Genome Sequence of Xanthomonas axonopodis pv. punicae Strain LMG 859

Sharma, Vikas; Midha, Samriti; Ranjan, Manish; Pinnaka, Anil Kumar; Patil, Prabhu B.

doi:10.1128/jb.00181-12

Cited by 20 publications

(15 citation statements)

References 6 publications

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“…From the present study, we report the genomes of 18 reference pathovar strains of XCPs and compare them with those of 4 publicly available XCPs (46)(47)(48)(49). However, these XCPs have historically been classified into three different species of Xanthomonas and one of these strains has been assigned to another genus, Pseudomonas ( Table 1).…”

Section: Importancementioning

confidence: 99%

Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity

Bansal

Midha

Patil

2017

Appl Environ Microbiol

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Citrus canker, caused by Xanthomonas citri pv. citri, is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed that X. citri pv. citri is related to many other pathovars, which can be collectively referred as Xanthomonas citri pathovars (XCPs). From the present study, we report the genome sequences of 18 XCPs and compared them with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster, suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, the majority of these XCPs were first noticed in India, corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role of interstrain genomic flux of these XCPs since their diversification from a common ancestor. Even though there are wide variations in type III gene effectomes, we identified three core effectors which can be valuable in resistance-breeding programs. Overall, genomic examination of ecological relatives allowed us to dissect the tremendous genomic potential of X. citri species to rapidly evolve into specialized strains infecting diverse crop plants.IMPORTANCE Host specialization is one of the characteristic features of highly evolved pathogens such as the Xanthomonas group of phytopathogenic bacteria. Since the hosts involve staple crops and economically important fruits such as citrus, detailed understanding of the diversity and evolution of such strains infecting diverse plants is important for quarantine purposes. In the present study, we carried out genomic investigation of members of a phylogenetically and ecologically defined group of Xanthomonas strains pathogenic to diverse plants, including citrus. This group includes the oldest Xanthomonas pathovars and also recently emerged pathovars in a particular country where they are endemic. Our high-throughput genomic study has provided novel insights into the evolution of a unique lineage consisting of serious pathogens and their ecological relatives, suggesting the nature, scope, and pattern of rapid and recent diversification. Further, from the level of species to that of clonal variants, the study revealed interesting genomic patterns in diversification of a Xanthomonas lineage and perhaps will inspire careful study of the host range of the included pathovars.

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Section: Importancementioning

confidence: 99%

Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity

Bansal

Midha

Patil

2017

Appl Environ Microbiol

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“…The Xac genome was one of the first plantpathogenic bacterial genomes to be sequenced (19). We have previously deposited and announced the whole-genome sequences of reference strains of pathovars Xmi and Xap (20,21). In this study, we sequenced the whole genome of the reference strain of Xvt.…”

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Genomic Insights into the Evolutionary Origin of Xanthomonas axonopodis pv. citri and Its Ecological Relatives

Midha

Patil

2014

Appl Environ Microbiol

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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.

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“…citri, the causal agent of citrus canker, and X. axonopodis pv. punicae, the causal agent of bacterial leaf blight in pomegranate (11). Further phylogenomic analysis using highly conserved housekeeping genes described earlier for xanthomonads (1) confirmed its close relationship with X. axonopodis pv.…”

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confidence: 74%

“…Moreover, the hosts of these pathovars also grow wild and are cultivated at a large scale in India. Hence, as hypothesized previously (11), this group of highly related phytopathogens may be dynamically exchanging their gene pool for fitness and virulence capabilities. The availability of the genome sequence of the reference strain of X. citri pv.…”

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Genome Sequence of Xanthomonas citri pv. mangiferaeindicae Strain LMG 941

et al. 2012

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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. Xanthomonas citri pv. mangiferaeindicae is one of the important pathovars belonging to the Xanthomonas axonopodis species complex. Even though this phytopathogen was first reported in South Africa in mango in 1915 (2), the disease was known much earlier in India (8, 9). It is a serious problem in mango cultivation and export in regions in which this pathogen is endemic. Moreover, the taxonomic relationship between X. citri pv. mangiferaeindicae and other closely related pathovars that infect citrus and other fruit crops is controversial. Hence the genome sequence of X. citri pv. mangiferaeindicae is an urgent requirement for gaining deeper insights into its phylogeny and taxonomy and also for identifying the determinants of its virulence.In this direction, we have sequenced the genome of LMG 941, the reference strain of X. citri pv. mangiferaeindicae, using the Roche 454 GS (FLX Titanium) pyrosequencing platform (Macrogen, Republic of Korea). The shotgun sequencing yielded 770,765 reads amounting to 345,463,238 bases and ϳ69-fold coverage. The GS de novo assembler (version 2.6) yielded 195 contigs of Ն500 bp with an average contig size of 26.213 kb and a largest contig of 169.379 kb. The percentage of bases that have a quality score of 40 or above was 99.98%. The genome of strain LMG 941 has a GϩC content of 64.85%, and annotation using the rapid annotation using subsystem technology (RAST) pipeline (7) and RNAmmer 1.2 (5) with further manual inspection revealed 4,521 predicted coding regions (CDSs), 51 tRNA genes, and 3 rRNA genes.BLAST analysis revealed that the 16S rRNA and complete rpoB gene sequences of X. citri pv. mangiferaeindicae are Ͼ99% identical to those of X. axonopodis pv. citri, the causal agent of citrus canker, and X. axonopodis pv. punicae, the causal agent of bacterial leaf blight in pomegranate (11). Further phylogenomic analysis using highly conserved housekeeping genes described earlier for xanthomonads (1) confirmed its close relationship with X. axonopodis pv. citri and X. axonopodis pv. punicae. Interestingly, the diseases caused by X. citri pv. mangiferaeindicae, X. axonopodis pv. citri, and X. axonopodis pv. punicae were all first noticed in India, which may also be the region of origin of these pathovars (3,4,6,8,9,10,11). Moreover, the hosts of these pathovars also grow wild and are cultivated at a large scale in India. Hence, as hypothesized previously (11), this group of highly related phytopathogens may be dynamically exchanging their gene pool for fitness and virulence capabilities. The availability of the genome sequence of the reference strain of X. citri pv. mangiferaeindicae, along with those of X. axonopodis pv. punicae and X. axonopodis pv. citri, will greatly aid in epidemiological/q...

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Genome Sequence of Xanthomonas axonopodis pv. punicae Strain LMG 859

Cited by 20 publications

References 6 publications

Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity

Ecological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity

Genomic Insights into the Evolutionary Origin of Xanthomonas axonopodis pv. citri and Its Ecological Relatives

Genome Sequence of Xanthomonas citri pv. mangiferaeindicae Strain LMG 941

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