Dataset Information

Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine.

ABSTRACT: Xanthomonas citri pv. viticola (Xcv) is the causal agent of bacterial canker in grapevine. The pathogen is restricted to India, where it was first reported in the 1970s, and Brazil. In the present study, we report the first complete genome sequence of Xcv LMG965, which is a reference pathotype strain. We also report genome sequences of additional isolates from India and comparative genome-based studies of isolates from Brazil. Apart from revealing the monophyletic origin of the pathovar, we could also confirm a common frameshift mutation in a gene that is part of the Xanthomonadin pigment biosynthetic gene cluster in all the isolates. The comparative study also revealed multiple intrinsic copper resistance-related genes in Brazilian isolates, suggesting intense selection, possibly because of heavy and indiscriminate usage of copper as an antimicrobial agent in the orchards. There is also the association of a Tn3-like transposase in the vicinity of the copper resistance genes, indicating a potential for rapid diversification through horizontal gene transfer events. The findings, along with genomic resources, will allow for systematic genetic and functional studies of Xcv.

SUBMITTER: Rana R

PROVIDER: S-EPMC10667641 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine.

Rana Rekha R Jaiswal Gagandeep G Bansal Kanika K Patil Prabhu B PB

Environmental microbiology reports 20230530 6

Xanthomonas citri pv. viticola (Xcv) is the causal agent of bacterial canker in grapevine. The pathogen is restricted to India, where it was first reported in the 1970s, and Brazil. In the present study, we report the first complete genome sequence of Xcv LMG965, which is a reference pathotype strain. We also report genome sequences of additional isolates from India and comparative genome-based studies of isolates from Brazil. Apart from revealing the monophyletic origin of the pathovar, we coul ...[more]

PMID: 37254648

Similar Datasets

Project description:The pathovar viticola of Xanthomonas citri causes bacterial canker of grapevine. This disease was first recorded in India in 1972, and later in Brazil in 1998, where its distribution is currently restricted to the northeastern region. A multilocus sequence analysis (MLSA) based on seven housekeeping genes and a multilocus variable number of tandem repeat analysis (MLVA) with eight loci were performed in order to assess the genetic relatedness among strains from India and Brazil. Strains isolated in India from three related pathovars affecting Vitaceae species and pathogenic strains isolated from Amaranthus sp. found in bacterial canker-infected vineyards in Brazil were also included. MLSA revealed lack of diversity in all seven genes and grouped grapevine and Amaranthus strains in a monophyletic group in X. citri. The VNTR (variable number of tandem repeat) typing scheme conducted on 107 strains detected 101 haplotypes. The total number of alleles per locus ranged from 5 to 12. A minimum spanning tree (MST) showed that Brazilian strains were clearly separated from Indian strains, which showed unique alleles at three loci. The two strains isolated from symptomatic Amaranthus sp. presented unique alleles at two loci. STRUCTURE analyses revealed three groups congruent with MST and a fourth group with strains from India and Brazil. Admixture among populations were observed in all groups. MST, STRUCTURE and e-BURST analyses showed that the strains collected in 1998 belong to two distinct groups, with predicted founder genotypes from two different vineyards in the same region. This suggest that one introduction of grape planting materials contaminated with genetically distinct strains took place, which was followed by pathogen adaptation. Genome sequencing of one Brazilian strain confirmed typical attributes of pathogenic xanthomonads and allowed the design of a complementary VNTR typing scheme dedicated to X. citri pv. viticola that will allow further epidemiological survey of this genetically monomorphic pathovar.

Project description:Effective systems for the analysis of molecular data are fundamental for monitoring the spread of infectious diseases and studying pathogen evolution. The rapid identification of emerging viral strains, and/or genetic variants potentially associated with novel phenotypic features is one of the most important objectives of genomic surveillance of human pathogens and represents one of the first lines of defense for the control of their spread. During the COVID 19 pandemic, several taxonomic frameworks have been proposed for the classification of SARS-Cov-2 isolates. These systems, which are typically based on phylogenetic approaches, represent essential tools for epidemiological studies as well as contributing to the study of the origin of the outbreak. Here, we propose an alternative, reproducible, and transparent phenetic method to study changes in SARS-CoV-2 genomic diversity over time. We suggest that our approach can complement other systems and facilitate the identification of biologically relevant variants in the viral genome. To demonstrate the validity of our approach, we present comparative genomic analyses of more than 175,000 genomes. Our method delineates 22 distinct SARS-CoV-2 haplogroups, which, based on the distribution of high-frequency genetic variants, fall into four major macrohaplogroups. We highlight biased spatiotemporal distributions of SARS-CoV-2 genetic profiles and show that seven of the 22 haplogroups (and of all of the four haplogroup clusters) showed a broad geographic distribution within China by the time the outbreak was widely recognized-suggesting early emergence and widespread cryptic circulation of the virus well before its isolation in January 2020. General patterns of genomic variability are remarkably similar within all major SARS-CoV-2 haplogroups, with UTRs consistently exhibiting the greatest variability, with s2m, a conserved secondary structure element of unknown function in the 3'-UTR of the viral genome showing evidence of a functional shift. Although several polymorphic sites that are specific to one or more haplogroups were predicted to be under positive or negative selection, overall our analyses suggest that the emergence of novel types is unlikely to be driven by convergent evolution and independent fixation of advantageous substitutions, or by selection of recombined strains. In the absence of extensive clinical metadata for most available genome sequences, and in the context of extensive geographic and temporal biases in the sampling, many questions regarding the evolution and clinical characteristics of SARS-CoV-2 isolates remain open. However, our data indicate that the approach outlined here can be usefully employed in the identification of candidate SARS-CoV-2 genetic variants of clinical and epidemiological importance.

Project description:BackgroundXanthomonas translucens pathovars differ in their individual host ranges among Poaceae. As the causal agent of bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.), X. translucens pv. graminis (Xtg) is one of the most important bacterial pathogens in temperate grassland regions. The genomes of six Xtg strains from Switzerland, Norway, and New Zealand were sequenced in order to gain insight into conserved genomic traits from organisms covering a wide geographical range. Subsequent comparative analysis with previously published genome data of seven non-graminis X. translucens strains including the pathovars arrhenatheri, poae, phlei, cerealis, undulosa, and translucens was conducted to identify candidate genes linked to the host adaptation of Xtg to Italian ryegrass.ResultsPhylogenetic analysis revealed a tight clustering of Xtg strains, which were found to share a large core genome. Conserved genomic traits included a non-canonical type III secretion system (T3SS) and a type IV pilus (T4P), which both revealed distinct primary structures of the pilins when compared to the non-graminis X. translucens strains. Xtg-specific traits that had no homologues in the other X. translucens strains were further found to comprise several hypothetical proteins, a TonB-dependent receptor, transporters, and effector proteins as well as toxin-antitoxin systems and DNA methyltransferases. While a nearly complete flagellar gene cluster was identified in one of the sequenced Xtg strains, phenotypic analysis pointed to swimming-deficiency as a common trait of the pathovar graminis.ConclusionOur study suggests that host adaptation of X. translucens pv. graminis may be conferred by a combination of pathovar-specific effector proteins, regulatory mechanisms, and adapted nutrient acquisition. Sequence deviations of pathogen-associated molecular patterns (PAMPs), as observed for the pilins of the T4P and T3SS, are moreover likely to impede perception by the plant defense machinery and thus facilitate successful host colonization of Italian ryegrass.

Dataset Information

Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine.

Publications

Comparative genomics reveals the emergence of copper resistance in a non-pigmented Xanthomonas pathogen of grapevine.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets