20 research outputs found
Analysis of the Lactobacilluscasei supragenome and its influence in species evolution and lifestyle adaptation
The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources. Results Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay. Conclusions Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria
ERIC, the Enteropathogen Resource Integration Center (www.ericbrc.org), is a new web portal serving as a rich source of information about enterobacteria on the NIAID established list of Select Agents related to biodefense—diarrheagenic Escherichia coli, Shigella spp., Salmonella spp., Yersinia enterocolitica and Yersinia pestis. More than 30 genomes have been completely sequenced, many more exist in draft form and additional projects are underway. These organisms are increasingly the focus of studies using high-throughput experimental technologies and computational approaches. This wealth of data provides unprecedented opportunities for understanding the workings of basic biological systems and discovery of novel targets for development of vaccines, diagnostics and therapeutics. ERIC brings information together from disparate sources and supports data comparison across different organisms, analysis of varying data types and visualization of analyses in human and computer-readable formats
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes
The Comprehensive Phytopathogen Genomics Resource (CPGR) provides a web-based portal for plant pathologists and diagnosticians to view the genome and trancriptome sequence status of 806 bacterial, fungal, oomycete, nematode, viral and viroid plant pathogens. Tools are available to search and analyze annotated genome sequences of 74 bacterial, fungal and oomycete pathogens. Oomycete and fungal genomes are obtained directly from GenBank, whereas bacterial genome sequences are downloaded from the A Systematic Annotation Package (ASAP) database that provides curation of genomes using comparative approaches. Curated lists of bacterial genes relevant to pathogenicity and avirulence are also provided. The Plant Pathogen Transcript Assemblies Database provides annotated assemblies of the transcribed regions of 82 eukaryotic genomes from publicly available single pass Expressed Sequence Tags. Data-mining tools are provided along with tools to create candidate diagnostic markers, an emerging use for genomic sequence data in plant pathology. The Plant Pathogen Ribosomal DNA (rDNA) database is a resource for pathogens that lack genome or transcriptome data sets and contains 131 755 rDNA sequences from GenBank for 17 613 species identified as plant pathogens and related genera
Annotation and overview of the Pseudomonas savastanoi pv. savastanoi NCPPB 3335 draft genome reveals the virulence gene complement of a tumour-inducing pathogen of woody hosts
Pseudomonas savastanoi pv. savastanoi is a tumour-inducing pathogen of Olea europaea L. causing oliveknot disease. Bioinformatic analysis of the draftgenome sequence of strain NCPPB 3335, whichencodes 5232 predicted coding genes on a totallength of 5856 998 bp and a 57.12% G + C, revealed alarge degree of conservation with Pseudomonassyringae pv. phaseolicola 1448A and P. syringae pv.tabaci 11528. However, NCPPB 3335 contains twelvevariable genomic regions, which are absent in all pre-viously sequenced P. syringae strains. Various fea-tures that could contribute to the ability of this strainto survive in a woody host were identified, includingbroad catabolic and transport capabilities for degrad-ing plant-derived aromatic compounds, the duplica-tion of sequences related to the biosynthesis of thephytohormone indoleacetic acid (iaaM, iaaH) and itsamino acid conjugate indoleacetic acid-lysine (iaaLgene), and the repertoire of strain-specific putativetype III secretion system effectors. Access to thisseventh genome sequence belonging to the ‘P. syrin-gae complex’ allowed us to identify 73 predictedcoding genes that are NCPPB 3335-specific. Resultsshown here provide the basis for detailed functionalanalysis of a tumour-inducing pathogen of woodyhosts and for the study of specific adaptations of a P.savastanoi pathovar