Dow JM

References (4)

Title : Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper - Potnis_2011_BMC.Genomics_12_146
Author(s) : Potnis N , Krasileva K , Chow V , Almeida NF , Patil PB , Ryan RP , Sharlach M , Behlau F , Dow JM , Momol M , White FF , Preston JF , Vinatzer BA , Koebnik R , Setubal JC , Norman DJ , Staskawicz BJ , Jones JB
Ref : BMC Genomics , 12 :146 , 2011
Abstract : BACKGROUND: Bacterial spot of tomato and pepper is caused by four Xanthomonas species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, Xanthomonas euvesicatoria (Xcv) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10.
RESULTS: We sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X. perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced Xcv strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from Xg strain 101 and Xv strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in Xcv. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity.
CONCLUSIONS: Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster, and genes unique to individual strains, such as novel type III effectors and bacteriocin genes, have been identified providing new clues for our understanding of pathogen virulence, aggressiveness, and host preference. These analyses will aid in efforts towards breeding for broad and durable resistance in economically important tomato and pepper cultivars.
ESTHER : Potnis_2011_BMC.Genomics_12_146
PubMedSearch : Potnis_2011_BMC.Genomics_12_146
PubMedID: 21396108
Gene_locus related to this paper: 9xant-f0bam8 , 9xant-f0bb73 , 9xant-f0bea2 , 9xant-f0bfp7 , 9xant-f0c1j5 , 9xant-f0c9f8 , 9xant-f0c729 , xanax-CATD , xanax-CPO , xanax-ENTF2 , xanax-estA1 , xanax-GAA , xanax-PTRB , xanax-XAC0198 , xanax-XAC0262 , xanax-XAC0515 , xanax-XAC0591 , xanax-XAC0619 , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC0753 , xanax-XAC0805 , xanax-XAC1213 , xanax-XAC1713 , xanax-XAC2532 , xanax-XAC2541 , xanax-XAC2987 , xanax-XAC2990 , xanax-XAC3315 , xanax-XAC4046 , xanax-XAC4055 , xanax-XAC4106 , xanax-XAC4316 , xanc5-q3bqi2 , xanca-impep , xanca-XCC0266 , xanca-XCC1105 , xanca-XCC2566 , xanca-XCC2722 , xanca-XCC3296 , xanca-XCC3961 , xanor-acvB , xanor-metx , 9xant-f0bgj0 , 9xant-f0cdj1 , 9xant-a0a0g8v5k2 , 9xant-f0cdg7

Title : Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp - Bogdanove_2011_J.Bacteriol_193_5450
Author(s) : Bogdanove AJ , Koebnik R , Lu H , Furutani A , Angiuoli SV , Patil PB , Van Sluys MA , Ryan RP , Meyer DF , Han SW , Aparna G , Rajaram M , Delcher AL , Phillippy AM , Puiu D , Schatz MC , Shumway M , Sommer DD , Trapnell C , Benahmed F , Dimitrov G , Madupu R , Radune D , Sullivan S , Jha G , Ishihara H , Lee SW , Pandey A , Sharma V , Sriariyanun M , Szurek B , Vera-Cruz CM , Dorman KS , Ronald PC , Verdier V , Dow JM , Sonti RV , Tsuge S , Brendel VP , Rabinowicz PD , Leach JE , White FF , Salzberg SL
Ref : Journal of Bacteriology , 193 :5450 , 2011
Abstract : Xanthomonas is a large genus of bacteria that collectively cause disease on more than 300 plant species. The broad host range of the genus contrasts with stringent host and tissue specificity for individual species and pathovars. Whole-genome sequences of Xanthomonas campestris pv. raphani strain 756C and X. oryzae pv. oryzicola strain BLS256, pathogens that infect the mesophyll tissue of the leading models for plant biology, Arabidopsis thaliana and rice, respectively, were determined and provided insight into the genetic determinants of host and tissue specificity. Comparisons were made with genomes of closely related strains that infect the vascular tissue of the same hosts and across a larger collection of complete Xanthomonas genomes. The results suggest a model in which complex sets of adaptations at the level of gene content account for host specificity and subtler adaptations at the level of amino acid or noncoding regulatory nucleotide sequence determine tissue specificity.
ESTHER : Bogdanove_2011_J.Bacteriol_193_5450
PubMedSearch : Bogdanove_2011_J.Bacteriol_193_5450
PubMedID: 21784931
Gene_locus related to this paper: xanax-XAC4055 , xanca-CATD , xanca-estA1 , xanca-XCC0080 , xanca-XCC3164 , xanor-q5h5n1

Title : The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants - Crossman_2008_Genome.Biol_9_R74
Author(s) : Crossman LC , Gould VC , Dow JM , Vernikos GS , Okazaki A , Sebaihia M , Saunders D , Arrowsmith C , Carver T , Peters N , Adlem E , Kerhornou A , Lord A , Murphy L , Seeger K , Squares R , Rutter S , Quail MA , Rajandream MA , Harris D , Churcher C , Bentley SD , Parkhill J , Thomson NR , Avison MB
Ref : Genome Biol , 9 :R74 , 2008
Abstract : BACKGROUND: Stenotrophomonas maltophilia is a nosocomial opportunistic pathogen of the Xanthomonadaceae. The organism has been isolated from both clinical and soil environments in addition to the sputum of cystic fibrosis patients and the immunocompromised. Whilst relatively distant phylogenetically, the closest sequenced relatives of S. maltophilia are the plant pathogenic xanthomonads. RESULTS: The genome of the bacteremia-associated isolate S. maltophilia K279a is 4,851,126 bp and of high G+C content. The sequence reveals an organism with a remarkable capacity for drug and heavy metal resistance. In addition to a number of genes conferring resistance to antimicrobial drugs of different classes via alternative mechanisms, nine resistance-nodulation-division (RND)-type putative antimicrobial efflux systems are present. Functional genomic analysis confirms a role in drug resistance for several of the novel RND efflux pumps. S. maltophilia possesses potentially mobile regions of DNA and encodes a number of pili and fimbriae likely to be involved in adhesion and biofilm formation that may also contribute to increased antimicrobial drug resistance. CONCLUSION: The panoply of antimicrobial drug resistance genes and mobile genetic elements found suggests that the organism can act as a reservoir of antimicrobial drug resistance determinants in a clinical environment, which is an issue of considerable concern.
ESTHER : Crossman_2008_Genome.Biol_9_R74
PubMedSearch : Crossman_2008_Genome.Biol_9_R74
PubMedID: 18419807
Gene_locus related to this paper: strm5-b4sjf3 , strm5-b4sly1 , strm5-b4smq6 , strm5-b4st20 , strm5-bioh , strmk-b2fhb1 , strmk-b2fju9 , strmk-b2fkx8 , strmk-b2fl50 , strmk-b2fl54 , strmk-b2flj0 , strmk-b2fnc5 , strmk-b2fre3 , strmk-b2frm1 , strmk-b2frs0 , strmk-b2fsp0 , strmk-b2ftw9 , strmk-b2fuf3 , strmk-metx , xanma-P95782 , strmk-b2fmj5 , strmk-b2fpy9 , strmk-b2ftk7 , strmk-b2frv5

Title : Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A - Salzberg_2008_BMC.Genomics_9_204
Author(s) : Salzberg SL , Sommer DD , Schatz MC , Phillippy AM , Rabinowicz PD , Tsuge S , Furutani A , Ochiai H , Delcher AL , Kelley D , Madupu R , Puiu D , Radune D , Shumway M , Trapnell C , Aparna G , Jha G , Pandey A , Patil PB , Ishihara H , Meyer DF , Szurek B , Verdier V , Koebnik R , Dow JM , Ryan RP , Hirata H , Tsuyumu S , Won Lee S , Seo YS , Sriariyanum M , Ronald PC , Sonti RV , Van Sluys MA , Leach JE , White FF , Bogdanove AJ
Ref : BMC Genomics , 9 :204 , 2008
Abstract : 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.
ESTHER : Salzberg_2008_BMC.Genomics_9_204
PubMedSearch : Salzberg_2008_BMC.Genomics_9_204
PubMedID: 18452608
Gene_locus related to this paper: xanax-GAA , xanax-PTRB , xanax-XAC0628 , xanax-XAC0736 , xanax-XAC1713 , xanca-impep , xanca-XCC1105 , xanor-acvB , xanor-bioh , xanor-metx , xanor-q5gu74 , xanor-q5gvh6 , xanor-q5gy36 , xanor-q5gy47 , xanor-q5gz98 , xanor-q5h3e8 , xanor-q5h5n1 , xanor-q5h5w8 , xanor-q5h5x9 , xanor-q5h236 , xanor-Q93M73 , xanop-a0a0k0gpc4