The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli.

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

Outbreaks of Bacterial Spot Caused by Xanthomonas gardneri on Processing Tomato in Central-West Brazil.

Severe epidemics of bacterial spot have been observed in central-west Brazil in fields of processing tomato. Several xanthomonads, Xanthomonas axonopodis pv. vesicatoria, X. vesicatoria, or X. gardneri, can cause the disease; therefore, attempts were made to identify the pathogen species present in this region. A total of 215 strains were obtained from 10 commercial areas in 1997, 1998, and 2000. The strains were characterized using pulsed-field gel electrophoresis (PFGE) and by their amylolytic and pectolytic activities. Representative strains from each PFGE haplotype then were tested for pathogenicity on tomato and pepper, carbon source utilization, and whole protein sodium dodecyl sulfate-polyacrylamide gel electrophoresis. rRNA sequence comparisons also were performed. All strains recovered from six fields were classified as X. gardneri, whereas X. vesicatoria and X. axonopodis pv. vesicatoria also were detected in the remaining four fields. Strains of X. gardneri, which could be grouped into two PFGE haplotypes, were unable to hydrolyze starch and pectate and to utilize gentiobiose and maltose. They expressed the ß protein of 27 kDa and were pathogenic on tomato but variable on pepper. This is the first report of outbreaks of bacterial spot on tomato caused by X. gardneri.

A homolog of the RPS2 disease resistance gene is constitutively expressed in Brassica oleracea

In this study, we identified disease resistance gene homologs in Brassica oleracea and assessed their expression in lines resistant and susceptible to Xanthomonas campestris pv. campestris (Xcc). Two DNA fragments of approximately 2.5 kb (BI-16/RPS2 and Lc201/RPS2) were amplified by PCR from two Brassica lines using primers based on an RPS2 homologous sequence previously described in the Brassica oleracea ecotype B117. The sequences of these fragments shared high similarity (95-98 percent) with RPS2 homologs from various Brassica species. The digestion of these fragments with restriction enzymes revealed polymorphisms at the Xba I restriction sites. The length polymorphisms were used as a co-dominant marker in an F2 population developed to segregate for resistance to Xcc, the causal agent of black rot. Linkage analysis showed no significant association between the marker and quantitative trait loci for black rot. RT-PCR with specific primers yielded an expected 453 bp fragment that corresponded to the RPS2 homologs in both resistant and susceptible lines inoculated with the pathogen, as well as in non-inoculated control plants. These results suggest that these homologs are constitutively expressed in B. oleracea.

Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane.

To contribute to our understanding of the genome complexity of sugarcane, we undertook a large-scale expressed sequence tag (EST) program. More than 260,000 cDNA clones were partially sequenced from 26 standard cDNA libraries generated from different sugarcane tissues. After the processing of the sequences, 237,954 high-quality ESTs were identified. These ESTs were assembled into 43,141 putative transcripts. Of the assembled sequences, 35.6% presented no matches with existing sequences in public databases. A global analysis of the whole SUCEST data set indicated that 14,409 assembled sequences (33% of the total) contained at least one cDNA clone with a full-length insert. Annotation of the 43,141 assembled sequences associated almost 50% of the putative identified sugarcane genes with protein metabolism, cellular communication/signal transduction, bioenergetics, and stress responses. Inspection of the translated assembled sequences for conserved protein domains revealed 40,821 amino acid sequences with 1415 Pfam domains. Reassembling the consensus sequences of the 43,141 transcripts revealed a 22% redundancy in the first assembling. This indicated that possibly 33,620 unique genes had been identified and indicated that >90% of the sugarcane expressed genes were tagged.