Patil PB

References (9)

Title : Genomic insights into the evolutionary origin of Xanthomonas axonopodis pv. citri and its ecological relatives - Midha_2014_Appl.Environ.Microbiol_80_6266
Author(s) : Midha S , Patil PB
Ref : Applied Environmental Microbiology , 80 :6266 , 2014
Abstract : Xanthomonas axonopodis pv. citri (Xac) is the causal agent of citrus bacterial canker (CBC) and is a serious problem worldwide. Like CBC, several important diseases in other fruits, such as mango, pomegranate, and grape, are also caused by Xanthomonas pathovars that display remarkable specificity toward their hosts. While citrus and mango diseases were documented more than 100 years ago, the pomegranate and grape diseases have been known only since the 1950s and 1970s, respectively. Interestingly, diseases caused by all these pathovars were noted first in India. Our genome-based phylogenetic studies suggest that these diverse pathogens belong to a single species and these pathovars may be just a group of rapidly evolving strains. Furthermore, the recently reported pathovars, such as those infecting grape and pomegranate, form independent clonal lineages, while the citrus and mango pathovars that have been known for a long time form one clonal lineage. Such an understanding of their phylogenomic relationship has further allowed us to understand major and unique variations in the lineages that give rise to these pathovars. Whole-genome sequencing studies including ecological relatives from their putative country of origin has allowed us to understand the evolutionary history of Xac and other pathovars that infect fruits.
ESTHER : Midha_2014_Appl.Environ.Microbiol_80_6266
PubMedSearch : Midha_2014_Appl.Environ.Microbiol_80_6266
PubMedID: 25085494
Gene_locus related to this paper: xanax-estA1 , xanax-XAC1213 , xanax-XAC3315 , xanor-q5h5n1

Title : Genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859 - Sharma_2012_J.Bacteriol_194_2395
Author(s) : Sharma V , Midha S , Ranjan M , Pinnaka AK , Patil PB
Ref : Journal of Bacteriology , 194 :2395 , 2012
Abstract : We report the 4.94-Mb genome sequence of Xanthomonas axonopodis pv. punicae strain LMG 859, the causal agent of bacterial leaf blight disease in pomegranate. The draft genome will aid in comparative genomics, epidemiological studies, and quarantine of this devastating phytopathogen.
ESTHER : Sharma_2012_J.Bacteriol_194_2395
PubMedSearch : Sharma_2012_J.Bacteriol_194_2395
PubMedID: 22493202
Gene_locus related to this paper: xanax-estA1 , xanax-XAC1213 , xanax-XAC2987 , xanax-XAC3315 , xanax-XAC4055 , xanor-q5h5n1

Title : Genome sequence of Xanthomonas citri pv. mangiferaeindicae strain LMG 941 - Midha_2012_J.Bacteriol_194_3031
Author(s) : Midha S , Ranjan M , Sharma V , Pinnaka AK , Patil PB
Ref : Journal of Bacteriology , 194 :3031 , 2012
Abstract : We report the 5.1-Mb genome sequence of Xanthomonas citri pv. mangiferaeindicae strain LMG 941, the causal agent of bacterial black spot in mango. Apart from evolutionary studies, the draft genome will be a valuable resource for the epidemiological studies and quarantine of this phytopathogen.
ESTHER : Midha_2012_J.Bacteriol_194_3031
PubMedSearch : Midha_2012_J.Bacteriol_194_3031
PubMedID: 22582385
Gene_locus related to this paper: xanax-estA1 , xanax-XAC1213 , xanax-XAC2987 , xanax-XAC3315 , xanax-XAC3371 , xanax-XAC4055 , xanor-q5h5n1

Title : Genome sequence of Brevibacillus laterosporus strain GI-9 - Sharma_2012_J.Bacteriol_194_1279
Author(s) : Sharma V , Singh PK , Midha S , Ranjan M , Korpole S , Patil PB
Ref : Journal of Bacteriology , 194 :1279 , 2012
Abstract : We report the 5.18-Mb genome sequence of Brevibacillus laterosporus strain GI-9, isolated from a subsurface soil sample during a screen for novel strains producing antimicrobial compounds. The draft genome of this strain will aid in biotechnological exploitation and comparative genomics of Brevibacillus laterosporus strains.
ESTHER : Sharma_2012_J.Bacteriol_194_1279
PubMedSearch : Sharma_2012_J.Bacteriol_194_1279
PubMedID: 22328768
Gene_locus related to this paper: brela-a0a075r7b1

Title : The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri - Frese_2011_PLoS.Genet_7_e1001314
Author(s) : Frese SA , Benson AK , Tannock GW , Loach DM , Kim J , Zhang M , Oh PL , Heng NC , Patil PB , Juge N , Mackenzie DA , Pearson BM , Lapidus A , Dalin E , Tice H , Goltsman E , Land M , Hauser L , Ivanova N , Kyrpides NC , Walter J
Ref : PLoS Genet , 7 :e1001314 , 2011
Abstract : Recent research has provided mechanistic insight into the important contributions of the gut microbiota to vertebrate biology, but questions remain about the evolutionary processes that have shaped this symbiosis. In the present study, we showed in experiments with gnotobiotic mice that the evolution of Lactobacillus reuteri with rodents resulted in the emergence of host specialization. To identify genomic events marking adaptations to the murine host, we compared the genome of the rodent isolate L. reuteri 100-23 with that of the human isolate L. reuteri F275, and we identified hundreds of genes that were specific to each strain. In order to differentiate true host-specific genome content from strain-level differences, comparative genome hybridizations were performed to query 57 L. reuteri strains originating from six different vertebrate hosts in combination with genome sequence comparisons of nine strains encompassing five phylogenetic lineages of the species. This approach revealed that rodent strains, although showing a high degree of genomic plasticity, possessed a specific genome inventory that was rare or absent in strains from other vertebrate hosts. The distinct genome content of L. reuteri lineages reflected the niche characteristics in the gastrointestinal tracts of their respective hosts, and inactivation of seven out of eight representative rodent-specific genes in L. reuteri 100-23 resulted in impaired ecological performance in the gut of mice. The comparative genomic analyses suggested fundamentally different trends of genome evolution in rodent and human L. reuteri populations, with the former possessing a large and adaptable pan-genome while the latter being subjected to a process of reductive evolution. In conclusion, this study provided experimental evidence and a molecular basis for the evolution of host specificity in a vertebrate gut symbiont, and it identified genomic events that have shaped this process.
ESTHER : Frese_2011_PLoS.Genet_7_e1001314
PubMedSearch : Frese_2011_PLoS.Genet_7_e1001314
PubMedID: 21379339
Gene_locus related to this paper: lacre-b3xl60 , lacrj-b2g622 , lacre-a0a0s4nmr3

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 : 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