(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) > cellular organisms: NE > Bacteria: NE > Proteobacteria: NE > Gammaproteobacteria: NE > Xanthomonadales: NE > Xanthomonadaceae: NE > Xanthomonas: NE > Xanthomonas oryzae: NE
Warning: This entry is a compilation of different species or line or strain with more than 90% amino acid identity. You can retrieve all strain data
(Below N is a link to NCBI taxonomic web page and E link to ESTHER at designed phylum.) Xanthomonas oryzae pv. oryzae: N, E.
Xanthomonas oryzae pv. oryzae MAFF 311018: N, E.
Xanthomonas oryzae pv. oryzae PXO99A: N, E.
Xanthomonas oryzae pv. oryzae KACC 10331: N, E.
Xanthomonas oryzae pv. oryzicola: N, E.
Xanthomonas oryzae pv. oryzicola BLS256: N, E.
LegendThis sequence has been compared to family alignement (MSA) red => minority aminoacid blue => majority aminoacid color intensity => conservation rate title => sequence position(MSA position)aminoacid rate Catalytic site Catalytic site in the MSA MLPGRCHLGLCLPDPLRTRLVPITLPAILPILPMPSRASRWFRPALLLLG SLPLTACSSVFFGGINAASSRAGIVEHHDQVFDPAHGLALDVYQPRGAVD APVVVFFYGGTWKRGSRANYRWVGRALARRGVVAMVADYRKYPQVGLHGF MSDAAGATAWSYRHAHEYGGDPKRMAVMGHSAGAHMAALLGTDARWLQAQ GLKPYQLCGVVGLAGPYDFMPMTDPELVEIFGDAPAAQRQSQPVRYVGGD EPPMLLLHGDADRVVELQNSISLQQALKRRGDSAELKVYPGIGHLGILLA LRQPPERSQVLSDTLQFVRQCRAH
BACKGROUND: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. RESULTS: The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus. CONCLUSION: Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.
The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, a bacterium that causes bacterial blight in rice (Oryza sativa L.). The genome is comprised of a single, 4 941 439 bp, circular chromosome that is G + C rich (63.7%). The genome includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be assigned putative function. Orthologs for 80% of the predicted Xoo genes were found in the previously reported X.axonopodis pv. citri (Xac) and X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently specific to Xoo were identified. Xoo genes likely to be associated with pathogenesis include eight with similarity to Xanthomonas avirulence (avr) genes, a set of hypersensitive reaction and pathogenicity (hrp) genes, genes for exopolysaccharide production, and genes encoding extracellular plant cell wall-degrading enzymes. The presence of these genes provides insights into the interactions of this pathogen with its gramineous host.
Title: Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity Inoue Y, Takeya M, Sasaki A, Kaki H Ref: , 39:275, 2005 : PubMed
The plant-pathogenic prokaryote Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, one of the most important diseases of rice. The bacterium is a model organism for the analysis of plant-pathogen interaction, because more than 30 races differing in virulence and 25 resistance genes in rice have been reported to date. We present here the complete genome sequence of Xoo strain MAFF 311018. The size of the genome was 4,940,217 bp, in a single circular chromosome. The genome structure of Xoo MAFF 311018 was characterized by large numbers of effector (avr) genes of the avrBs3/pth family and insertion sequences (ISs). RFLP analysis of diverse strains using ISXo1 as a probe suggests that the prevalence of mobile elements in this species, which can bring about genome inversions and rearrangement, may have played a major role in generating the high degree of genetic diversity and race differentiation characteristic of this pathogen. The Xoo MAFF 311018 sequence was also highly similar to those of X. axonopodis pv. citri and X. campestris pv. campestris with the exception of the large number of effectors and IS elements, and numerous inversions and rearrangements.
Transcription activator-like effectors (TALEs) are virulence factors, produced by the bacterial plant-pathogen Xanthomonas, that function as gene activators inside plant cells. Although the contribution of individual TALEs to infectivity has been shown, the specific roles of most TALEs, and the overall TALE diversity in Xanthomonas spp. is not known. TALEs possess a highly repetitive DNA-binding domain, which is notoriously difficult to sequence. Here, we describe an improved method for characterizing TALE genes by the use of PacBio sequencing. We present 'AnnoTALE', a suite of applications for the analysis and annotation of TALE genes from Xanthomonas genomes, and for grouping similar TALEs into classes. Based on these classes, we propose a unified nomenclature for Xanthomonas TALEs that reveals similarities pointing to related functionalities. This new classification enables us to compare related TALEs and to identify base substitutions responsible for the evolution of TALE specificities.
BACKGROUND: Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. RESULTS: The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus. CONCLUSION: Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world.
The nucleotide sequence was determined for the genome of Xanthomonas oryzae pathovar oryzae (Xoo) KACC10331, a bacterium that causes bacterial blight in rice (Oryza sativa L.). The genome is comprised of a single, 4 941 439 bp, circular chromosome that is G + C rich (63.7%). The genome includes 4637 open reading frames (ORFs) of which 3340 (72.0%) could be assigned putative function. Orthologs for 80% of the predicted Xoo genes were found in the previously reported X.axonopodis pv. citri (Xac) and X.campestris pv. campestris (Xcc) genomes, but 245 genes apparently specific to Xoo were identified. Xoo genes likely to be associated with pathogenesis include eight with similarity to Xanthomonas avirulence (avr) genes, a set of hypersensitive reaction and pathogenicity (hrp) genes, genes for exopolysaccharide production, and genes encoding extracellular plant cell wall-degrading enzymes. The presence of these genes provides insights into the interactions of this pathogen with its gramineous host.
Title: Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity Inoue Y, Takeya M, Sasaki A, Kaki H Ref: , 39:275, 2005 : PubMed
The plant-pathogenic prokaryote Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight, one of the most important diseases of rice. The bacterium is a model organism for the analysis of plant-pathogen interaction, because more than 30 races differing in virulence and 25 resistance genes in rice have been reported to date. We present here the complete genome sequence of Xoo strain MAFF 311018. The size of the genome was 4,940,217 bp, in a single circular chromosome. The genome structure of Xoo MAFF 311018 was characterized by large numbers of effector (avr) genes of the avrBs3/pth family and insertion sequences (ISs). RFLP analysis of diverse strains using ISXo1 as a probe suggests that the prevalence of mobile elements in this species, which can bring about genome inversions and rearrangement, may have played a major role in generating the high degree of genetic diversity and race differentiation characteristic of this pathogen. The Xoo MAFF 311018 sequence was also highly similar to those of X. axonopodis pv. citri and X. campestris pv. campestris with the exception of the large number of effectors and IS elements, and numerous inversions and rearrangements.
