Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed

Fang, Yunxia; Lin, Haiyan; Wu, Liwen; Ren, Deyong; Ye, Weijun; Dong, Guanping; Zhu, Lan; Guo, Longbiao

doi:10.1016/j.jbiotec.2015.04.014

Cited by 28 publications

(26 citation statements)

References 13 publications

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“…Similar results with species like X. albilineans, X. theicola, X. hyacinthy, and X. translucens were found in previous studies forming a basal clade in the phylogeny of Xanthomonas [4,43,44]. Additionally, X. albilineans and X. sacchari presents a reduced genome comparing to the other species of the genus [24,25] comparable to Xylella fastidiosa [45].…”

Section: Discussionsupporting

confidence: 87%

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Comparative genome analysis and phylogenomic of Xanthomonas citri pv. viticola lead to new taxonomic insights about species of Xanthomonas

Farias

Silva

Nascimento

et al. 2020

Preprint

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Background Xanthomonas citri pv. viticola is one of the most critical grapevine diseases in the Northeast of Brazil, presenting a high risk to Brazilian and worldwide areas of grape production. The X.citri pv. viticola epithet was recently proposed to be changed from X. campestris pv. v iticola based on multilocus sequence analysis and whole-genome sequences. Besides, genomics has revolutionized the field of bacteriology, by associating genome sequencing with comparative analysis such as in silico analysis such as DNA-DNA hybridization, average nucleotide identity, distance between genomes, pan-genomic approach, and phylogenomic, providing valuable insights and knowledge about virulence factors and contributing to increase the understanding and clarifying the taxonomic relationship of Xanthomonas and others prokaryotic species.Results We used the whole-genome sequence of three Brazilian strains and the pathotype to characterize X.citri pv. viticola accessions plus 124 whole-genome sequences of Xanthomonas species available in NCBI, comprising 13 species and 15 pathovars. The whole-genome sequence structure of X. citri pv. viticola was shown presents a high level of conservation concerning other X. citri species. Pan-genomic approaches, average nucleotide identity analysis, and in silico DNA-DNA hybridization were carried out, allowing X.citri pv. viticola characterization and inferences on the phylogenetic relationships within Xanthomonas . The analysis of the sequence of the 128 genomes clustered the Xanthomonas strains in eight main groups according to the recently proposed classification in all approaches used. Also, the analysis revealed that X. hortorum and X. gardneri should be classified as a single species, and the strain 17 of X. campestris and XC01 of X. citri pv. mangiferaeindicae widely described in the literature are misclassified.Conclusions We performed the genomic characterization of three representative Brazilian strains of Xcv . The genomic approaches based in the pan-genome, average nucleotide identity, and in silico DNA-DNA hybridization support the proposed taxonomic position of X.citri pv. viticola and of the recently proposed Xanthomonas species and pathovars. In addition, we detected species delimitation of the misclassified Xanthomonas strains with extensive studies reported in the literature.

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Section: Discussionsupporting

confidence: 87%

“…fragariae [24][25][26][27][28][29]. In this way, we found that the genome of the XC01 strain of X. citri pv.…”

Section: Discussionmentioning

confidence: 97%

Comparative genome analysis and phylogenomic of Xanthomonas citri pv. viticola lead to new taxonomic insights about species of Xanthomonas

Farias

Silva

Nascimento

et al. 2020

Preprint

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“…These strains are isolated from surface-sterilized rice seeds. X. sontii strains are reported to be non-pathogenic towards rice, however, pathogenicity status of remaining isolates is unknown (Fang, Lin et al 2015, Bansal, Kaur et al 2019).…”

Section: Resultsmentioning

confidence: 99%

“…However, X. sontii, X. maliensis and some strains of X. sacchari , other Xanthomonas sp. were found to be associated with healthy rice seeds or leaves (Vauterin, Yang et al 1996, Fang, Lin et al 2015, Triplett, Verdier et al 2015, Bansal, Kaur et al 2019). Rice pathogenic Xanthomonas are widely studied, however, their non-pathogenic counterparts isolated from healthy plants are vastly overlooked.…”

Section: Introductionmentioning

confidence: 99%

Ecological and evolutionary insights into pathogenic and non-pathogenic rice associatedXanthomonas

Bansal

Midha

Kaur

et al. 2018

Preprint

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Xanthomonas oryzae is a devastating pathogen of rice worldwide, however, X. sontii and X. maliensis are its non-pathogenic counterparts from the same host. So far, these non-pathogenic isolates were overlooked due to their less economic importance and lack of genomic information. We have carried out detailed ecological and evolutionary study focusing on diverse lifestyles of these strains. Phylogenomic analysis revealed two major lineages corresponding to X. sontii (ML-I) and X. oryzae (ML-II) species. Interestingly, one of the non-pathogenic Xanthomonas strains belonging to X. maliensis is intermediary to both the major lineages/species suggesting on-going diversification and selection. Accordingly, pangenome analysis revealed large number of lifestyle specific genes with atypical GC content indicating role of horizontal gene transfer in genome diversification. Our comprehensive comparative genomic investigation of major lineages has revealed that impact of recombination is more for X. sontii as compared to X. oryzae. Acquisition of type III secretion system and its effectome along with a type VI secretion system also seem to have played a major role in the pathogenic lineage. Other known key pathogenicity clusters or genes like biofilm forming cluster, cellobiohydrolase and non-fimbrial adhesin (yapH) are exclusive to pathogenic lineage. However, commonality of loci encoding exopolysacharide, rpf signalling molecule, iron-uptake, xanthomonadin pigment, etc. suggests their essentiality in host adaptation. Overall, this study reveals evolutionary history of pathogenic and non-pathogenic strains and will further open up a new avenue for better management of pathogenic strains for sustainable cultivation of a major staple food crop.

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“…Xanthomonas arboricola is known to comprise pathogenic strains of different pathovars affecting stone and nut fruit trees (13); nonpathogenic X. arboricola strains are also isolated from walnut trees (11,12). Another well-studied nonpathogenic strain, Xanthomonas sacchari R1, was isolated from rice seeds and is known to be antagonistic to rice pathogens, which was later identified as a misclassified strain of X. sontii (14,15). In addition to these, there are various unclassified and unexplored nonpathogenic isolates reported from a diversity of host plants (16).…”

mentioning

confidence: 99%

Phylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with Citrus

Bansal

Patil

2020

mSphere

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Xanthomonas species are primarily known as a group of phytopathogens infecting diverse plants. Recent molecular studies reveal the existence of potential novel species and strains of Xanthomonas following a nonpathogenic lifestyle. In the present study, we report whole-genome sequences of four nonpathogenic strains from citrus (NPXc). Taxonogenomics revealed the surprising diversity, as each of these three isolates were found to be potential novel species that together form a citrus-associated nonpathogenic Xanthomonas species complex (NPXc complex). Interestingly, this NPXc complex is related to another nonpathogenic species, Xanthomonas sontii, from rice (NPXr). On the other hand, the fourth NPXc isolate was found to be related to nonpathogenic isolates from walnut (NPXw); altogether, they form a potential taxonomic outlier of pathogenic Xanthomonas arboricola species. Furthermore, genomic investigation of well-characterized pathogenicity clusters in NPXc isolates revealed lifestyle-specific gene content dynamics. Primarily, genes essential for virulence (i.e., type 1 secretion system [T1SS], T2SS and its effectors, T3SS and its effectors, T4SS, T6SS, adhesins, and rpf gene cluster) and adaptation (i.e., gum, iron uptake and utilization, xanthomonadin, and two-component systems) were depicted by comparative genomics of a Xanthomonas community comprising diverse lifestyles. Overall, the present analysis confers that nonpathogenic isolates of diverse hosts phylogenomically converge and are evolving in parallel with their pathogenic counterparts. Hence, there is a need to understand the world of nonpathogenic isolates from diverse and economically important hosts. Genomic knowledge and resources of nonpathogenic strains will be invaluable in both basic and applied research of the genus Xanthomonas. IMPORTANCE Xanthomonas citri is one of the top phytopathogenic bacteria and is the causal agent of citrus canker. Interestingly, Xanthomonas is also reported to be associated with healthy citrus plants. The advent of the genomic era enabled us to carry out a detailed evolutionary study of a Xanthomonas community associated with citrus and other plants. Our genome-based investigations have revealed hidden and extreme interstrain diversity of nonpathogenic Xanthomonas strains from citrus plants, warranting further large-scale studies. This indicates an unexplored world of Xanthomonas from healthy citrus plant species that may be coevolving as a species complex with the host, unlike the variant pathogenic species. The knowledge and genomic resources will be valuable in evolutionary studies exploring its hidden potential and management of pathogenic species.

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Genome sequence of Xanthomonas sacchari R1, a biocontrol bacterium isolated from the rice seed

Cited by 28 publications

References 13 publications

Comparative genome analysis and phylogenomic of Xanthomonas citri pv. viticola lead to new taxonomic insights about species of Xanthomonas

Comparative genome analysis and phylogenomic of Xanthomonas citri pv. viticola lead to new taxonomic insights about species of Xanthomonas

Ecological and evolutionary insights into pathogenic and non-pathogenic rice associatedXanthomonas

Phylogenomic Insights into Diversity and Evolution of Nonpathogenic Xanthomonas Strains Associated with Citrus

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