.
sbra - s. brasiliensis, ssch – s. schenckii, gcla – g. clavigera, mory – m. oryzae, pans – p. anserina, ncra – n. crassa, vdah - v. dahliae, fgra – f. graminearum, afum – a. fumigatus, pmar – p. marneffei, cim – c. immitis, pbra – p. brasiliensis, plut – p. lutzii, bder – b. dermatitidis, hcap – h. capsulatum.
the reported p-values were used for multiple testing using q-value.
we have not observed the enrichment of peptidases genes in sporothrix lineage, specifically the merops families m <dig> or m <dig>  which are expanded in dimorphic fungal pathogens as adaptation to mammalian hosts  <cit> .
on the other hand, we observe a lack of polysaccharide lyase genes which are associated with decay of plants  when compared to other sordariomycetes .
the subfamilies pl <dig>  pl <dig> and pl <dig> are broadly distributed among sordariomycetes, but were not observed in the sporothrix species.
interestingly loss of plant degrading enzymes were also observed in other dimorphic fungal pathogens such as h. capsulatum and c. immitis , which has also been previously interpreted as adaptation from plants to animals  <cit> .
as an alternative for the absence of pl proteins, it may be hypothesized that sporothrix may digest pectin by using polygalactouronase  as a replacement strategy.
additionally, we didn’t detect any gh <dig> genes in sporothrix genomes although those genes were found in all remaining analyzed fungi .figure  <dig>
gene expansion/contraction of carbohydrate-active enzymes  in the genus sporothrix.
overall comparison of glycoside hydrolases , glycosyl transferases , polysaccharide lyases , carbohydrate esterases , auxiliary activities  and carbohydrate-binding modules  against other thermo dimorphic fungi and closely related sordariomycetes.
cbm  <dig> gene family is highly expanded in the sporothrix lineage.
lysm domain-containing proteins display carbohydrate binding modules, usually 42– <dig> amino acids residues in length, found in prokaryotes and eukaryotes.
these proteins are classified in the cazy database as cbm family  <dig> and harbor n-acetylglucosamine  binding characteristics.
according to pfam and cazy counts, a marked expansion of the lysm domain pf <dig>  was detected in the sporothrix lineage.
the phylogenetic tree clearly showed highly expanded branches in the sporothrix lineage when compared to other sordariomycetes and thermo dimorphic fungal pathogens .
moreover, the comparative analysis of cazy cbm family  <dig> also revealed a high expansion of this domain .
recent events of duplications of lysm homologs subsequent to a speciation event were detected in the sporothrix lineage using reconciled tree approach .
the first duplication  is related to genes containing single or multiple repetitions of lysm domains, chitin-binding module type  <dig>  plus glycoside hydrolase .
the second event of duplication was observed in genes harboring multiple copies of lysm, providing evidence of recent intergene duplication of this domain within paralogues .
the structure of sporothrix lysm domain-containing genes are presented separately in additional file 3: figure s <dig> figure  <dig>
unrooted maximum likelihood tree revealing lysm expansions in the
sporothrix
lineage.
two major expansions were detected: the first duplication is related to genes containing single or multiple repetitions of lysm domains , chitin binding module type  <dig>  plus glycoside hydrolase  – clade i. the second event of duplication was observed in genes presenting multiple copies of lysm , and is evidence of recent intergene duplication of this domain within paralogous - clade ii.
chitin is a linear polymer of β--linked glcnac, and is one of the major components of fungal cell wall.
the absence of chitin in mammalian cells makes this polymer a potential targets for the innate immune system  <cit> .
chitin can be recognized by mammalian cells, and is bound and degraded by chitin-binding proteins gh <dig>  playing an important role in inflammation and innate and adaptive immunity based on their modulation on various disease states  <cit> .
chitin can mask immune recognition by blocking dectin-1-mediated interaction with fungal cell walls  <cit> .
also, chitin modulates epithelial immunity of the skin expressing high levels of cytokine and chemokine and increases tlr <dig> expression on keratinocytes  <cit> .
possibly these proteins are present to bind the own sporothrix chitin exposed upon cell damage, and in this way it may protect itself against recognition of this polymer by keratinocytes.
lysm effector  from cladosporium fulvum was characterized as a virulence factor of this phytopathogenic fungus on tomato plants.
carbohydrate binding assays have shown that ecp <dig> specifically binds to chitin, the major constituent of the fungal cell wall, acting as a pamp upon recognition by the plant during fungal invasion.
the presence of chitin-binding effector ecp <dig> in the apoplast masks the perception of chitin by plant receptors preventing the activation of defense responses  <cit> .
in addition significant expansion of the lysm domain was detected in dermatophytes, compared to the thermodimorphic fungi  <cit> .
dermatophytosis and sporotrichosis are characterized as cutaneous mycoses and the infection is acquired after contact and/or trauma of skin.
lysm domain containing proteins have not been characterized as virulence factors in human or animal fungal pathogens so far, and the role of those proteins requires further investigation and could be a novel mechanism for fungal evasion in mammalian host tissue.
small gtpases are an independent superfamily of gtp-binding proteins, sharing a common enzymatic activity and producing gdp by the hydrolysis of gtp, and play pivotal roles in cell division and signaling, vesicle fusion and protein synthesis  <cit> .
these proteins are also involved in filamentation, mating, growth at 37°c and virulence in c. neoformans
<cit> .
significant expansions in ras, rho and rab small gtpase superfamilies  were observed in the sporothrix lineage when compared to other ascomycetes .
judging from the phylogenetic trees of small gtpases, the majority of branches harboring sporothrix homologues suggests a higher diversity among the ascomycetes we analyzed .
reconciliation of small gtpases gene trees and species tree do not indicate sporothrix-specific duplications, that instead independent gene losses in other species explain the increased copy number in sporothrix .
an alternative hypothesis is that the sporothrix ras, rho and rab genes have duplicated recently and rapidly diverged creating the observed long branch lengths.
in addition we detected highly supported clades containing sporothrix and other pathogenic dimorphic fungi, suggesting convergent evolution of small gtpases, reinforcing the high plasticity of signal transduction in the sporothrix lineage .
to date, such a high diversity of small gtpase proteins as found in the sporothrix lineage has not been reported from any other class of fungi.
another group that was expanded by interpro and smart domain counts in the sporothrix lineage is the polyketide synthase , enoylreductase  family .
polyketides comprises diverse fungal secondary metabolites such as antibiotics, pigments, and mycotoxins that are formed from simple carbon precursor acids catalyzed by polyketide synthases   <cit> .
filamentous fungi are producers of polyketide metabolites, several of which of pharmacological or agricultural interest  <cit> .
fungal pkss are in general a linear succession of ketosynthetase , acyltransferase , dehydratase , enoyl reductase , ketoreductase , acyl carrier protein , and thioesterase  domains  <cit> .
er domains reduce enoyl groups to alkyl groups  during production of secondary metabolites.
among fungal genomes, few potential pks orthologous genes are shared, even between closely related taxa  <cit> .
we identified various paralogous duplications in the phylogenetic analysis of pks-containing protein, and the sporothrix lineage appears to have of pks-encoding genes that is at least 3-fold larger than that of the other species analyzed .
this was confirmed using the reconciled approach of pks gene tree with the species tree analyzed .
convergent branches linking sporothrix and other pathogenic dimorphic fungi were also observed.
we identified discontinuous distributions of pks homologs among the analyzed fungal species, with low bootstrap values, that can be explained by gene duplication, divergence, and gene loss  <cit> .
we also identified expanded clades harboring sporothrix and dimorphic fungi with high branch support values, suggesting a great diversity of this protein family.figure  <dig>
unrooted maximum likelihood tree of polyketide synthase  enoylreductase  family showing expansions in the
sporothrix
lineage.
paralogous duplications are displayed in the related branches suggesting vast genomic apparatus of pks containing genes in the sporothrix lineage.
clades harboring sporothrix and dimorphic fungi are displayed in red.
another large expansion found in the sporothrix lineage is a fungal trichothecene efflux pump , an evidence of detoxification via mycotoxin pump  <cit> .
apart from that, fungal genomes generally harbor a lower content of leucine-rich repeat  proteins than other ophistokonts  <cit> .
gene expansions of several lrr superfamilies were identified in the sporothrix lineage .
lrr proteins expansions are commonly found in eukaryotic parasites such as trypanosoma and giardia
<cit>
.
these domains consist of 2– <dig> motifs of 20– <dig> amino acids in length providing a structural framework for protein-protein interactions.
lrr proteins are involved in a variety of biological processes and are source of genetic variation for the ongoing process of antigenic variability in pathogens  <cit> .
in addition expansion of lrr proteins was described for candida species as a virulence factor  <cit> .
the role of these proteins should be further investigated in the genus sporothrix.
cellular processes and dimorphism
the basic mechanisms of dna repair in sporothrix do not deviate from the eukaryotic consensus, as expected, but neither s. brasiliensis nor s. schenckii seem to have a homolog to the neurospora crassa rip-defective  methyl-transferase  <cit> .
this suggests that rip-like mutation patterns found in transposable elements in this fungus are not generated by the classical, rid-dependent mechanism.
this is not a surprise, given that at least one previous report  <cit>  pointed to the possibility of alternative pathways for repetitive dna quelling via rip.
this is in contrast to other sordariomycetes and even more distantly related members of the ascomycota, such as p. brasiliensis and h. capsulatum, for which the tblastn tool yielded hits with high homology.
since the number of degenerate tes and overall evidence of transposon activity in sporothrix spp.
genomes is low, it would be interesting to identify which pathway is responsible for te suppression in this genus instead of rip.
we also note the absence of a mus- <dig> homologue for the alternative, uv damage-related nucleotide excision repair pathway  <cit> , found in neurospora crassa.
among transcription factors, the recent discovery of the ryp <dig> protein in h. capsulatum
<cit>  is of interest for the study of adaptive processes in fungi.
ryp <dig> and its homologues in c. albicans and s. cerevisiae
<cit>  are all implicated in morphogenetic changes of their respective species in response to environmental stimuli.
we have also found an ortholog of ryp <dig> in sporothrix.
given that ryp <dig> and the hybrid histidine-kinase drk <dig> are two determinants of mold-to-yeast transition in dimorphic fungi, and that sporothrix also has homologues for the latter  <cit> , it seems reasonable to speculate that both also have been coopted by this genus to coordinate dimorphic transition.
cell wall assembly
the cell wall of fungi is a dynamic organelle, which is constantly adjusted depending on environmental insults.
fungal cell wall components are considered relevant for virulence, have antigenic properties and participate in the modulation of the host immune response by being recognized by innate immunity receptors  <cit> .
current models propose an arrangement of several stratified layers composed of structural polysaccharides, mainly β-glucans and chitin, proteins and glycoproteins, generally known as mannoproteins, and other minor components.
cell wall proteins  are either covalently linked to the cell wall β -glucans by a glycophosphatidylinositol  moiety or linked via an alkali sensitive linkage to β -glucans.
the sugar moieties in cwp are n– and/or o- linked to the protein core  <cit> .
despite the importance of those components, little is known about the surface protein composition of s. schenckii and s. brasiliensis.
a) adhesins and/or cell surface proteins
previous studies searching for adhesins and antigens in cell extracts of sporothrix demonstrated the presence of a main antigen on both species, known as gp <dig>  a secreted antigen that is also present on the cell surface acting as an adhesin .
the genomes of s. schenckii and s. brasiliensis were investigated with different predictors to ascertain the presence of these cell wall components.
an in silico comparative analysis was performed in order to determine the putative adhesins and/or cell surface proteins bearing a gpi-anchor.
according to profasta and fungalrv, s. schenckii harbors  <dig> and  <dig> surface proteins, respectively, that have adhesin properties .
of these,  <dig> were found by both predictors  totalizing  <dig> unique predicted proteins in the cell wall of s. schenckii.
for s. brasiliensis we have identified  <dig> and  <dig> cell wall proteins , respectively,  <dig> of which were predicted by both algorithms.
for this species, a total of  <dig> unique predicted proteins .
the protein sequence relative to the previously proven cell surface/adhesin gp <dig> was not predicted to possess this function or to be present in the surface location by any of the predictors used  <cit> .
previous studies described several other important, non-classical surface proteins present in other fungi but which were not recognized in sporothrix by fungalrv and profasta .
the major classes of proteins predicted in s. schenckii and s. brasiliensis, by both profasta and fungalrv, are currently annotated either as hypothetical proteins or belonging to a protein family with unknown function .
this indicates that proteomic studies are needed to validate the expression of such proteins and biochemical functional studies are necessary to clarify their role on the fungal cell surface.
the cell wall proteins and/or adhesins predicted for these species were blasted against  <dig> fungi for comparative analysis, and each protein was blasted against the two sporothrix species .
eight proteins were found exclusively in s. brasiliensis and eight proteins were present only in s. schenckii.
sixteen sporothrix-specific proteins were annotated as hypothetical proteins.
none of the proteins described are specific to the group of human pathogenic fungi, but interestingly there are some proteins putatively present in the cell wall of sporothrix that share homology with those of plant and insect-associated fungi.figure  <dig>
putative adhesins identified and/or cell wall gpi-anchored proteins in
s. schenckii
and
s. brasiliensis
predicted by profasta and fungalrv.
putative adhesins were classified by their biological function using gene ontology  and interpro databases.
b) glucan and chitin metabolism
in s. schenckii, β-glucans are major components of the cell wall  <cit> , and are present as alkali-insoluble and alkali-soluble glucans, containing predominantly β--linkages in both cases  <cit> .
in s. schenckii, no genes related to the synthesis or degradation of β-glucans have been reported to date.
genomic data analysis revealed a single fks ortholog in s. schenckii and s. brasiliensis genomes, as well as single orthologs in the genomes of the other  <dig> fungal species studied here .
no genes related to the synthesis of either β- <dig> - or β- <dig> -glucans were identified, although hydrolase orthologs for the three types of β-glucan linkages in the s. schenckii cell wall, are present in both genomes .
chitin synthesis in fungi is a rather complex process, regulated by multigene families encoding chitin synthase isoenzymes, whose activities may be spatially regulated to fulfill the multitude of roles ascribed to them  <cit> .
based on differences in regions of high sequence conservation, chitin synthases have been attributed to seven classes  <cit> , whose functional implications are not yet clear in all cases.
despite the low chitin content reported for s. schenckii
<cit> , genomic analysis showed the presence of seven chs genes, in s. schenckii as well as in s. brasiliensis genomes.
a cluster analysis of their putative products, including  <dig> fungal chitin synthases, revealed that each of the translation products of the seven chs sporothrix genes identified in genomic databases , could be ascribed to each of the seven chitin synthase classes known  .
it is worth noting that class iii chitin synthases were thought to occurr exclusively in filamentous fungi  <cit> .
in our analysis, genes for class iii chitin synthases were found in the sporothrix genomes as well as the genomes of other dimorphic fungi , an indication that class iii fungal chitin synthases might be more widespread in fungi.
another interesting finding was the head-to-head arrangement in the s. schenckii and s. brasiliensis genomes of the chs <dig> and chs <dig> genes, whose putative translated products are class v and vii chitin synthases .
a similar arrangement was reported for genes coding for classes v and vii of chitin synthases in p. brasiliensis, a. nidulans, c. posadasii and f. oxysporum
.
the meaning of such arrangement is unclear, although a common transcriptional regulation for these genes has been suggested for a. nidulans and p. brasiliensis
<cit> .
in agreement with the large number of chs genes in the sporothrix genomes, genomic analysis showed the presence of ten and nine chitinase genes, respectively, in the s. schenckii and s. brasiliensis genomes .
polysaccharide synthesis and hydrolysis-related genes identified in s. schenckii and s. brasiliensis genomes correlate with the biochemical composition of the cell wall as reported by previato et al.
<cit> .
it remains to be determined which individual synthase and/or hydrolase gene might be involved in shaping the yeast, mycelial and spore  walls of sporothrix species, or even whether any of them might have any role in survival and would provide potential targets for the development of specific antifungal drugs.
c) protein glycosylation
glycoproteins are key components of the s. schenckii cell wall, but thus far little is known about their biosynthetic pathways  <cit> .
the genomes of s. schenckii and s. brasiliensis contained the orthologs involved in elaboration of the n-linked glycan core, its transference to proteins and in early trimming.
these genes are also known to be involved in glycoprotein endoplasmic reticulum-associated degradation, a quality control system for proteins synthesized within the secretory pathway  .
furthermore, the genomes contain the putative orthologs encoding golgi-resident glycosidases and glycosyltransferases that further modify n-linked glycans, generating both hybrid and complex n-linked glycans.
the presence of a gene with significant similarity to those encoding the n-acetylglucosaminidase iii , which adds the bisecting glcnac residue found in both hybrid and complex n-linked glycans  <cit> , suggests an ability to elaborate more complex oligosaccharides than those found in s. cerevisiae
<cit> .
moreover, our analysis revealed genes encoding putative golgi udp-galactose and cmp-sialic acid transporters, suggesting the ability of these fungi to add these sugars to their glycans.
s. schenckii and s. brasiliensis also contain an ortholog of a. nidulans ugma, whose product generates the galactomannan-building sugar donor  <cit> , and some putative galactosyltransferases .
however, it remains to be addressed whether these enzymes participate in elaboration of glycoproteins and/or glycolipids.
sialic acid has previously been reported as a component of s. schenckii cell wall glycolipids  <cit> , so it is likely that the putative golgi cmp-sialic acid transporter is involved in modification of such lipids.
the biosynthetic pathway for o-linked glycans can also be predicted from the analysis of s. schenckii and s. brasiliensis genomes .
optimal characterization of o-linked glycans is via isolation from peptide-rhamnomannans  <cit> .
they contain an α <dig> .mannobiose core, an α <dig> -glucuronic acid unit, and one or two rhamnose residues.
the s. schenckii and s. brasiliensis genomes contain three putative glucuronosyl transferases that might participate in the elaboration of this o-linked glycan .
our genomic analysis could not find any obvious ortholog for rhamnosyl transferases, but sporothrix contains all the required genes for synthesis of udp-l-rhamnose   <cit> , the sugar donor in the enzyme reaction catalyzed by rhamnosyltransferases  <cit> .
synthesis of gpi is quite conserved in eukaryotic cells and the sporothrix genome contains all genes to elaborate this glycolipid .
melanin metabolism
melanins are dark pigments formed by phenolic and indolic oxidation.
these biopolymers are produced by a wide range of organisms, possibly contributing to the maintenance of several species throughout evolution  <cit> .
in fungi, the expression of these pigments has been associated with virulence  <cit> .
fungi may synthesize melanin by several pathways: in pathogenic fungi, most commonly from endogenous substrate via the  <dig> -dihydroxynaphthalene  pathway or the l- <dig> -dihydroxyphenylalanine  pathways  <cit> .
the latter type is prevalent in basidiomycetes.
however, evidence of both pathways has been found in s. schenckii by means of specific substrate supplementation or drug-related inhibition of the respective pathways  <cit> .
melanins are found in s. schenckii spores and yeast cells and are produced in vitro and during infection using hamsters as host model.
its detection has also been confirmed by immunofluorescence with monoclonal antibodies raised against s. schenckii melanin  <cit> .
in s. schenckii, melanin pigments can protect the fungus from the mammalian host’s innate immune responses providing resistance to killing by phagocytosis and oxidizing agents  <cit> .
recently it was reported that s. schenckii and s. brasiliensis also produce pyomelanin, a melanoid pigment derived from the degradation of l-tyrosine via a 4-hydroxyphenylpyruvate dioxygenase  <cit> .
genomic comparison showed that both s. schenckii and s. brasiliensis possess enzymes with central roles in melanin synthesis via dhn and dopa pathways, and also in pyomelanin synthesis.
sporothrix schenckii and s. brasiliensis loci which are postulated to be involved in the melanin biosynthesis pathway are described in additional file 2: table s <dig>  we found  <dig> loci related to melanin biosynthesis in s. schenckii and  <dig> in s. brasiliensis.
homology with previously described melanin-related enzymes found in the sequence analyses are: pigment biosynthesis protein yellowish-green  <dig>  polyketide synthase i and iii, tetrahydroxynaphthalene/trihydroxinaphtalene reductase, scytalone dehydratase, laccase, tyrosinase and 4-hydroxyphenylpyruvate dioxygenase, as illustrated in additional file 13: figure s <dig>  the multiple functions of melanin in a cell and, especially, the resistance to antifungal drugs and survival of the host immune system, are a strong motivation for the study of the genetic characteristics of melanin biosythesis.
CONCLUSIONS
in this study we provide high quality genomic sequence assemblies and annotations for s. schenckii and s. brasiliensis.
genomic analyses showed a convergent evolutionary fate compared to other dimorphic fungi, even though sporothrix is a close relative of plant-associated sordariomycetes.
similar to other dimorphic fungal pathogens we have observed a lack of polysaccharide lyase genes which are associated with decay of plants, suggesting evolutionary adaptations from a plant pathogenic or saprobic to an animal pathogenic life style.
in addition, convergent branches linking sporothrix and other pathogenic dimorphic fungi were also observed in genes involved in signal transduction and secondary metabolism which suggest similar evolutionary traits.
the recent hypothesis of habitat shift from a saprobic life style in fermented plant material to mammal transmission may explain numerous plant/related atavisms.
comparative genomics reveals a certain degree of specialization in the sporothrix lineage which may contribute to our understanding of how fungal-environment-human interactions lead to the selection of pathogenic phenotypes of these species.
the sporothrix system may bring new opportunities for functional studies in order to understand the biology of fungi and infection.

 the fungal genus sporothrix includes about species found on all inhabited continents mainly occurring as environmental saprobes, living in association with plants or decaying matter. one lineage within the genus is composed of at least four pathogenic species associated with human and animal sporotrichosis: sporothrix schenckii sensu stricto, s. brasiliensis, s. globosa, and s. luriei. subcutaneous infections caused by s. schenckii are globally endemic. additionally, outbreaks have been described from south africa, australia, china and india. during the last two decades, an ongoing zoonotic outbreak of sporotrichosis has been observed in brazil. initially thought to be caused by sporothrix schenckii, detailed studies demonstrated that most outbreak isolates were actually s. brasiliensis. sporothricosis is classically associated with rural activities such as agriculture, floriculture or hunting, but more recently felines have emerged as source of human infection. the most common clinical form is a chronic subcutaneous/lymphocutaneous disease acquired after inoculation of fungal material into the skin. extracutaneous and disseminated forms secondary to cutaneous infection have been described in patients who are immunocompromised as a result of aids, chronic alcoholism and diabetes. rarely, severe cases involving pulmonary infection are noted. the pathogens of the genus sporothrix exhibit a thermo-dimorphic phenotype: in its saprophytic stage or in in vitro culture at 25°c the fungus grows with its filamentous form characterized by hyaline, septate hyphae with sympodial conidiogenous cells that produce two types of spores: hyaline conidia that form clusters and brown, thick-walled spores that are distributed perpendicularly alongside the hyphae. during the parasitic stage, the fungus is found as cigar-shaped yeast cells that can also be obtained in vitro by switching the temperature to 37°c. this dimorphism is essential for virulence in the mammalian host and is also found in other human pathogenic fungi such as blastomyces dermatitidis, b. gilchristii, histoplasma capsulatum, paracoccidioides brasiliensis, p. lutzii, coccidioides immitis and c. posadasi. however, all of these other dimorphic fungi are members of the order onygenales, phylogenetically distant from sporothrix in the ophiostomatales. the long genetic distance between these two orders suggests that thermo-dimorphism is a convergent phenotype shared by only a few members of these two orders. genes such as histidine kinase regulates the transition of mycelium to yeast and consequently the maintenance of virulence in b. dermatitidis and h. capsulatum. this gene, also identified in s. schenckii, shows 65% of identity with its ortholog in b.dermatitidis and seems to be highly expressed during the yeast stage. besides dimorphism and thermo-tolerance, current knowledge about virulence factors of sporothrix remains scant. the cell surface of pathogenic fungi plays a key role in the host-fungus interplay, mediating various processes associated with pathogenesis. the fungal cell wall is mainly composed of glycoconjugates: structural polysaccharides such as chitin and β-glucans, and cell wall glycoproteins. few proteins and glycoconjugates have been identified so far in the s. schenckii cell wall and their relevance for the host-fungus interaction and stimulation of the host immune system was reinforced by recent studies. however, the identity of the enzymes involved in biosynthetic pathways of cell wall components is still lacking. another cell wall virulence factor, melanin, was found in s. schenckii conidia and yeast cells being produced in vitro or in vivo during infection. melanin pigments protect the fungus from the mammalian host’s innate immune responses providing resistance to oxidizing agents and fungal cell death during phagocytosis. members of the pathogenic lineage in sporothrix seem to behave in the host remarkably different from ophiostoma species, suggesting a fundamental habitat shift from a plant- to a mammal-associated life style. remarkably, most fungi from the order ophiostomatales live in association with bark beetles in woody plants, displaying adaptation strategies for insect transmission that are very different from those of s. schenckii and their relatives. the main biological questions of this work revolve around the dimorphic and pathogenic status of the two sporothrix species, which are phenotypically similar to human/animal pathogenic onygenales but philogenetically closely related to plant-associated sordariomycetes. to address these questions, we performed a comparative genomic analysis of the pathogens with other fungi, either dimorphic pathogens or plant-associated sordariomycetes. of these, we chose the closest relative to the sporothrix lineage, grosmannia clavigera, for more detailed comparison. g. clavigera is a tree-pathogenic and insect-associated fungus from a related genus from the ophiostomatales order. it is a haploid filamentous ascomycete and a symbiont of the bark beetle dendroctonus ponderosae, which affects commercial conifer forests, parks, protected areas and urban forests across north america. these genomic analyses allowed us to identify the core genes for general and secondary metabolism as well genes related to autophagy, adhesion, cell wall assembly and melanin biosynthetic processes. we have also shown that genomic adaptation in the sporothrix lineage has led to expansion of some protein domains and lack of genes associated with plant biomass decay when compared to other sordariomycetes, which can be interpreted as an adaptation from plant to an animal associated life style.  genomes features, assemblies and synteny the s. schenckii and s. brasiliensis genomes were each pyrosequenced to ~20x coverage. the s. schenckii genome yielded scaffolds with n of  mb, containing contigs comprising a total size of  mb. the s. brasiliensis genome yielded scaffolds with n of  mb, containing contigs, had a total genome size of  mb, and shared similar genomic characteristics with g. clavigera. telomeric repeats n were found at 5’ or 3’ terminal ends of out of scaffolds in the s. schenckii and out of scaffolds in the s. brasiliensis genome. terminal repeats were found in both ends of and scaffolds of s. schenckii and s. brasiliensis respectively, revealing the presence of complete linear chromosomes. pair-wise genome alignments showed that both sporothrix species are highly syntenic sharing % average sequence identity. according to the genomic alignments long inverted segments were found in the two sporothrix genomes. s. schenckii and s. brasiliensis were predicted to have and protein coding genes respectively, similar to other eurotiomycetes and sordariomycetes, and slightly higher than g. clavigera. the g + c content in s. schenckii and s. brasiliensis genomes is one of the highest in ascomycota. s. schenckii and s. brasiliensis genomes display 62% of g + c contents in both species, which is considerably higher than g. clavigera and 50–52% in most other fungi in pezizomycotina. we detected similar distributions of transcript lengths, but we found less introns per gene in sporothrix genomes than in those of g. clavigera. the trna contents revealed a great discrepancy among the analyzed fungi; g. clavigera harbors at least 2-fold more trnas than sporothrix genomes. we analyzed the homology relationships among fungi from the ophiostomataceae family, comparing the gene content of s. schenckii, s. brasiliensis and g. clavigera by bidirectional-best blast hits. a total of genes were found in all three genomes and were found to be sporothrix-restricted genes, indicating a high content of specific genes in the sporothrix lineage. a total of and genes were considered orphan sequences in s. schenckii and s. brasiliensis, respectively. we have performed the comparative analysis of core genes involved in general and secondary metabolism, as well genes involved in transport and catabolism showing a high degree of conservation when compared to those present in other ascomycetes. genomes from s. schenckii and s. brasiliensis were deposited in the genbank under respectively accession numbers: axcr and awtv table sporothrix genome characteristics s. schenckii s. brasiliensis g. clavigera* *genomic information collected according previously published g. clavirera genome. genomic alignments, synteny and homology of s. schenckii and s. brasiliensis. a) dot-plot of s. schenckii and s. brasiliensis using ordered scaffold sequences. b) predicted proteins in s. schenckii and s. brasiliensis were compared with the predicted proteins of g. clavigera. the venn diagram was built using minimum query/subject coverage of 50% and e-value of e ≤ 1×10− c) genomic alignments of s. schenckii and s. brasiliensis showing chromosomal inversions in the genomes of these pathogens. phylogenomic analysis a total of orthologous protein clusters were identified by bbh after searching fungal genomes, including ascomycetes, basidiomycetes and chytridiomycetes. a maximum likelihood phylogenomic tree was generated using a amino acids position alignment and calibrated with the origin of ascomycota clade around 500– mya. the phylogenomic tree, as expected, placed s. schenckii and s. brasiliensis in a monophyletic clade closest to g. clavigera being apart from other sordariomycetes. according to the phylogenomic tree, s. schenckii and s. brasiliensis diverged about - mya suggesting a recent event of speciation in the genus sporothrix. additionally, evolutionary origin of the ophiostomatoid fungi was dated to - mya, being highly divergent from the plant pathogen g. clavigera. the divergence time varied across sister species of fungal pathogens along the ascomycota phylum, such as c. immitis vs. c. posadasii diverged about mya and p. brasiliensis vs. p. lutzii about to mya.figure phylogenomic relationships of sporothrix species and other thermodimorphic fungal pathogens. the phylogenetic tree was constructed from an alignment of amino acids of orthologous protein clusters. the tree was inferred by maximum likelihood method implemented in raxml and dayhoff amino acid substitution was used as the best protein substitution model. the tree was calibrated with the origin of the ascomycota clade around 500– mya. mitochondrial genomic comparisons the mitochondrial genome assembly of s. schenckii strain 1099– is kb in size and shares 99-100% average sequence identity and 97-100% coverage in comparison to that of previously published s. schenckii strains atcc and kmu. the mitochondrial genome assembly of s. brasiliensis strain spans kb but covers only 71-75% of the three s. schenckii mentioned genomes before. despite the high similarity between the two analyzed mitochondrial genomes, s. brasiliensis harbors parasitic group-i intron encoding homing endonucleases which is responsible for the higher mitochondrial genome size in this species. those elements were detected in the cytochrome c oxidase atp synthase subunit and between nadh dehydrogenase subunits and orf’s. these he’s found in the s. brasiliensis mitochondrial genome were classified into two families according interpro domain screening: laglidadg and giy-yig. mitochondrial laglidadg he’s from s. brasiliensis shared 75%, 84% and 78% of identity to madurella mycetomatis, fusarium graminearum and f. solani, respectively. the s. brasiliensis mitochondrial giy-yig he is highly conserved among other sordarimycetes, sharing 72% and 77% of identity to podospora anserina and ceratocystis cacofunesta, respectively. c. cacofunesta contains intronic orfs, thus being responsible for one of the largest mitochondrial genomes among sordariomycetes. fungal mitochondrial genomes present a constant genetic mobility, probably due to the activity of group-i intron encoding homing endonucleases. mitochondrial introns and their orfs have been associated with mitochondrial parasitism and genomic size changes thus causing genomic instability, which was reported before in s. cereviseae, p. anserina, neurospora crassa, ophiostoma and aspergillus. according to the phylogenetic tree, no common ancestor was found in sordariomycetes class, suggesting an independent or convergent evolution of group-i intron encoding laglidadg and giy-yig elements in ascomycota.figure comparative analysis of mitochondrial genomes of s. schenckii and s. brasiliensis. gene content and order in mitochondrial genomes of s. schenckii vs. s. brasiliensis showing high synteny despite the considerable difference in size. insertions of laglidadg and giy-yig intron i type homing endonucleases in s. brasiliensis are present inside cytochrome c oxidase atp synthase subunit and nadh dehydrogenase subunits and genes. phylogenetic analysis was performed using the five laglidadg or giy-yig elements found in s. brasiliensis showing no pattern of ancestry with other close related species. transposable elements expansions in s. brasiliensisgenome transposable elements comprise % and % of the s. schenckii and s. brasiliensis genomes, respectively. fungal genomes contain substantially different amounts of repetitive dna sequences. the assembled genome of magnaporthe oryzae contains % of repetitive dna sequences, in m. grisea it is %, in n. crassa is 10% and in s. cerevisiae almost 6%. differences in the te contents are observed even between closely related species, e.g. in the genus paracoccidioides. in p. brasiliensis tes correspond to 8-9% of the genome and twice this amount in p. lutzii. although less common, lower te contents have been described in other fungi, for example % of trichoderma and % of fusarium graminearum genomes assemblies.table transposable element composition in sporothrix genomes s. schenckii s. brasiliensis athe number of potentially functional elements is shown in parentheses. despite their lower content in sporothrix genome, all classes of tes have been detected with large variation in number and diversity between s. schenckii and s. brasiliensis. two major types of retrotransposons, lines and ltrs, were found in s. schenckii and s. brasiliensis, but no sine elements were found. in s. brasiliensis, a five-fold expansion of gypsy-like elements was observed compared to s. schenckii and both genomes contain more gypsy-like elements than copia-like elements. we have observed a and fold-change between gypsy-like and copia-like elements for s. schenckii and s. brasiliensis respectively, as usual for fungal genomes. the overall 2-fold expansion of repetitive sequence content between sporothrix species may reflect an expansion of retrotransposons in the s. brasiliensis genome or either a contraction in that of s. schenckii. according to population genomics studies and mating type distribution, the s. brasiliensis population appears to be clonal and no recombination events were detected. we observed a predominance of a single mating clone in epidemics of sporotrichosis and no or limiting sex could favor the accumulation of repetitive elements in microorganisms genomes. assexual propagation could lead extinction due inability to control proliferation of vertically transmitted tes, as accumulation occurs due to the inefficiency of purifying selection in clonal species.figure transposable element content in sporothrix schenckii and s. brasiliensis genomes. the number of potentially functional elements is shown in parentheses. equivalent numbers of dna transposons were found in s. schenckii and s. brasiliensis genomes. hat-like elements were the most prevalent in both species. transposons from tc1/mariner and mutator superfamilies were also found in both genomes. four copies of helitrons were identified in s. brasiliensis while a piggybac-like element was detected only in s. schenckii. almost all tes identified in sporothrix genomes corresponded to defective and truncated copies, with exception of one line-like element found in s. schenckii, suggesting that sporothrix species are able to control their proliferation. this finding suggests that tes are present in sporothrix but with low transposition activity. we discuss why this could be below. protein family expansion and contraction in the sporothrixlineages gene duplications are an important source of evolutionary innovation and new gene copies can evolve new adaptive functions shaping an organism’s gene content. the differences among gene families have been related to emerging processes due to differential degrees of genetic drift, and thus the effectiveness of selection, acting on genomes. the pathogenic phenotypes of s. schenckii and s. brasiliensis could result of expansion in specific gene families that confer advantages in the interaction with human/animal hosts. on the other hand, gene families that ate necessary for the plant-associated lifestyles of other sordariomycetes could be contracted. to test these hypotheses, we have compared the genomes from closely related sordariomycetes and dimorphic fungal pathogens. changes in s. schenckii and s. brasiliensis gene families were inferred based on domain expansions or contractions assigned by interpro, pfam and smart databases and statistically tested by hypergeometric comparisons and the reported p-values were used for multiple testing using q-value.figure interpro domains most enriched or depleted in sporothrix lineages compared to other thermo dimorphic fungi and close related sordariomycetes. sbra - s. brasiliensis, ssch – s. schenckii, gcla – g. clavigera, mory – m. oryzae, pans – p. anserina, ncra – n. crassa, vdah - v. dahliae, fgra – f. graminearum, afum – a. fumigatus, pmar – p. marneffei, cim – c. immitis, pbra – p. brasiliensis, plut – p. lutzii, bder – b. dermatitidis, hcap – h. capsulatum. the reported p-values were used for multiple testing using q-value. we have not observed the enrichment of peptidases genes in sporothrix lineage, specifically the merops families m or m which are expanded in dimorphic fungal pathogens as adaptation to mammalian hosts. on the other hand, we observe a lack of polysaccharide lyase genes which are associated with decay of plants when compared to other sordariomycetes. the subfamilies pl pl and pl are broadly distributed among sordariomycetes, but were not observed in the sporothrix species. interestingly loss of plant degrading enzymes were also observed in other dimorphic fungal pathogens such as h. capsulatum and c. immitis, which has also been previously interpreted as adaptation from plants to animals. as an alternative for the absence of pl proteins, it may be hypothesized that sporothrix may digest pectin by using polygalactouronase as a replacement strategy. additionally, we didn’t detect any gh genes in sporothrix genomes although those genes were found in all remaining analyzed fungi.figure gene expansion/contraction of carbohydrate-active enzymes in the genus sporothrix. overall comparison of glycoside hydrolases, glycosyl transferases, polysaccharide lyases, carbohydrate esterases, auxiliary activities and carbohydrate-binding modules against other thermo dimorphic fungi and closely related sordariomycetes. cbm gene family is highly expanded in the sporothrix lineage. lysm domain-containing proteins display carbohydrate binding modules, usually 42– amino acids residues in length, found in prokaryotes and eukaryotes. these proteins are classified in the cazy database as cbm family and harbor n-acetylglucosamine binding characteristics. according to pfam and cazy counts, a marked expansion of the lysm domain pf was detected in the sporothrix lineage. the phylogenetic tree clearly showed highly expanded branches in the sporothrix lineage when compared to other sordariomycetes and thermo dimorphic fungal pathogens. moreover, the comparative analysis of cazy cbm family also revealed a high expansion of this domain. recent events of duplications of lysm homologs subsequent to a speciation event were detected in the sporothrix lineage using reconciled tree approach. the first duplication is related to genes containing single or multiple repetitions of lysm domains, chitin-binding module type plus glycoside hydrolase. the second event of duplication was observed in genes harboring multiple copies of lysm, providing evidence of recent intergene duplication of this domain within paralogues. the structure of sporothrix lysm domain-containing genes are presented separately in additional file 3: figure s figure unrooted maximum likelihood tree revealing lysm expansions in the sporothrix lineage. two major expansions were detected: the first duplication is related to genes containing single or multiple repetitions of lysm domains, chitin binding module type plus glycoside hydrolase – clade i. the second event of duplication was observed in genes presenting multiple copies of lysm, and is evidence of recent intergene duplication of this domain within paralogous - clade ii. chitin is a linear polymer of β--linked glcnac, and is one of the major components of fungal cell wall. the absence of chitin in mammalian cells makes this polymer a potential targets for the innate immune system. chitin can be recognized by mammalian cells, and is bound and degraded by chitin-binding proteins gh playing an important role in inflammation and innate and adaptive immunity based on their modulation on various disease states. chitin can mask immune recognition by blocking dectin-1-mediated interaction with fungal cell walls. also, chitin modulates epithelial immunity of the skin expressing high levels of cytokine and chemokine and increases tlr expression on keratinocytes. possibly these proteins are present to bind the own sporothrix chitin exposed upon cell damage, and in this way it may protect itself against recognition of this polymer by keratinocytes. lysm effector from cladosporium fulvum was characterized as a virulence factor of this phytopathogenic fungus on tomato plants. carbohydrate binding assays have shown that ecp specifically binds to chitin, the major constituent of the fungal cell wall, acting as a pamp upon recognition by the plant during fungal invasion. the presence of chitin-binding effector ecp in the apoplast masks the perception of chitin by plant receptors preventing the activation of defense responses. in addition significant expansion of the lysm domain was detected in dermatophytes, compared to the thermodimorphic fungi. dermatophytosis and sporotrichosis are characterized as cutaneous mycoses and the infection is acquired after contact and/or trauma of skin. lysm domain containing proteins have not been characterized as virulence factors in human or animal fungal pathogens so far, and the role of those proteins requires further investigation and could be a novel mechanism for fungal evasion in mammalian host tissue. small gtpases are an independent superfamily of gtp-binding proteins, sharing a common enzymatic activity and producing gdp by the hydrolysis of gtp, and play pivotal roles in cell division and signaling, vesicle fusion and protein synthesis. these proteins are also involved in filamentation, mating, growth at 37°c and virulence in c. neoformans. significant expansions in ras, rho and rab small gtpase superfamilies were observed in the sporothrix lineage when compared to other ascomycetes. judging from the phylogenetic trees of small gtpases, the majority of branches harboring sporothrix homologues suggests a higher diversity among the ascomycetes we analyzed. reconciliation of small gtpases gene trees and species tree do not indicate sporothrix-specific duplications, that instead independent gene losses in other species explain the increased copy number in sporothrix. an alternative hypothesis is that the sporothrix ras, rho and rab genes have duplicated recently and rapidly diverged creating the observed long branch lengths. in addition we detected highly supported clades containing sporothrix and other pathogenic dimorphic fungi, suggesting convergent evolution of small gtpases, reinforcing the high plasticity of signal transduction in the sporothrix lineage. to date, such a high diversity of small gtpase proteins as found in the sporothrix lineage has not been reported from any other class of fungi. another group that was expanded by interpro and smart domain counts in the sporothrix lineage is the polyketide synthase, enoylreductase family. polyketides comprises diverse fungal secondary metabolites such as antibiotics, pigments, and mycotoxins that are formed from simple carbon precursor acids catalyzed by polyketide synthases. filamentous fungi are producers of polyketide metabolites, several of which of pharmacological or agricultural interest. fungal pkss are in general a linear succession of ketosynthetase, acyltransferase, dehydratase, enoyl reductase, ketoreductase, acyl carrier protein, and thioesterase domains. er domains reduce enoyl groups to alkyl groups during production of secondary metabolites. among fungal genomes, few potential pks orthologous genes are shared, even between closely related taxa. we identified various paralogous duplications in the phylogenetic analysis of pks-containing protein, and the sporothrix lineage appears to have of pks-encoding genes that is at least 3-fold larger than that of the other species analyzed. this was confirmed using the reconciled approach of pks gene tree with the species tree analyzed. convergent branches linking sporothrix and other pathogenic dimorphic fungi were also observed. we identified discontinuous distributions of pks homologs among the analyzed fungal species, with low bootstrap values, that can be explained by gene duplication, divergence, and gene loss. we also identified expanded clades harboring sporothrix and dimorphic fungi with high branch support values, suggesting a great diversity of this protein family.figure unrooted maximum likelihood tree of polyketide synthase enoylreductase family showing expansions in the sporothrix lineage. paralogous duplications are displayed in the related branches suggesting vast genomic apparatus of pks containing genes in the sporothrix lineage. clades harboring sporothrix and dimorphic fungi are displayed in red. another large expansion found in the sporothrix lineage is a fungal trichothecene efflux pump, an evidence of detoxification via mycotoxin pump. apart from that, fungal genomes generally harbor a lower content of leucine-rich repeat proteins than other ophistokonts. gene expansions of several lrr superfamilies were identified in the sporothrix lineage. lrr proteins expansions are commonly found in eukaryotic parasites such as trypanosoma and giardia. these domains consist of 2– motifs of 20– amino acids in length providing a structural framework for protein-protein interactions. lrr proteins are involved in a variety of biological processes and are source of genetic variation for the ongoing process of antigenic variability in pathogens. in addition expansion of lrr proteins was described for candida species as a virulence factor. the role of these proteins should be further investigated in the genus sporothrix. cellular processes and dimorphism the basic mechanisms of dna repair in sporothrix do not deviate from the eukaryotic consensus, as expected, but neither s. brasiliensis nor s. schenckii seem to have a homolog to the neurospora crassa rip-defective methyl-transferase. this suggests that rip-like mutation patterns found in transposable elements in this fungus are not generated by the classical, rid-dependent mechanism. this is not a surprise, given that at least one previous report pointed to the possibility of alternative pathways for repetitive dna quelling via rip. this is in contrast to other sordariomycetes and even more distantly related members of the ascomycota, such as p. brasiliensis and h. capsulatum, for which the tblastn tool yielded hits with high homology. since the number of degenerate tes and overall evidence of transposon activity in sporothrix spp. genomes is low, it would be interesting to identify which pathway is responsible for te suppression in this genus instead of rip. we also note the absence of a mus- homologue for the alternative, uv damage-related nucleotide excision repair pathway, found in neurospora crassa. among transcription factors, the recent discovery of the ryp protein in h. capsulatum is of interest for the study of adaptive processes in fungi. ryp and its homologues in c. albicans and s. cerevisiae are all implicated in morphogenetic changes of their respective species in response to environmental stimuli. we have also found an ortholog of ryp in sporothrix. given that ryp and the hybrid histidine-kinase drk are two determinants of mold-to-yeast transition in dimorphic fungi, and that sporothrix also has homologues for the latter, it seems reasonable to speculate that both also have been coopted by this genus to coordinate dimorphic transition. cell wall assembly the cell wall of fungi is a dynamic organelle, which is constantly adjusted depending on environmental insults. fungal cell wall components are considered relevant for virulence, have antigenic properties and participate in the modulation of the host immune response by being recognized by innate immunity receptors. current models propose an arrangement of several stratified layers composed of structural polysaccharides, mainly β-glucans and chitin, proteins and glycoproteins, generally known as mannoproteins, and other minor components. cell wall proteins are either covalently linked to the cell wall β -glucans by a glycophosphatidylinositol moiety or linked via an alkali sensitive linkage to β -glucans. the sugar moieties in cwp are n– and/or o- linked to the protein core. despite the importance of those components, little is known about the surface protein composition of s. schenckii and s. brasiliensis. a) adhesins and/or cell surface proteins previous studies searching for adhesins and antigens in cell extracts of sporothrix demonstrated the presence of a main antigen on both species, known as gp a secreted antigen that is also present on the cell surface acting as an adhesin. the genomes of s. schenckii and s. brasiliensis were investigated with different predictors to ascertain the presence of these cell wall components. an in silico comparative analysis was performed in order to determine the putative adhesins and/or cell surface proteins bearing a gpi-anchor. according to profasta and fungalrv, s. schenckii harbors and surface proteins, respectively, that have adhesin properties. of these, were found by both predictors totalizing unique predicted proteins in the cell wall of s. schenckii. for s. brasiliensis we have identified and cell wall proteins, respectively, of which were predicted by both algorithms. for this species, a total of unique predicted proteins. the protein sequence relative to the previously proven cell surface/adhesin gp was not predicted to possess this function or to be present in the surface location by any of the predictors used. previous studies described several other important, non-classical surface proteins present in other fungi but which were not recognized in sporothrix by fungalrv and profasta. the major classes of proteins predicted in s. schenckii and s. brasiliensis, by both profasta and fungalrv, are currently annotated either as hypothetical proteins or belonging to a protein family with unknown function. this indicates that proteomic studies are needed to validate the expression of such proteins and biochemical functional studies are necessary to clarify their role on the fungal cell surface. the cell wall proteins and/or adhesins predicted for these species were blasted against fungi for comparative analysis, and each protein was blasted against the two sporothrix species. eight proteins were found exclusively in s. brasiliensis and eight proteins were present only in s. schenckii. sixteen sporothrix-specific proteins were annotated as hypothetical proteins. none of the proteins described are specific to the group of human pathogenic fungi, but interestingly there are some proteins putatively present in the cell wall of sporothrix that share homology with those of plant and insect-associated fungi.figure putative adhesins identified and/or cell wall gpi-anchored proteins in s. schenckii and s. brasiliensis predicted by profasta and fungalrv. putative adhesins were classified by their biological function using gene ontology and interpro databases. b) glucan and chitin metabolism in s. schenckii, β-glucans are major components of the cell wall, and are present as alkali-insoluble and alkali-soluble glucans, containing predominantly β--linkages in both cases. in s. schenckii, no genes related to the synthesis or degradation of β-glucans have been reported to date. genomic data analysis revealed a single fks ortholog in s. schenckii and s. brasiliensis genomes, as well as single orthologs in the genomes of the other fungal species studied here. no genes related to the synthesis of either β- - or β- -glucans were identified, although hydrolase orthologs for the three types of β-glucan linkages in the s. schenckii cell wall, are present in both genomes. chitin synthesis in fungi is a rather complex process, regulated by multigene families encoding chitin synthase isoenzymes, whose activities may be spatially regulated to fulfill the multitude of roles ascribed to them. based on differences in regions of high sequence conservation, chitin synthases have been attributed to seven classes, whose functional implications are not yet clear in all cases. despite the low chitin content reported for s. schenckii, genomic analysis showed the presence of seven chs genes, in s. schenckii as well as in s. brasiliensis genomes. a cluster analysis of their putative products, including fungal chitin synthases, revealed that each of the translation products of the seven chs sporothrix genes identified in genomic databases, could be ascribed to each of the seven chitin synthase classes known. it is worth noting that class iii chitin synthases were thought to occurr exclusively in filamentous fungi. in our analysis, genes for class iii chitin synthases were found in the sporothrix genomes as well as the genomes of other dimorphic fungi, an indication that class iii fungal chitin synthases might be more widespread in fungi. another interesting finding was the head-to-head arrangement in the s. schenckii and s. brasiliensis genomes of the chs and chs genes, whose putative translated products are class v and vii chitin synthases. a similar arrangement was reported for genes coding for classes v and vii of chitin synthases in p. brasiliensis, a. nidulans, c. posadasii and f. oxysporum. the meaning of such arrangement is unclear, although a common transcriptional regulation for these genes has been suggested for a. nidulans and p. brasiliensis. in agreement with the large number of chs genes in the sporothrix genomes, genomic analysis showed the presence of ten and nine chitinase genes, respectively, in the s. schenckii and s. brasiliensis genomes. polysaccharide synthesis and hydrolysis-related genes identified in s. schenckii and s. brasiliensis genomes correlate with the biochemical composition of the cell wall as reported by previato et al.. it remains to be determined which individual synthase and/or hydrolase gene might be involved in shaping the yeast, mycelial and spore walls of sporothrix species, or even whether any of them might have any role in survival and would provide potential targets for the development of specific antifungal drugs. c) protein glycosylation glycoproteins are key components of the s. schenckii cell wall, but thus far little is known about their biosynthetic pathways. the genomes of s. schenckii and s. brasiliensis contained the orthologs involved in elaboration of the n-linked glycan core, its transference to proteins and in early trimming. these genes are also known to be involved in glycoprotein endoplasmic reticulum-associated degradation, a quality control system for proteins synthesized within the secretory pathway. furthermore, the genomes contain the putative orthologs encoding golgi-resident glycosidases and glycosyltransferases that further modify n-linked glycans, generating both hybrid and complex n-linked glycans. the presence of a gene with significant similarity to those encoding the n-acetylglucosaminidase iii, which adds the bisecting glcnac residue found in both hybrid and complex n-linked glycans, suggests an ability to elaborate more complex oligosaccharides than those found in s. cerevisiae. moreover, our analysis revealed genes encoding putative golgi udp-galactose and cmp-sialic acid transporters, suggesting the ability of these fungi to add these sugars to their glycans. s. schenckii and s. brasiliensis also contain an ortholog of a. nidulans ugma, whose product generates the galactomannan-building sugar donor, and some putative galactosyltransferases. however, it remains to be addressed whether these enzymes participate in elaboration of glycoproteins and/or glycolipids. sialic acid has previously been reported as a component of s. schenckii cell wall glycolipids, so it is likely that the putative golgi cmp-sialic acid transporter is involved in modification of such lipids. the biosynthetic pathway for o-linked glycans can also be predicted from the analysis of s. schenckii and s. brasiliensis genomes. optimal characterization of o-linked glycans is via isolation from peptide-rhamnomannans. they contain an α.mannobiose core, an α -glucuronic acid unit, and one or two rhamnose residues. the s. schenckii and s. brasiliensis genomes contain three putative glucuronosyl transferases that might participate in the elaboration of this o-linked glycan. our genomic analysis could not find any obvious ortholog for rhamnosyl transferases, but sporothrix contains all the required genes for synthesis of udp-l-rhamnose, the sugar donor in the enzyme reaction catalyzed by rhamnosyltransferases. synthesis of gpi is quite conserved in eukaryotic cells and the sporothrix genome contains all genes to elaborate this glycolipid. melanin metabolism melanins are dark pigments formed by phenolic and indolic oxidation. these biopolymers are produced by a wide range of organisms, possibly contributing to the maintenance of several species throughout evolution. in fungi, the expression of these pigments has been associated with virulence. fungi may synthesize melanin by several pathways: in pathogenic fungi, most commonly from endogenous substrate via the -dihydroxynaphthalene pathway or the l- -dihydroxyphenylalanine pathways. the latter type is prevalent in basidiomycetes. however, evidence of both pathways has been found in s. schenckii by means of specific substrate supplementation or drug-related inhibition of the respective pathways. melanins are found in s. schenckii spores and yeast cells and are produced in vitro and during infection using hamsters as host model. its detection has also been confirmed by immunofluorescence with monoclonal antibodies raised against s. schenckii melanin. in s. schenckii, melanin pigments can protect the fungus from the mammalian host’s innate immune responses providing resistance to killing by phagocytosis and oxidizing agents. recently it was reported that s. schenckii and s. brasiliensis also produce pyomelanin, a melanoid pigment derived from the degradation of l-tyrosine via a 4-hydroxyphenylpyruvate dioxygenase. genomic comparison showed that both s. schenckii and s. brasiliensis possess enzymes with central roles in melanin synthesis via dhn and dopa pathways, and also in pyomelanin synthesis. sporothrix schenckii and s. brasiliensis loci which are postulated to be involved in the melanin biosynthesis pathway are described in additional file 2: table s we found loci related to melanin biosynthesis in s. schenckii and in s. brasiliensis. homology with previously described melanin-related enzymes found in the sequence analyses are: pigment biosynthesis protein yellowish-green polyketide synthase i and iii, tetrahydroxynaphthalene/trihydroxinaphtalene reductase, scytalone dehydratase, laccase, tyrosinase and 4-hydroxyphenylpyruvate dioxygenase, as illustrated in additional file 13: figure s the multiple functions of melanin in a cell and, especially, the resistance to antifungal drugs and survival of the host immune system, are a strong motivation for the study of the genetic characteristics of melanin biosythesis.  in this study we provide high quality genomic sequence assemblies and annotations for s. schenckii and s. brasiliensis. genomic analyses showed a convergent evolutionary fate compared to other dimorphic fungi, even though sporothrix is a close relative of plant-associated sordariomycetes. similar to other dimorphic fungal pathogens we have observed a lack of polysaccharide lyase genes which are associated with decay of plants, suggesting evolutionary adaptations from a plant pathogenic or saprobic to an animal pathogenic life style. in addition, convergent branches linking sporothrix and other pathogenic dimorphic fungi were also observed in genes involved in signal transduction and secondary metabolism which suggest similar evolutionary traits. the recent hypothesis of habitat shift from a saprobic life style in fermented plant material to mammal transmission may explain numerous plant/related atavisms. comparative genomics reveals a certain degree of specialization in the sporothrix lineage which may contribute to our understanding of how fungal-environment-human interactions lead to the selection of pathogenic phenotypes of these species. the sporothrix system may bring new opportunities for functional studies in order to understand the biology of fungi and infection. 
transposable elements comprise respectively % and % of the s. schenckii and s. brasiliensis genomes and expansions of gypsy-like elements was observed reflecting the accumulation of repetitive elements in the s. brasiliensis genome. in contrast, a lack of polysaccharide lyase genes that are associated with decay of plants was observed when compared to other sordariomycetes and dimorphic fungal pathogens, suggesting evolutionary adaptations from a plant pathogenic or saprobic to an animal pathogenic life style. mitochondrial genomic comparisons showed the presence of group-i intron encoding homing endonucleases exclusively in s. brasiliensis. moreover, the striking differences found in comparison with other dimorphic fungi revealed that dimorphism in these close relatives of plant-associated sordariomycetes is a case of convergent evolution, stressing the importance of this morphogenetic change in fungal pathogenesis. analysis of protein family expansions and contractions in the sporothrix lineage revealed expansion of lysm domain-containing proteins, small gtpases, pks type and leucin-rich proteins. elsewhere, sapronoses are caused by s. schenckii and s. globosa. one of these species, s. brasiliensis, is the causal agent of a major ongoing zoonotic outbreak of sporotrichosis in brazil. pair-wise genome alignments revealed that the two species are highly syntenic showing % average sequence identity. the major aims on this comparative genomic study are: 1) to explore the presence of virulence factors in s. schenckii and s. brasiliensis; 2) to compare s. brasiliensis, which is cat-transmitted and infects both humans and cats with s. schenckii, mainly a human pathogen; 3) to compare these two species to other human pathogens with similar thermo-dimorphic behavior and to other plant-associated sordariomycetes. the genomes of s. schenckii and s. brasiliensis were pyrosequenced to 17x and 20x coverage comprising a total of  mb and  mb, respectively. the fungal genus sporothrix includes at least four human pathogenic species. comparative genomic data suggest a unique ecological shift in the sporothrix lineage from plant-association to mammalian parasitism, which contributes to the understanding of how environmental interactions may shape fungal virulence. phylogenomic analysis reveals that both species diverged about - mya suggesting a recent event of speciation.
 the fungal genus sporothrix includes at least four human pathogenic species. one of these species, s. brasiliensis, is the causal agent of a major ongoing zoonotic outbreak of sporotrichosis in brazil. elsewhere, sapronoses are caused by s. schenckii and s. globosa. the major aims on this comparative genomic study are: 1) to explore the presence of virulence factors in s. schenckii and s. brasiliensis; 2) to compare s. brasiliensis, which is cat-transmitted and infects both humans and cats with s. schenckii, mainly a human pathogen; 3) to compare these two species to other human pathogens with similar thermo-dimorphic behavior and to other plant-associated sordariomycetes.  the genomes of s. schenckii and s. brasiliensis were pyrosequenced to 17x and 20x coverage comprising a total of  mb and  mb, respectively. pair-wise genome alignments revealed that the two species are highly syntenic showing % average sequence identity. phylogenomic analysis reveals that both species diverged about - mya suggesting a recent event of speciation. transposable elements comprise respectively % and % of the s. schenckii and s. brasiliensis genomes and expansions of gypsy-like elements was observed reflecting the accumulation of repetitive elements in the s. brasiliensis genome. mitochondrial genomic comparisons showed the presence of group-i intron encoding homing endonucleases exclusively in s. brasiliensis. analysis of protein family expansions and contractions in the sporothrix lineage revealed expansion of lysm domain-containing proteins, small gtpases, pks type and leucin-rich proteins. in contrast, a lack of polysaccharide lyase genes that are associated with decay of plants was observed when compared to other sordariomycetes and dimorphic fungal pathogens, suggesting evolutionary adaptations from a plant pathogenic or saprobic to an animal pathogenic life style.  comparative genomic data suggest a unique ecological shift in the sporothrix lineage from plant-association to mammalian parasitism, which contributes to the understanding of how environmental interactions may shape fungal virulence.. moreover, the striking differences found in comparison with other dimorphic fungi revealed that dimorphism in these close relatives of plant-associated sordariomycetes is a case of convergent evolution, stressing the importance of this morphogenetic change in fungal pathogenesis. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords sporothrix schenckiisporothrix brasiliensiscomparative genomicsfungal evolutionissue-copyright-statement© the author 2014 