BACKGROUND
the xanthomonadaceae are a family of gram negative bacteria belonging to the order xanthomonadales in the gamma subdivision of the proteobacteria  <cit> .
members of this family are typically characterized as environmental organisms and occupy diverse ecological niches, such as soil and water, as well as plant tissues.
many xanthomonadaceae, especially species from the genera xanthomonas and xylella, cause plant diseases and only one, stenotrophomonas maltophilia, is known to be an opportunistic human pathogen.
complete genome sequences of several xanthomonas species and xylella fastidiosa strains have been determined, making those bacteria attractive models for study of plant-pathogen interactions  <cit> .
x. fastidiosa was the first completely sequenced plant pathogen.
sequence analysis showed that this xylem-limited bacterium, which is insect-vectored to a variety of diverse hosts, had a reduced genome and did not possess hrp genes, which encode a type iii secretion system  found in most gram negative plant pathogenic bacteria  <cit> .
phylogenetic analysis with rrna sequences showed that the two major genera of xanthomonadaceae, xanthomonas and stenotrophomonas, form a coherent group excluding x. fastidiosa  <cit> .
these characteristics suggested the hypothesis that this species evolved from an ancestor shared with xanthomonas and stenotrophomonas by genome reduction during adaptation to life within its hosts  <cit> .
xanthomonas albilineans is a systemic, xylem-limited pathogen that causes leaf scald, one of the major diseases of sugarcane   <cit> .
leaf scald symptoms vary from a single, white, narrow, sharply defined stripe to complete wilting and necrosis of infected leaves, leading to plant death.
x. albilineans produces the toxin albicidin that has phytotoxic and antibiotic properties  <cit> .
albicidin is a potent dna gyrase inhibitor that targets the chloroplastic dna gyrase a, inhibits chloroplast dna replication and blocks chloroplast differentiation, resulting in the white foliar stripe symptoms  <cit> .
all attempts to identify hrp genes in x. albilineans failed so far  <cit> .
a phylogenetic study with the housekeeping genes ihfa and efp, which did not include s. maltophilia sequences, suggested that x. albilineans was an evolutionary intermediate between several xanthomonas species and x. fastidiosa  <cit> .
unlike other xylem-invading xanthomonads that interact with living plant tissues, such as x. campestris pv.
campestris or x. oryzae pv.
oryzae, x. fastidiosa and x. albilineans appear to be strictly xylem-limited, living only in dead xylem cells or tracheary elements.
in order to better understand the evolution of these two xylem-limited xanthomonadaceae, we sequenced the genome of x. albilineans strain gpe pc <dig> from guadeloupe  <cit> .
this sequence was compared to complete genome sequences of other closely related members of the xanthomonadaceae.
this comparative analysis revealed that x. albilineans and x. fastidiosa experienced a convergent reductive genome evolution from a common ancestral parent of the xanthomonas genus.
RESULTS
general genomic features of x. albilineans
the genome of x. albilineans strain gpe pc <dig> consists of one circular chromosome of  <dig> , <dig> bp and three extrachromosomal plasmids of  <dig>   <dig> and  <dig> kbp, respectively.
the chromosome exhibits a gc skew pattern typical of prokaryotic genomes that have two major shifts, one near the origin and one near the terminus of replication, with dnaa assigned as base pair  <dig> of the chromosome .
the gc skew pattern of x. albilineans contains a lower number of diagram distortions and has much lower amplitude than the gc skew pattern of x. fastidiosa .
however, the amplitude of the gc skew pattern of x. albilineans is significantly higher than the one of other xanthomonads and s. maltophilia .
of the  <dig> putative protein-coding sequences  manually annotated on the chromosome of x. albilineans strain gpe pc <dig>   <dig>  were assigned putative functions based on homology to other known proteins and domain analyses.
the general features of the x. albilineans chromosome were compared to those of the chromosomes of the following eight xanthomonadaceae strains: x. oryzae pv.
oryzae strain maff  <dig> , x. campestris pv.
campestris strain atcc  <dig> , x. axonopodis pv.
vesicatoria strain 85- <dig> , x. axonopodis pv.
citri strain  <dig> , s. maltophilia strain k279a , s. maltophilia strain r551- <dig> , x. fastidiosa strain 9a5c  and x. fastidiosa strain temecula <dig> .
the chromosome of x. albilineans is  <dig>  mb smaller than the chromosomes of x. axonopodis pv.
vesicatoria strain 85- <dig> and x. axonopodis pv.
citri strain  <dig>  but it is  <dig>  mb bigger than the chromosome of x. fastidiosa strain temecula <dig> .
the g+c content of the chromosome of x. albilineans averages 63%.
this value is similar to those of other xanthomonas strains, but it is 12% higher than the g+c content of the chromosome of x. fastidiosa strain temecula <dig>  the chromosome of x. albilineans shows an average coding density of 84%, which is also similar to other xanthomonads.
acore genome cds correspond to the  <dig> orthologs shared by the nine xanthomonadaceae
comparative genomic analyses
in order to assess phylogenetic relationships among the nine xanthomonadaceae mentioned above , we performed multilocus sequence analysis .
the phylogenetic tree obtained with the concatenated data set of seven housekeeping genes showed that x. albilineans belongs to the same clade as x. fastidiosa .
the clade containing x. albilineans and x. fastidiosa is clearly distinct from the clade containing the four xanthomonads of the hrp xanthomonas group .
on the basis of this phylogenetic tree, we conclude that x. albilineans and x. fastidiosa derived from the progenitor of the xanthomonas genus .
in order to identify orthologs shared by the nine xanthomonadaceae strains , we performed orthomcl comparative analyses  <cit> .
the x. albilineans cdss shared with x. fastidiosa strain 9a5c, s. maltophilia strain k279a or x. axonopodis pv.
vesicatoria strain 85- <dig> are represented on the circular chromosome .
interestingly, the chromosome of x. albilineans harbours several large regions that do not contain any genes present in the other eight xanthomonadaceae strains.
these regions correspond either to phage related sequences or to large genes encoding proteins that contain repeated rhs elements that are known to be frequently transferred by horizontal genetic transfer  <cit> .
they also contain several gene clusters specific to x. albilineans:  the albicidin biosynthesis gene cluster xalb <dig> which was previously sequenced from x. albilineans strain xa23r <dig>  <cit>  and which contains three nonribosomal peptide synthetases  genes;  three additional nrps gene clusters to which cannot be ascribed a precise function as they have not been previously identified and no strictly orthologous genes were found in other bacteria; and  a gene cluster encoding a t3ss of the spi- <dig>  family that is mainly found in free-living animal pathogens  <cit> .
the orthomcl analyses identified a total of  <dig> cdss of the genome of x. albilineans strain gpe pc <dig> that are not shared with any of the other eight xanthomonadaceae complete genome sequences compared in this study.
they also identified  <dig> cdss shared by the nine xanthomonadaceae, which represent a xanthomonadaceae core gene set which was likely inherited from a common ancestor.
evidence of convergent genome reductive evolution of x. albilineans and x. fastidiosa
the phylogenetic tree presented in figure  <dig> suggests that x. albilineans, x. fastidiosa and the hrp xanthomonas group derived from a common ancestor shared with stenotrophomonas.
the chromosome sizes of x. albilineans and x. fastidiosa are smaller than those of any other xanthomonad , suggesting that both species evolved from the progenitor of xanthomonads by genome reduction.
to examine how the chromosomes of x. albilineans and x. fastidiosa have evolved to result in these different sizes, we determined the order of divergence of x. albilineans, x. fastidiosa, the four xanthomonads of the hrp xanthomonas group and s. maltophilia .
orthologous genes shared by s. maltophilia and a species of the hrp xanthomonas group, but missing in x. albilineans or x. fastidiosa, may be assumed to have been lost by x. albilineans or x. fastidiosa, respectively.
inversely, genes of a species of the hrp xanthomonas group that are shared with s. maltophilia, x. albilineans or x. fastidiosa may be assumed to have been inherited from the progenitor of the xanthomonas genus.
on the basis of orthomcl analysis, the numbers of genes lost by x. albilineans strain gpe pc <dig> and x. fastidiosa strain 9a5c are at least  <dig> and  <dig>  respectively .
the number of ancestral genes inherited from the progenitor of the xanthomonas genus is higher in x. axonopodis pv.
vesicatoria than in any other species of the hrp xanthomonas group .
interestingly, x. oryzae pv.
oryzae strain maff  <dig> contains the smallest number of genes lost by x. albilineans or x. fastidiosa, indicating that a significant number of genes lost by x. albilineans or x. fastidiosa were also lost by the xylem-invading pathogen x. oryzae pv.
oryzae .
on the basis of orthomcl analysis including both x. albilineans strain gpe pc <dig> and x. fastidiosa strain 9a5c,  <dig> ancestral genes were lost by both x. albilineans and x. fastidiosa ,  <dig> ancestral genes were lost only by x. fastidiosa , and  <dig> ancestral genes were lost only by x. albilineans .
comparison of the reductive evolutions of x. albilineans and x. fastidiosa
further comparative analyses were performed to compare genome erosion in x. albilineans and x. fastidiosa.
for these analyses, we selected the genome of x. axonopodis pv.
vesicatoria, which contains the highest number of genes inherited from the progenitor of the xanthomonas genus .
orthomcl analysis identified  <dig> cdss of x. axonopodis pv.
vesicatoria that do not include any transposase genes and that are shared either by x. albilineans strain gpe pc <dig>  x. fastidiosa strain 9a5c or one of the two s. maltophilia strains k279a and r551- <dig>  for each of the  <dig> cdss, we looked for the best blast hit within a database that included:  all annotated cdss from the genome sequence of x. albilineans strain gpe pc <dig> and  all available sequences from public databases excluding all sequences from the xanthomonads.
on the basis of these analyses and among the  <dig> cdss, we selected the genes for which the best blast hit belonged to x. albilineans, x. fastidiosa or s. maltophilia.
we made the hypothesis that these genes were inherited by x. axonopodis pv.
vesicatoria from the ancestor of the xanthomonads.
these best blast hit analyses confirmed that  <dig> of these  <dig> cdss have the same ancestor as genes present either in x. albilineans, x. fastidiosa or s. maltophilia and were therefore inherited by x. axonopodis pv.
vesicatoria from the progenitor of the xanthomonas genus.
the elimination of paralogs present in at least two copies in x. axonopodis pv.
vesicatoria generated a list of  <dig> cdss representing one copy of each gene inherited by x. axonopodis pv.
vesicatoria from the progenitor of the xanthomonas genus.
these  <dig> cdss are listed and individually analysed in additional file  <dig>  among them,  <dig> cdss are shared by both x. fastidiosa and x. albilineans ,  <dig> cdss are shared only with one of the two s. maltophilia strains ,  <dig> cdss are shared with x. fastidiosa but not with x. albilineans  and  <dig> cdss are shared with x. albilineans but not with x. fastidiosa .
the distribution in functional cog categories of these  <dig> cdss is illustrated in figure  <dig>
analyses of the arrangement of these  <dig> ancestral genes on the chromosome of x. axonopodis pv.
vesicatoria strain 85- <dig> led to the identification of dna regions constituting contiguous ancestral genes that are missing in x. albilineans or x. fastidiosa .
during the speciation of x. fastidiosa or x. albilineans, the loss of these dna regions was due either to a single event of deletion or to the cumulative effect of multiple events .
for example, the loss in x. fastidiosa of the large dna region constituted by ancestral genes from xcv <dig> to xcv <dig> seems to be due to a single event of deletion since all these ancestral genes are missing in x. fastidiosa .
this large dna region lost by x. fastidiosa encodes all flagellar proteins and several chemotaxis proteins.
the sum of the length of the ancestral genes present in this dna region is  <dig>  bp, strongly suggesting that x. fastidiosa experienced a single deletion of a dna fragment of a larger size.
the other dna regions constituting contiguous ancestral genes that are missing in x. albilineans or x. fastidiosa are shorter and, for this reason, their loss may result either from a single event of deletion or from multiple mutational events.
analysis of the arrangement on the chromosome of x. axonopodis pv.
vesicatoria strain 85- <dig> of ancestral genes absent in x. albilineans or x. fastidiosa did not allow us to determine if the genes absent in both xylem-limited xanthomonadaceae were lost by their common ancestor or were lost independently after their divergence.
the loss of genes by pseudogenization and short deletions should not affect the position on the chromosome of the genes that precede or follow the lost genes.
in order to identify ancestral genes putatively lost by pseudogenization and short deletions, we looked for ancestral lost genes that are present on the chromosome of x. axonopodis pv.
vesicatoria between the orthologs of two ancestral genes that are contiguous and conserved in x. fastidiosa or x. albilineans.
for example, the rpf  gene cluster contains in x. axonopodis pv.
vesicatoria two ancestral genes  that are missing in both x. albilineans and x. fastidiosa.
the ancestral genes xcv <dig> and xcv <dig> that precede and follow respectively these two lost genes are orthologs of either xalc_ <dig> and xalc_ <dig> or xf <dig> and xf <dig> that are contiguous in x. albilineans and x. fastidiosa, respectively.
using the same strategy we identified  <dig> and  <dig> ancestral genes potentially lost by pseudogenization by x. fastidiosa and x. albilineans, respectively .
common genomic features of x. fastidiosa and x. albilineans
the close relationship between x. albilineans and x. fastidiosa is illustrated by the common unique characteristics of their enzymes involved in cellulose degradation.
in these two xylem-limited xanthomonadaceae, endoglucanase engxca and  <dig> -beta cellobiosidase cbha possess a cellulose binding domain  and a long polyserine linker  at their c termini .
the endoglucanase engxca is conserved in all other xanthomonas species and also has a cbd, but the linker is much shorter and its serine content is much lower .
the  <dig> -beta cellobiosidase cbha is conserved in the xylem-invading xanthomonads x. campestris pv.
campestris and x. oryzae pv.
oryzae but, in these two species, cbha does not possess any linker nor any cbd .
the presence of a cbd is known to increase catalytic activity by reducing the "substrate accessibility problem"  <cit> .
the long flexible psl was proposed to enhance substrate accessibility  <cit> .
the presence of genes encoding enzymes harbouring a psl and a cbd provides evidence that both x. fastidiosa and x. albilineans are adapted to use plant cell breakdown products as carbon sources.
apsl = polyserine linker; bcbd = cellulose binding domain
the orthomcl analyses identified  <dig> orthologs shared only by x. fastidiosa strain 9a5c, x. fastidiosa strain temecula <dig> and x. albilineans gpe pc <dig> .
blast analyses confirmed that  <dig> of these  <dig> cdss are unique to x. albilineans and x. fastidiosa .
interestingly, they include the gene mete which encodes the 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase.
this enzyme is absolutely required for the biosynthesis of methionine and is therefore present in all xanthomonadaceae.
however, the mete gene present in the two xylem-limited xanthomonadaceae is closer to the gene mete of mesorhizobium sp.
than the mete present in the other xanthomonas species and in s. maltophilia .
this strongly suggests that the progenitor of the two xylem-limited xanthomonadaceae lost the ancestral mete gene  and acquired another mete by horizontal genetic transfer.
the  <dig> genes unique to x. albilineans and x. fastidiosa also include one cysteine protease gene, one abc transporter gene, one polysaccharide deacetylase gene, one glycosyl transferase gene, one hydrolase gene, one cell filamentation protein gene and four hypothetical protein genes .
blast analyses confirmed that x. albilineans, like x. fastidiosa, lacks the hrp t3ss that is present in other xanthomonas species and does not possess any of the known hrp type iii effectors.
the hrp t3ss, which plays a major role in suppressing host plant defense responses in most other pathogenic xanthomonas strains  <cit> , was therefore probably acquired after the divergence of the hrp xanthomonas group and xylem-limited xanthomonadaceae lineages.
no remains of the hrp gene cluster were found in the complete genome sequence of x. albilineans strain gpe pc <dig> nor in the available complete genome sequences of x. fastidiosa.
discussion
in their rather cloistered environmental niche inside xylem vessels, x. albilineans and x. fastidiosa may have largely avoided surveillance by general and specific plant defense systems.
their lack of a t3ss of the hrp <dig> or hrp <dig> families may be explained by the fact that x. albilineans and x. fastidiosa live and multiply essentially in a dead-cell environment.
however, like other bacterial vascular pathogens, they may interact with living xylem parenchyma cells through pit membranes  <cit> .
if they do, they do not use a hrp ttss but another system that remains to be identified.
the adaptation of x. albilineans and x. fastidiosa to a xylem-limited lifestyle is also illustrated by their enzymes adapted to the use of plant cell breakdown products as carbon sources.
the low number of genes unique to both x. albilineans and x. fastidiosa  may be explained by a very early divergence of the two xylem-limited xanthomonadaceae lineages, possibly followed by strong selective pressure to adapt to their different biological niches and lifestyles.
x. fastidiosa is vector-transmitted by various xylem sap-feeding insects and is able to colonize many plant species  .
on the other hand, x. albilineans is mainly transmitted by mechanical means and is not known to be insect-transmitted, and is able to colonize only sugarcane and few other monocots in the poaceae family .
the genome of x. albilineans encodes a t3ss that displays similarities with the burkholderia pseudomallei bsa t3ss which belongs to the injectisome family spi- <dig>  and which is required for the virulence of this human pathogen.
the spi- <dig> injectisome family mainly includes t3sss from human and insect bacterial pathogens or symbionts  <cit> .
interestingly, the genomes of erwinia amylovora strain ea <dig> and erwinia tasmaniensis strain et1/ <dig> both contain two copies of a spi- <dig> t3ss  <cit> .
the role of these spi- <dig> t3sss in these plant-invading erwinia spp.
remains unknown.
e. amylovora is insect-disseminated, although the interactions between this pathogen and its insect hosts remain poorly understood.
it was suggested that the presence of a spi- <dig> t3ss in erwinia spp.
indicates a common ancestry and close phylogenetic relationship between erwinia spp.
and insect-related enteric bacteria, raising the possibility that an insect host might be serving as a mixing vessel for the exchange of genes between erwinia strains and other enteric bacteria  <cit> .
similarly, the presence of a spi- <dig> t3ss in the genome of x. albilineans could indicate an insect-associated life style of this plant pathogen.
the mlsa performed herein resulted in a phylogenetic tree that included x. fastidiosa into the xanthomonas group.
this phylogenetic tree is in accordance with the presence of the unique gum genes in both x. fastidiosa and xanthomonas species of the hrp xanthomonas group.
the gum genes, which are involved in the biosynthesis of extracellular polysaccharides and the formation of biofilms, play a key role in pathogenicity of these xanthomonadaceae.
these genes, which were probably acquired by the progenitor of the xanthomonas genus, were most likely lost by x. albilineans and conserved by x. fastidiosa during their speciation.
our mlsa phylogenetic tree is also in accordance with i/the presence of  <dig> unique genes, including mete, in x. albilineans and x. fastidiosa, and ii/the alignment of the 5' end of the 16s rna of xanthomonadaceae .
additionally, based on this mlsa, the same  <dig> ancestral genes appeared to be lost by both x. albilineans and x. fastidiosa.
interestingly,  <dig> of the  <dig> ancestral genes lost by both x. albilineans and x. fastidiosa are also absent in x. oryzae pv.
oryzae , indicating that independent but convergent evolution events were involved in genome erosion of x. oryzae pv.
oryzae and the xylem-limited xanthomonadaceae.
some of these genes lost by three xylem-invading pathogens are orthologous of genes with assigned functions and are organized into clusters.
the five following ancestral gene clusters were lost by x. albilineans, x. fastidiosa and x. oryzae pv.
oryzae: i/ the ancestral genes xcv <dig> to xcv <dig> encoding enzymes involved in the glyoxylate cycle; ii/ the ancestral genes xcv <dig> to xcv <dig> encoding enzymes involved in malonate metabolism; iii/ the ancestral genes xcv <dig> to xcv <dig> including one tonb-dependant receptor gene, a two component signal transduction system  and chemotaxis genes, iv/ the ancestral genes xcv <dig> to xcv <dig> including one tcsts and a type i secretion system and v/ the ancestral genes xcv <dig> to xcv <dig> encoding enzymes involved in catabolism of polysaccharides .
these examples support the hypothesis of a link between the convergent erosion of three xylem-invading xanthomonadaceae and the adaptation to a same restricted environment  in which these lost functions are useless.
however, only  <dig> of the  <dig> ancestral genes lost by both x. albilineans and x. fastidiosa are also absent in another xylem invading pathogen, x. campestris pv.
campestris, indicating that adaptation to xylem lifestyle favoured or allowed genome erosion, but did not necessarily induce it.
alternatively, the convergent genome erosion of the two xylem-limited xanthomonadaceae may be linked to similar insect-associated lifestyles that may have favoured genome erosion because most of the genes required for a plant-associated life style are most likely not required for an insect-associated life style.
similar striking convergence in fundamental genomic features associated with a restricted lifestyle is very well documented for obligate animal symbionts and pathogens, especially for buchnera .
in these bacteria, gene losses are non-random but can affect all functional categories.
the most dramatic losses affect genes that are involved in metabolism but are not required for survival.
another general feature is the loss of most dna repair systems and transcriptional regulatory mechanisms, indicating that there is reduced need for transcriptional regulation in a stable environment  <cit> .
in x. fastidiosa, and to a lesser extent in x. albilineans, losses also affected genes involved in metabolism and transcriptional regulatory mechanisms .
metabolic capabilities essential for other habitats may have been lost in the genome reduction process coincidently with the adaptation of x. fastidiosa and x. albilineans to the nutrient-poor xylem environment.
for x. fastidiosa, genome erosion has been extreme.
for example, x. fastidiosa retained only one transcriptional sigma factor gene and one outer membrane efflux protein tolc gene, and it lost all genes involved in synthesis of the flagellar apparatus.
this extreme erosion allowed x. fastidiosa to save energy .
in obligate animal symbionts and pathogens, the process of genome shrinkage might have taken place in two separate stages  <cit> .
a massive gene loss must have occurred soon after the establishment of the obligate symbiosis, probably by means of large deletions that eliminated a series of contiguous genes.
the large dna region containing the flagellar genes was probably lost by x. fastidiosa during a similar stage.
the accumulation of mobile elements, representing a source of chromosomal rearrangements and gene inactivation, seems to have an important role in this first stage.
a similar process is likely responsible for the limited genome erosion of x. oryzae pv.
oryzae, which possesses a very high number of insertion sequences  covering 20% of the genome  <cit> .
during the second stage of genome reduction in obligate animal symbionts and pathogens, genome shrinkage seems to have mostly occurred through a process of gradual gene loss, scattered along the genome.
such losses seem to follow a pattern that starts with the inactivation of a gene  by single-nucleotide mutations, and continues with a rapid reduction in length until the original gene is completely eroded  <cit> .
a similar process is likely responsible for the genome erosions of x. fastidiosa and x. albilineans .
furthermore, the coding density of x. fastidiosa strain temecula <dig> is significantly smaller than that of xanthomonads probably because of the degradation of ancestral genes.
in x. fastidiosa strain 9a5c, the number of short annotated cdss is considerably higher than in other xanthomonadaceae , although the functionality of these shortened cdss, which may result from the degradation of ancestral genes, is questionable.
obligate animal symbionts and pathogens display rapid evolution and have highly biased nucleotide base compositions with elevated frequencies of adenine and thymine  .
x. fastidiosa also displays rapid evolution  and has a high a+t content in comparison with other xanthomonadaceae .
furthermore, the gc skew pattern of the chromosome of x. fastidiosa has very high amplitude and contains a high number of diagram distortions .
a similar atypical gc skew pattern was observed for the chromosome of a buchnera aphidicola strain  <cit> .
this latter atypical gc skew coincides with the loss of genes involved in the replication restart process  and may be explained by a higher frequency of cytosine deaminations  <cit> .
the loss of dna repair genes recx, ding and dinp may explain, similarly, the very high gc skew of x. fastidiosa.
it may also explain the more extensive genome erosion of x. fastidiosa, compared to x. albilineans and x. oryzae pv.
oryzae.
alternatively, the most important factor affecting genome erosion of x. fastidiosa may reflect the insect-associated lifestyle specific to this xanthomonadaceae  <cit> .
the gc skew pattern of the x. albilineans chromosome contains a lower number of distortions and has a significantly higher amplitude than the gc skew pattern of other xanthomonas species , indicating that no recent events of recombination have occurred in x. albilineans.
furthermore, the synteny between the chromosomes of x. albilineans strain gpe pc <dig> and x. axonopodis pv.
vesicatoria strain 85- <dig> also indicated that recombination events were limited during the speciation of x. albilineans .
the limited recombination of the chromosome of x. albilineans, its limited erosion, its high g+c content and its low number of is elements may indicate that a distinctive process was responsible for the reductive genome evolution of this pathogen.
we propose a unique mechanism of genome erosion involving the unique toxin albicidin produced by x. albilineans.
albicidin is a potent dna gyrase inhibitor with 50% inhibitory concentrations  lower than those of most quinolones  <cit> .
dna gyrase inhibitors block the religation of cleaved dna intermediate during gyrase catalysis, resulting in lethal double-stranded dna breaks  <cit> .
in the presence of subinhibitory doses of dna gyrase inhibitors, the sos response mediates survival of the bacteria by allowing dna replication to continue past breaks that would normally block it.
in exchange for this survival advantage, there is an increased mutation rate because the polymerases that perform the repair are prone to error  <cit> .
several studies showed that subinhibitory doses of quinolones result in an increased mutation rate in escherichia coli, staphylococcus aureus, pseudomonas aeruginosa and mycobacterium tuberculosis  <cit> .
x. albilineans has two genes conferring resistance to albicidin: an albicidin efflux pump gene that is present in the albicidin biosynthesis gene cluster xalb <dig>  <cit>  and an albicidin-resistant dna gyrase a gene elsewhere on the chromosome.
this albicidin-resistant dna gyrase a is unique to x. albilineans  <cit> .
it contains a unique insertion of  <dig> amino-acids length close to the albicidin binding site.
production of albicidin in ancestral bacteria that possessed both the albicidin biosynthesis gene cluster and a dna gyrase a sensitive to albicidin may have induced genome erosion.
in these ancestral bacteria, most of the albicidin molecules were secreted by the albicidin efflux pump.
occasionally, molecules of albicidin that were not secreted most likely had the same effect as subinhibitory doses of quinolones: the sos response was induced, thus resulting in dna repair, recombination and mutagenesis.
successive and cumulative effect of albicidin at each replication cycle eventually resulted in genome erosion.
the genome erosion induced by albicidin was likely arrested by evolution of the albicidin-resistant dna gyrase a.
acquisition of the albicidin biosynthesis genes by the ancestor of x. albilineans conferred a selective advantage because of the potent antibiotic activity of albicidin.
the dna damage caused by albicidin may rapidly have induced the mutation of dna gyrase a gene and thus stopped the process of genome erosion, possibly explaining the distinctive genomic characteristics of x. albilineans.
albicidin inhibits the growth of x. axonopodis pv.
vesicatoria , suggesting that the dna gyrase a of the ancestral xanthomonas was sensitive to albicidin.
transfer of the albicidin biosynthesis gene cluster to x. axonopodis pv.
vesicatoria led to production of functional albicidin  <cit> , demonstrating that the production of albicidin per se is not lethal for a producer that possesses an albicidin-sensitive dna gyrase a. no remains of the albicidin biosynthesis genes were found in the complete genome sequences of x. fastidiosa.
therefore, albicidin is most likely not responsible for genome erosion of x. fastidiosa.
however, we cannot exclude the hypothesis that albicidin biosynthesis genes were lost during evolution of x. fastidiosa.
for example, cluster xalb <dig> could have been lost concurrently with the flagellar biosynthesis gene cluster because these two gene clusters are close on the chromosome of x. albilineans.
CONCLUSIONS
during their descent from a common ancestral parent, the two xylem-limited xanthomonadaceae experienced a convergent reductive evolution.
adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution.
alternatively, the most important factor affecting genome erosion of x. fastidiosa and x. albilineans may reflect insect-associated lifestyles specific to these xanthomonadaceae.
x. albilineans and x. fastidiosa evolved differently: genome erosion has occurred to different extents and specific genes have been acquired independently by x. albilineans and x. fastidiosa.
for example, x. albilineans has acquired a t3ss of the spi- <dig> family that is mainly found in free-living animal pathogens and four nrps gene clusters that are involved in the biosynthesis of albicidin and probably other unknown small molecules.
the toxin albicidin may be responsible for the distinctive genome erosion of x. albilineans.
much progress has been recently made in understanding how x. fastidiosa spreads within the xylem vessels as well as the traits that contribute to its acquisition and transmission by sharpshooter vectors .
a similar in-depth functional analysis will be necessary to identify the genes that are required for x. albilineans to spread and succeed within sugarcane xylem vessels.

 the xanthomonadaceae are a family of gram negative bacteria belonging to the order xanthomonadales in the gamma subdivision of the proteobacteria. members of this family are typically characterized as environmental organisms and occupy diverse ecological niches, such as soil and water, as well as plant tissues. many xanthomonadaceae, especially species from the genera xanthomonas and xylella, cause plant diseases and only one, stenotrophomonas maltophilia, is known to be an opportunistic human pathogen. complete genome sequences of several xanthomonas species and xylella fastidiosa strains have been determined, making those bacteria attractive models for study of plant-pathogen interactions. x. fastidiosa was the first completely sequenced plant pathogen. sequence analysis showed that this xylem-limited bacterium, which is insect-vectored to a variety of diverse hosts, had a reduced genome and did not possess hrp genes, which encode a type iii secretion system found in most gram negative plant pathogenic bacteria. phylogenetic analysis with rrna sequences showed that the two major genera of xanthomonadaceae, xanthomonas and stenotrophomonas, form a coherent group excluding x. fastidiosa. these characteristics suggested the hypothesis that this species evolved from an ancestor shared with xanthomonas and stenotrophomonas by genome reduction during adaptation to life within its hosts. xanthomonas albilineans is a systemic, xylem-limited pathogen that causes leaf scald, one of the major diseases of sugarcane. leaf scald symptoms vary from a single, white, narrow, sharply defined stripe to complete wilting and necrosis of infected leaves, leading to plant death. x. albilineans produces the toxin albicidin that has phytotoxic and antibiotic properties. albicidin is a potent dna gyrase inhibitor that targets the chloroplastic dna gyrase a, inhibits chloroplast dna replication and blocks chloroplast differentiation, resulting in the white foliar stripe symptoms. all attempts to identify hrp genes in x. albilineans failed so far. a phylogenetic study with the housekeeping genes ihfa and efp, which did not include s. maltophilia sequences, suggested that x. albilineans was an evolutionary intermediate between several xanthomonas species and x. fastidiosa. unlike other xylem-invading xanthomonads that interact with living plant tissues, such as x. campestris pv. campestris or x. oryzae pv. oryzae, x. fastidiosa and x. albilineans appear to be strictly xylem-limited, living only in dead xylem cells or tracheary elements. in order to better understand the evolution of these two xylem-limited xanthomonadaceae, we sequenced the genome of x. albilineans strain gpe pc from guadeloupe. this sequence was compared to complete genome sequences of other closely related members of the xanthomonadaceae. this comparative analysis revealed that x. albilineans and x. fastidiosa experienced a convergent reductive genome evolution from a common ancestral parent of the xanthomonas genus.  general genomic features of x. albilineans the genome of x. albilineans strain gpe pc consists of one circular chromosome of, bp and three extrachromosomal plasmids of and kbp, respectively. the chromosome exhibits a gc skew pattern typical of prokaryotic genomes that have two major shifts, one near the origin and one near the terminus of replication, with dnaa assigned as base pair of the chromosome. the gc skew pattern of x. albilineans contains a lower number of diagram distortions and has much lower amplitude than the gc skew pattern of x. fastidiosa. however, the amplitude of the gc skew pattern of x. albilineans is significantly higher than the one of other xanthomonads and s. maltophilia. of the putative protein-coding sequences manually annotated on the chromosome of x. albilineans strain gpe pc were assigned putative functions based on homology to other known proteins and domain analyses. the general features of the x. albilineans chromosome were compared to those of the chromosomes of the following eight xanthomonadaceae strains: x. oryzae pv. oryzae strain maff, x. campestris pv. campestris strain atcc, x. axonopodis pv. vesicatoria strain 85-, x. axonopodis pv. citri strain, s. maltophilia strain k279a, s. maltophilia strain r551-, x. fastidiosa strain 9a5c and x. fastidiosa strain temecula. the chromosome of x. albilineans is mb smaller than the chromosomes of x. axonopodis pv. vesicatoria strain 85- and x. axonopodis pv. citri strain but it is mb bigger than the chromosome of x. fastidiosa strain temecula. the g+c content of the chromosome of x. albilineans averages 63%. this value is similar to those of other xanthomonas strains, but it is 12% higher than the g+c content of the chromosome of x. fastidiosa strain temecula the chromosome of x. albilineans shows an average coding density of 84%, which is also similar to other xanthomonads. acore genome cds correspond to the orthologs shared by the nine xanthomonadaceae comparative genomic analyses in order to assess phylogenetic relationships among the nine xanthomonadaceae mentioned above, we performed multilocus sequence analysis. the phylogenetic tree obtained with the concatenated data set of seven housekeeping genes showed that x. albilineans belongs to the same clade as x. fastidiosa. the clade containing x. albilineans and x. fastidiosa is clearly distinct from the clade containing the four xanthomonads of the hrp xanthomonas group. on the basis of this phylogenetic tree, we conclude that x. albilineans and x. fastidiosa derived from the progenitor of the xanthomonas genus. in order to identify orthologs shared by the nine xanthomonadaceae strains, we performed orthomcl comparative analyses. the x. albilineans cdss shared with x. fastidiosa strain 9a5c, s. maltophilia strain k279a or x. axonopodis pv. vesicatoria strain 85- are represented on the circular chromosome. interestingly, the chromosome of x. albilineans harbours several large regions that do not contain any genes present in the other eight xanthomonadaceae strains. these regions correspond either to phage related sequences or to large genes encoding proteins that contain repeated rhs elements that are known to be frequently transferred by horizontal genetic transfer. they also contain several gene clusters specific to x. albilineans: the albicidin biosynthesis gene cluster xalb which was previously sequenced from x. albilineans strain xa23r and which contains three nonribosomal peptide synthetases genes; three additional nrps gene clusters to which cannot be ascribed a precise function as they have not been previously identified and no strictly orthologous genes were found in other bacteria; and a gene cluster encoding a t3ss of the spi- family that is mainly found in free-living animal pathogens. the orthomcl analyses identified a total of cdss of the genome of x. albilineans strain gpe pc that are not shared with any of the other eight xanthomonadaceae complete genome sequences compared in this study. they also identified cdss shared by the nine xanthomonadaceae, which represent a xanthomonadaceae core gene set which was likely inherited from a common ancestor. evidence of convergent genome reductive evolution of x. albilineans and x. fastidiosa the phylogenetic tree presented in figure suggests that x. albilineans, x. fastidiosa and the hrp xanthomonas group derived from a common ancestor shared with stenotrophomonas. the chromosome sizes of x. albilineans and x. fastidiosa are smaller than those of any other xanthomonad, suggesting that both species evolved from the progenitor of xanthomonads by genome reduction. to examine how the chromosomes of x. albilineans and x. fastidiosa have evolved to result in these different sizes, we determined the order of divergence of x. albilineans, x. fastidiosa, the four xanthomonads of the hrp xanthomonas group and s. maltophilia. orthologous genes shared by s. maltophilia and a species of the hrp xanthomonas group, but missing in x. albilineans or x. fastidiosa, may be assumed to have been lost by x. albilineans or x. fastidiosa, respectively. inversely, genes of a species of the hrp xanthomonas group that are shared with s. maltophilia, x. albilineans or x. fastidiosa may be assumed to have been inherited from the progenitor of the xanthomonas genus. on the basis of orthomcl analysis, the numbers of genes lost by x. albilineans strain gpe pc and x. fastidiosa strain 9a5c are at least and respectively. the number of ancestral genes inherited from the progenitor of the xanthomonas genus is higher in x. axonopodis pv. vesicatoria than in any other species of the hrp xanthomonas group. interestingly, x. oryzae pv. oryzae strain maff contains the smallest number of genes lost by x. albilineans or x. fastidiosa, indicating that a significant number of genes lost by x. albilineans or x. fastidiosa were also lost by the xylem-invading pathogen x. oryzae pv. oryzae. on the basis of orthomcl analysis including both x. albilineans strain gpe pc and x. fastidiosa strain 9a5c, ancestral genes were lost by both x. albilineans and x. fastidiosa, ancestral genes were lost only by x. fastidiosa, and ancestral genes were lost only by x. albilineans. comparison of the reductive evolutions of x. albilineans and x. fastidiosa further comparative analyses were performed to compare genome erosion in x. albilineans and x. fastidiosa. for these analyses, we selected the genome of x. axonopodis pv. vesicatoria, which contains the highest number of genes inherited from the progenitor of the xanthomonas genus. orthomcl analysis identified cdss of x. axonopodis pv. vesicatoria that do not include any transposase genes and that are shared either by x. albilineans strain gpe pc x. fastidiosa strain 9a5c or one of the two s. maltophilia strains k279a and r551- for each of the cdss, we looked for the best blast hit within a database that included: all annotated cdss from the genome sequence of x. albilineans strain gpe pc and all available sequences from public databases excluding all sequences from the xanthomonads. on the basis of these analyses and among the cdss, we selected the genes for which the best blast hit belonged to x. albilineans, x. fastidiosa or s. maltophilia. we made the hypothesis that these genes were inherited by x. axonopodis pv. vesicatoria from the ancestor of the xanthomonads. these best blast hit analyses confirmed that of these cdss have the same ancestor as genes present either in x. albilineans, x. fastidiosa or s. maltophilia and were therefore inherited by x. axonopodis pv. vesicatoria from the progenitor of the xanthomonas genus. the elimination of paralogs present in at least two copies in x. axonopodis pv. vesicatoria generated a list of cdss representing one copy of each gene inherited by x. axonopodis pv. vesicatoria from the progenitor of the xanthomonas genus. these cdss are listed and individually analysed in additional file among them, cdss are shared by both x. fastidiosa and x. albilineans, cdss are shared only with one of the two s. maltophilia strains, cdss are shared with x. fastidiosa but not with x. albilineans and cdss are shared with x. albilineans but not with x. fastidiosa. the distribution in functional cog categories of these cdss is illustrated in figure analyses of the arrangement of these ancestral genes on the chromosome of x. axonopodis pv. vesicatoria strain 85- led to the identification of dna regions constituting contiguous ancestral genes that are missing in x. albilineans or x. fastidiosa. during the speciation of x. fastidiosa or x. albilineans, the loss of these dna regions was due either to a single event of deletion or to the cumulative effect of multiple events. for example, the loss in x. fastidiosa of the large dna region constituted by ancestral genes from xcv to xcv seems to be due to a single event of deletion since all these ancestral genes are missing in x. fastidiosa. this large dna region lost by x. fastidiosa encodes all flagellar proteins and several chemotaxis proteins. the sum of the length of the ancestral genes present in this dna region is bp, strongly suggesting that x. fastidiosa experienced a single deletion of a dna fragment of a larger size. the other dna regions constituting contiguous ancestral genes that are missing in x. albilineans or x. fastidiosa are shorter and, for this reason, their loss may result either from a single event of deletion or from multiple mutational events. analysis of the arrangement on the chromosome of x. axonopodis pv. vesicatoria strain 85- of ancestral genes absent in x. albilineans or x. fastidiosa did not allow us to determine if the genes absent in both xylem-limited xanthomonadaceae were lost by their common ancestor or were lost independently after their divergence. the loss of genes by pseudogenization and short deletions should not affect the position on the chromosome of the genes that precede or follow the lost genes. in order to identify ancestral genes putatively lost by pseudogenization and short deletions, we looked for ancestral lost genes that are present on the chromosome of x. axonopodis pv. vesicatoria between the orthologs of two ancestral genes that are contiguous and conserved in x. fastidiosa or x. albilineans. for example, the rpf gene cluster contains in x. axonopodis pv. vesicatoria two ancestral genes that are missing in both x. albilineans and x. fastidiosa. the ancestral genes xcv and xcv that precede and follow respectively these two lost genes are orthologs of either xalc_ and xalc_ or xf and xf that are contiguous in x. albilineans and x. fastidiosa, respectively. using the same strategy we identified and ancestral genes potentially lost by pseudogenization by x. fastidiosa and x. albilineans, respectively. common genomic features of x. fastidiosa and x. albilineans the close relationship between x. albilineans and x. fastidiosa is illustrated by the common unique characteristics of their enzymes involved in cellulose degradation. in these two xylem-limited xanthomonadaceae, endoglucanase engxca and -beta cellobiosidase cbha possess a cellulose binding domain and a long polyserine linker at their c termini. the endoglucanase engxca is conserved in all other xanthomonas species and also has a cbd, but the linker is much shorter and its serine content is much lower. the -beta cellobiosidase cbha is conserved in the xylem-invading xanthomonads x. campestris pv. campestris and x. oryzae pv. oryzae but, in these two species, cbha does not possess any linker nor any cbd. the presence of a cbd is known to increase catalytic activity by reducing the "substrate accessibility problem". the long flexible psl was proposed to enhance substrate accessibility. the presence of genes encoding enzymes harbouring a psl and a cbd provides evidence that both x. fastidiosa and x. albilineans are adapted to use plant cell breakdown products as carbon sources. apsl = polyserine linker; bcbd = cellulose binding domain the orthomcl analyses identified orthologs shared only by x. fastidiosa strain 9a5c, x. fastidiosa strain temecula and x. albilineans gpe pc. blast analyses confirmed that of these cdss are unique to x. albilineans and x. fastidiosa. interestingly, they include the gene mete which encodes the 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase. this enzyme is absolutely required for the biosynthesis of methionine and is therefore present in all xanthomonadaceae. however, the mete gene present in the two xylem-limited xanthomonadaceae is closer to the gene mete of mesorhizobium sp. than the mete present in the other xanthomonas species and in s. maltophilia. this strongly suggests that the progenitor of the two xylem-limited xanthomonadaceae lost the ancestral mete gene and acquired another mete by horizontal genetic transfer. the genes unique to x. albilineans and x. fastidiosa also include one cysteine protease gene, one abc transporter gene, one polysaccharide deacetylase gene, one glycosyl transferase gene, one hydrolase gene, one cell filamentation protein gene and four hypothetical protein genes. blast analyses confirmed that x. albilineans, like x. fastidiosa, lacks the hrp t3ss that is present in other xanthomonas species and does not possess any of the known hrp type iii effectors. the hrp t3ss, which plays a major role in suppressing host plant defense responses in most other pathogenic xanthomonas strains, was therefore probably acquired after the divergence of the hrp xanthomonas group and xylem-limited xanthomonadaceae lineages. no remains of the hrp gene cluster were found in the complete genome sequence of x. albilineans strain gpe pc nor in the available complete genome sequences of x. fastidiosa. discussion in their rather cloistered environmental niche inside xylem vessels, x. albilineans and x. fastidiosa may have largely avoided surveillance by general and specific plant defense systems. their lack of a t3ss of the hrp or hrp families may be explained by the fact that x. albilineans and x. fastidiosa live and multiply essentially in a dead-cell environment. however, like other bacterial vascular pathogens, they may interact with living xylem parenchyma cells through pit membranes. if they do, they do not use a hrp ttss but another system that remains to be identified. the adaptation of x. albilineans and x. fastidiosa to a xylem-limited lifestyle is also illustrated by their enzymes adapted to the use of plant cell breakdown products as carbon sources. the low number of genes unique to both x. albilineans and x. fastidiosa may be explained by a very early divergence of the two xylem-limited xanthomonadaceae lineages, possibly followed by strong selective pressure to adapt to their different biological niches and lifestyles. x. fastidiosa is vector-transmitted by various xylem sap-feeding insects and is able to colonize many plant species. on the other hand, x. albilineans is mainly transmitted by mechanical means and is not known to be insect-transmitted, and is able to colonize only sugarcane and few other monocots in the poaceae family. the genome of x. albilineans encodes a t3ss that displays similarities with the burkholderia pseudomallei bsa t3ss which belongs to the injectisome family spi- and which is required for the virulence of this human pathogen. the spi- injectisome family mainly includes t3sss from human and insect bacterial pathogens or symbionts. interestingly, the genomes of erwinia amylovora strain ea and erwinia tasmaniensis strain et1/ both contain two copies of a spi- t3ss. the role of these spi- t3sss in these plant-invading erwinia spp. remains unknown. e. amylovora is insect-disseminated, although the interactions between this pathogen and its insect hosts remain poorly understood. it was suggested that the presence of a spi- t3ss in erwinia spp. indicates a common ancestry and close phylogenetic relationship between erwinia spp. and insect-related enteric bacteria, raising the possibility that an insect host might be serving as a mixing vessel for the exchange of genes between erwinia strains and other enteric bacteria. similarly, the presence of a spi- t3ss in the genome of x. albilineans could indicate an insect-associated life style of this plant pathogen. the mlsa performed herein resulted in a phylogenetic tree that included x. fastidiosa into the xanthomonas group. this phylogenetic tree is in accordance with the presence of the unique gum genes in both x. fastidiosa and xanthomonas species of the hrp xanthomonas group. the gum genes, which are involved in the biosynthesis of extracellular polysaccharides and the formation of biofilms, play a key role in pathogenicity of these xanthomonadaceae. these genes, which were probably acquired by the progenitor of the xanthomonas genus, were most likely lost by x. albilineans and conserved by x. fastidiosa during their speciation. our mlsa phylogenetic tree is also in accordance with i/the presence of unique genes, including mete, in x. albilineans and x. fastidiosa, and ii/the alignment of the 5' end of the 16s rna of xanthomonadaceae. additionally, based on this mlsa, the same ancestral genes appeared to be lost by both x. albilineans and x. fastidiosa. interestingly, of the ancestral genes lost by both x. albilineans and x. fastidiosa are also absent in x. oryzae pv. oryzae, indicating that independent but convergent evolution events were involved in genome erosion of x. oryzae pv. oryzae and the xylem-limited xanthomonadaceae. some of these genes lost by three xylem-invading pathogens are orthologous of genes with assigned functions and are organized into clusters. the five following ancestral gene clusters were lost by x. albilineans, x. fastidiosa and x. oryzae pv. oryzae: i/ the ancestral genes xcv to xcv encoding enzymes involved in the glyoxylate cycle; ii/ the ancestral genes xcv to xcv encoding enzymes involved in malonate metabolism; iii/ the ancestral genes xcv to xcv including one tonb-dependant receptor gene, a two component signal transduction system and chemotaxis genes, iv/ the ancestral genes xcv to xcv including one tcsts and a type i secretion system and v/ the ancestral genes xcv to xcv encoding enzymes involved in catabolism of polysaccharides. these examples support the hypothesis of a link between the convergent erosion of three xylem-invading xanthomonadaceae and the adaptation to a same restricted environment in which these lost functions are useless. however, only of the ancestral genes lost by both x. albilineans and x. fastidiosa are also absent in another xylem invading pathogen, x. campestris pv. campestris, indicating that adaptation to xylem lifestyle favoured or allowed genome erosion, but did not necessarily induce it. alternatively, the convergent genome erosion of the two xylem-limited xanthomonadaceae may be linked to similar insect-associated lifestyles that may have favoured genome erosion because most of the genes required for a plant-associated life style are most likely not required for an insect-associated life style. similar striking convergence in fundamental genomic features associated with a restricted lifestyle is very well documented for obligate animal symbionts and pathogens, especially for buchnera. in these bacteria, gene losses are non-random but can affect all functional categories. the most dramatic losses affect genes that are involved in metabolism but are not required for survival. another general feature is the loss of most dna repair systems and transcriptional regulatory mechanisms, indicating that there is reduced need for transcriptional regulation in a stable environment. in x. fastidiosa, and to a lesser extent in x. albilineans, losses also affected genes involved in metabolism and transcriptional regulatory mechanisms. metabolic capabilities essential for other habitats may have been lost in the genome reduction process coincidently with the adaptation of x. fastidiosa and x. albilineans to the nutrient-poor xylem environment. for x. fastidiosa, genome erosion has been extreme. for example, x. fastidiosa retained only one transcriptional sigma factor gene and one outer membrane efflux protein tolc gene, and it lost all genes involved in synthesis of the flagellar apparatus. this extreme erosion allowed x. fastidiosa to save energy. in obligate animal symbionts and pathogens, the process of genome shrinkage might have taken place in two separate stages. a massive gene loss must have occurred soon after the establishment of the obligate symbiosis, probably by means of large deletions that eliminated a series of contiguous genes. the large dna region containing the flagellar genes was probably lost by x. fastidiosa during a similar stage. the accumulation of mobile elements, representing a source of chromosomal rearrangements and gene inactivation, seems to have an important role in this first stage. a similar process is likely responsible for the limited genome erosion of x. oryzae pv. oryzae, which possesses a very high number of insertion sequences covering 20% of the genome. during the second stage of genome reduction in obligate animal symbionts and pathogens, genome shrinkage seems to have mostly occurred through a process of gradual gene loss, scattered along the genome. such losses seem to follow a pattern that starts with the inactivation of a gene by single-nucleotide mutations, and continues with a rapid reduction in length until the original gene is completely eroded. a similar process is likely responsible for the genome erosions of x. fastidiosa and x. albilineans. furthermore, the coding density of x. fastidiosa strain temecula is significantly smaller than that of xanthomonads probably because of the degradation of ancestral genes. in x. fastidiosa strain 9a5c, the number of short annotated cdss is considerably higher than in other xanthomonadaceae, although the functionality of these shortened cdss, which may result from the degradation of ancestral genes, is questionable. obligate animal symbionts and pathogens display rapid evolution and have highly biased nucleotide base compositions with elevated frequencies of adenine and thymine. x. fastidiosa also displays rapid evolution and has a high a+t content in comparison with other xanthomonadaceae. furthermore, the gc skew pattern of the chromosome of x. fastidiosa has very high amplitude and contains a high number of diagram distortions. a similar atypical gc skew pattern was observed for the chromosome of a buchnera aphidicola strain. this latter atypical gc skew coincides with the loss of genes involved in the replication restart process and may be explained by a higher frequency of cytosine deaminations. the loss of dna repair genes recx, ding and dinp may explain, similarly, the very high gc skew of x. fastidiosa. it may also explain the more extensive genome erosion of x. fastidiosa, compared to x. albilineans and x. oryzae pv. oryzae. alternatively, the most important factor affecting genome erosion of x. fastidiosa may reflect the insect-associated lifestyle specific to this xanthomonadaceae. the gc skew pattern of the x. albilineans chromosome contains a lower number of distortions and has a significantly higher amplitude than the gc skew pattern of other xanthomonas species, indicating that no recent events of recombination have occurred in x. albilineans. furthermore, the synteny between the chromosomes of x. albilineans strain gpe pc and x. axonopodis pv. vesicatoria strain 85- also indicated that recombination events were limited during the speciation of x. albilineans. the limited recombination of the chromosome of x. albilineans, its limited erosion, its high g+c content and its low number of is elements may indicate that a distinctive process was responsible for the reductive genome evolution of this pathogen. we propose a unique mechanism of genome erosion involving the unique toxin albicidin produced by x. albilineans. albicidin is a potent dna gyrase inhibitor with 50% inhibitory concentrations lower than those of most quinolones. dna gyrase inhibitors block the religation of cleaved dna intermediate during gyrase catalysis, resulting in lethal double-stranded dna breaks. in the presence of subinhibitory doses of dna gyrase inhibitors, the sos response mediates survival of the bacteria by allowing dna replication to continue past breaks that would normally block it. in exchange for this survival advantage, there is an increased mutation rate because the polymerases that perform the repair are prone to error. several studies showed that subinhibitory doses of quinolones result in an increased mutation rate in escherichia coli, staphylococcus aureus, pseudomonas aeruginosa and mycobacterium tuberculosis. x. albilineans has two genes conferring resistance to albicidin: an albicidin efflux pump gene that is present in the albicidin biosynthesis gene cluster xalb and an albicidin-resistant dna gyrase a gene elsewhere on the chromosome. this albicidin-resistant dna gyrase a is unique to x. albilineans. it contains a unique insertion of amino-acids length close to the albicidin binding site. production of albicidin in ancestral bacteria that possessed both the albicidin biosynthesis gene cluster and a dna gyrase a sensitive to albicidin may have induced genome erosion. in these ancestral bacteria, most of the albicidin molecules were secreted by the albicidin efflux pump. occasionally, molecules of albicidin that were not secreted most likely had the same effect as subinhibitory doses of quinolones: the sos response was induced, thus resulting in dna repair, recombination and mutagenesis. successive and cumulative effect of albicidin at each replication cycle eventually resulted in genome erosion. the genome erosion induced by albicidin was likely arrested by evolution of the albicidin-resistant dna gyrase a. acquisition of the albicidin biosynthesis genes by the ancestor of x. albilineans conferred a selective advantage because of the potent antibiotic activity of albicidin. the dna damage caused by albicidin may rapidly have induced the mutation of dna gyrase a gene and thus stopped the process of genome erosion, possibly explaining the distinctive genomic characteristics of x. albilineans. albicidin inhibits the growth of x. axonopodis pv. vesicatoria, suggesting that the dna gyrase a of the ancestral xanthomonas was sensitive to albicidin. transfer of the albicidin biosynthesis gene cluster to x. axonopodis pv. vesicatoria led to production of functional albicidin, demonstrating that the production of albicidin per se is not lethal for a producer that possesses an albicidin-sensitive dna gyrase a. no remains of the albicidin biosynthesis genes were found in the complete genome sequences of x. fastidiosa. therefore, albicidin is most likely not responsible for genome erosion of x. fastidiosa. however, we cannot exclude the hypothesis that albicidin biosynthesis genes were lost during evolution of x. fastidiosa. for example, cluster xalb could have been lost concurrently with the flagellar biosynthesis gene cluster because these two gene clusters are close on the chromosome of x. albilineans.  during their descent from a common ancestral parent, the two xylem-limited xanthomonadaceae experienced a convergent reductive evolution. adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. alternatively, the most important factor affecting genome erosion of x. fastidiosa and x. albilineans may reflect insect-associated lifestyles specific to these xanthomonadaceae. x. albilineans and x. fastidiosa evolved differently: genome erosion has occurred to different extents and specific genes have been acquired independently by x. albilineans and x. fastidiosa. for example, x. albilineans has acquired a t3ss of the spi- family that is mainly found in free-living animal pathogens and four nrps gene clusters that are involved in the biosynthesis of albicidin and probably other unknown small molecules. the toxin albicidin may be responsible for the distinctive genome erosion of x. albilineans. much progress has been recently made in understanding how x. fastidiosa spreads within the xylem vessels as well as the traits that contribute to its acquisition and transmission by sharpshooter vectors. a similar in-depth functional analysis will be necessary to identify the genes that are required for x. albilineans to spread and succeed within sugarcane xylem vessels. 
x. fastidiosa was the first completely sequenced plant pathogen. x. fastidiosa was excluded from the xanthomonas group based on phylogenetic analyses with rrna sequences. phylogenetic analysis using x. albilineans genomic sequences showed that x. fastidiosa belongs to the xanthomonas group. order of divergence of the xanthomonadaceae revealed that x. albilineans and x. fastidiosa experienced a convergent reductive genome evolution during their descent from the progenitor of the xanthomonas genus. however, genome characteristics of x. albilineans differ from those of x. fastidiosa and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. it is insect-vectored, has a reduced genome and does not possess hrp genes which encode a type iii secretion system found in most plant pathogenic bacteria. x. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possess hrp genes. adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. the complete genome of x. albilineans was sequenced and annotated. the possible role in genome reduction of the unique toxin albicidin, produced by x. albilineans, is discussed. the xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, xanthomonas albilineans and xylella fastidiosa. reductive genome evolutions of the two xylem-limited xanthomonadaceae were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens. the two xylem-limited xanthomonadaceae, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution.
 the xanthomonadaceae family contains two xylem-limited plant pathogenic bacterial species, xanthomonas albilineans and xylella fastidiosa. x. fastidiosa was the first completely sequenced plant pathogen. it is insect-vectored, has a reduced genome and does not possess hrp genes which encode a type iii secretion system found in most plant pathogenic bacteria. x. fastidiosa was excluded from the xanthomonas group based on phylogenetic analyses with rrna sequences.  the complete genome of x. albilineans was sequenced and annotated. x. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possess hrp genes. phylogenetic analysis using x. albilineans genomic sequences showed that x. fastidiosa belongs to the xanthomonas group. order of divergence of the xanthomonadaceae revealed that x. albilineans and x. fastidiosa experienced a convergent reductive genome evolution during their descent from the progenitor of the xanthomonas genus. reductive genome evolutions of the two xylem-limited xanthomonadaceae were compared in light of their genome characteristics and those of obligate animal symbionts and pathogens.  the two xylem-limited xanthomonadaceae, during their descent from a common ancestral parent, experienced a convergent reductive genome evolution. adaptation to the nutrient-poor xylem elements and to the cloistered environmental niche of xylem vessels probably favoured this convergent evolution. however, genome characteristics of x. albilineans differ from those of x. fastidiosa and obligate animal symbionts and pathogens, indicating that a distinctive process was responsible for the reductive genome evolution in this pathogen. the possible role in genome reduction of the unique toxin albicidin, produced by x. albilineans, is discussed. 