Background: TheXanthomonadaceaefamily contains two xylem-limited plant pathogenic bacterial species,Xanthomonas albilineansandXylella fastidiosa.X. fastidiosawas the first completely sequenced plant pathogen. It is insect-vectored, has a reduced genome and does not possesshrpgenes which encode a Type III secretion system found in most plant pathogenic bacteria.X. fastidiosawas excluded from theXanthomonasgroup based on phylogenetic analyses with rRNA sequences.Results: The complete genome ofX. albilineanswas sequenced and annotated.X. albilineans, which is not known to be insect-vectored, also has a reduced genome and does not possesshrpgenes. Phylogenetic analysis usingX. albilineansgenomic sequences showed thatX. fastidiosabelongs to theXanthomonasgroup. Order of divergence of theXanthomonadaceaerevealed thatX. albilineansandX. fastidiosaexperienced a convergent reductive genome evolution during their descent from the progenitor of theXanthomonasgenus. Reductive genome evolutions of the two xylem-limitedXanthomonadaceaewere compared in light of their genome characteristics and those of obligate animal symbionts and pathogens.Conclusion: The two xylem-limitedXanthomonadaceae, 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 ofX. albilineansdiffer from those ofX. fastidiosaand 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 byX. albilineans, is discussed.

Background: Xanthomonads are plant-associated bacteria responsible for diseases on economically important crops. Xanthomonas fuscans subsp. fuscans (Xff) is one of the causal agents of common bacterial blight of bean. In this study, the complete genome sequence of strain Xff 4834-R was determined and compared to other Xanthomonas genome sequences. Results: Comparative genomics analyses revealed core characteristics shared between Xff 4834-R and other xanthomonads including chemotaxis elements, two-component systems, TonB-dependent transporters, secretion systems (from T1SS to T6SS) and multiple effectors. For instance a repertoire of 29 Type 3 Effectors (T3Es) with two Transcription Activator-Like Effectors was predicted. Mobile elements were associated with major modifications in the genome structure and gene content in comparison to other Xanthomonas genomes. Notably, a deletion of 33 kbp affects flagellum biosynthesis in Xff 4834-R. The presence of a complete flagellar cluster was assessed in a collection of more than 300 strains representing different species and pathovars of Xanthomonas. Five percent of the tested strains presented a deletion in the flagellar cluster and were non-motile. Moreover, half of the Xff strains isolated from the same epidemic than 4834-R was non-motile and this ratio was conserved in the strains colonizing the next bean seed generations. Conclusions: This work describes the first genome of a Xanthomonas strain pathogenic on bean and reports the existence of non-motile xanthomonads belonging to different species and pathovars. Isolation of such Xff variants from a natural epidemic may suggest that flagellar motility is not a key function for in planta fitness.

Background: Xanthomonas albilineanscauses leaf scald, a lethal disease of sugarcane.X. albilineansexhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species ofXanthomonas. For example, this species produces a potent DNA gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. A first manuscript on the complete genome sequence of the highly pathogenicX. albilineansstrain GPE PC73 focused exclusively on distinctive genomic features shared withXylella fastidiosa—another xylem-limitedXanthomonadaceae. The present manuscript on the same genome sequence aims to describe all other pathogenicity-related genomic features ofX. albilineans, and to compare, using suppression subtractive hybridization (SSH), genomic features of two strains differing in pathogenicity.Results: Comparative genomic analyses showed that most of the known pathogenicity factors from otherXanthomonasspecies are conserved inX. albilineans, with the notable absence of two major determinants of the “artillery” of other plant pathogenic species ofXanthomonas: the xanthan gum biosynthesis gene cluster, and the type III secretion system Hrp (hypersensitive response and pathogenicity). Genomic features specific toX. albilineansthat may contribute to specific adaptation of this pathogen to sugarcane xylem vessels were also revealed. SSH experiments led to the identification of 20 genes common to three highly pathogenic strains but missing in a less pathogenic strain. These 20 genes, which include four ABC transporter genes, a methyl-accepting chemotaxis protein gene and an oxidoreductase gene, could play a key role in pathogenicity. With the exception of hypothetical proteins revealed by our comparative genomic analyses and SSH experiments, no genes potentially involved in any offensive or counter-defensive mechanism specific toX. albilineanswere identified, supposing thatX. albilineanshas a reduced artillery compared to other pathogenicXanthomonasspecies. Particular attention has therefore been given to genomic features specific toX. albilineansmaking it more capable of evading sugarcane surveillance systems or resisting sugarcane defense systems.Conclusions: This study confirms thatX. albilineansis a highly distinctive species within the genusXanthomonas, and opens new perpectives towards a greater understanding of the pathogenicity of this destructive sugarcane pathogen.

Specific primer pairs were designed to distinguish four genotypes (BRA for Brazil, CUB for Cuba, PER for Peru, and REU for Réunion Island) of Sugarcane yellow leaf virus (SCYLV) by reverse transcription-polymerase chain reaction (RT-PCR). A unique genome fragment was amplified from each genotype, with the exception of genotypes BRA and PER that are phylogenetically relatively close and were designated genotype BRA-PER. These RT-PCR primers were then used to identify the SCYLV genotype(s) present in 18 different sugarcane growing locations in the world, and 245 leaf samples infected by the virus were analyzed. Most samples were infected by only one of the three genotypes, but mixed infections occurred. Genotype BRA-PER was found in all sugarcane growing locations, whereas genotypes CUB and REU were each found in four geographical locations only. Genotypes BRA-PER, CUB, and REU were all three detected in locally bred sugarcane cultivars in Guadeloupe, indicating local transmission of these genotypes. In contrast, only genotypes BRA-PER and CUB were found in locally bred cultivars in Brazil, whereas genotype REU was detected in this country in cultivar R570 imported from Réunion. Similarly, genotypes BRA-PER and REU are both present in Réunion, but genotype BRA-PER has not, as of yet, spread on this island. Presence of several SCYLV genotypes in Brazil, Colombia, Guadeloupe, Mauritius, and Réunion suggests different virus introductions and/or different evolution histories of the virus after its introduction into a new environment.

The spread of Sugarcane yellow leaf virus (SCYLV) in sugarcane plants was studied on Réunion using virus‐infected cuttings from four cultivars (R570, R575, R577 and R579). One month after the germination of cuttings in an insect‐proof glasshouse, SCYLV was detected by reverse‐transcription polymerase chain reaction (RT‐PCR) and tissue‐blot immunoassay (TBIA) in the leaves, shoots and roots of all cultivars. The distribution of SCYLV in the whole plant did not vary over a 10‐ to 11‐month period of growth. In addition, the spread of SCYLV in sugarcane fields on Réunion was investigated during a survey conducted from 1998 to 2001. Samples were taken in three sugarcane‐growing areas, and TBIA was used to detect SCYLV in the three major cultivars (R570, R575 and R579). The percentage of infected stalks varied according to cultivar and growing area, but remained relatively stable for a given cultivar in a given growing area over the 30‐month survey period. Cultivar R575 was the most infected cultivar in all three growing areas (mean of 98% infected stalks). The percentage of infected stalks ranged from 16 to 94% in cv. R570 and from 21 to 92% in cv. R579. These results suggested that on Réunion: (i) infected sugarcane stools do not recover from the disease after harvesting; and (ii) the virus is mainly propagated by planting infected cuttings. SCYLV was detected by RT‐PCR in the aphid Melanaphis sacchari , a potential vector of this virus. Two months after planting virus‐free plants of susceptible cv. R575 in a field surrounded by sugarcane infected with SCYLV, 14% of plants were found infected with the virus. Four months later, 25% of plants were found infected with SCYLV, but no new infections were detected between 6 and 12 months after planting. In the first ratoon crop, 42% of plants were infected with SCYLV after 6 months of growth. Spatial distribution of infected plants suggested that, on Réunion, a small window of time (between 0 and 2 months after planting cuttings) exists during which primary infection can occur. Based on the results obtained in this study, the use of clean planting material for some cultivars and the use of tolerant cultivars should be an efficient means of controlling sugarcane yellow leaf on Réunion.