Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

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Abstract

Whole genome comparisons provide a quantitative, objective basis for taxonomic classification of bacterial pathogens important to food security.

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Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

David Bryant, Vincent Moulton (2004)

We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the data that can guide more detailed analysis. Unlike split decomposition, Neighbor-Net scales well and can quickly produce detailed and informative networks for several hundred taxa. We illustrate the method by reanalyzing three published data sets: a collection of 110 highly recombinant Salmonella multi-locus sequence typing sequences, the 135 "African Eve" human mitochondrial sequences published by Vigilant et al., and a collection of 12 Archeal chaperonin sequences demonstrating strong evidence for gene conversion. Neighbor-Net is available as part of the SplitsTree4 software package.

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Pseudomonas genomes: diverse and adaptable.

Mark W. Silby, Craig Winstanley, Scott A C Godfrey … (2011)

Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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PGAP: pan-genomes analysis pipeline

Yongbing Zhao, Jiayan Wu, Junhui Yang … (2011)

Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We have developed a new pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. PGAP's performance has been evaluated on 11 Streptococcus pyogenes strains. Availability:PGAP is developed with Perl script on the Linux Platform and the package is freely available from http://pgap.sf.net. Contact: junyu@big.ac.cn; xiaojingfa@big.ac.cn Supplementary information: Supplementary data are available at Bioinformatics online.

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Journal

Journal ID (publisher-id): AMNECT

Title: Anal. Methods

Abbreviated Title: Anal. Methods

Publisher: Royal Society of Chemistry (RSC)

ISSN (Print): 1759-9660

ISSN (Electronic): 1759-9679

Publication date Created: 2016

Publication date (Print): 2016

Volume: 8

Issue: 1

Pages: 12-24

Article

DOI: 10.1039/C5AY02550H

PubMed ID: 26585518

SO-VID: 1ec9eb92-97d7-4c39-83b3-6342048ae782

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Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

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Most cited references 52

Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

Pseudomonas genomes: diverse and adaptable.

PGAP: pan-genomes analysis pipeline

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