Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus

Microorganisms
Jarred Yasuhara-BellJames P Stack

Abstract

Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV ↔ RT-I ↔ RT-II ↔ RT-III ↔ RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require un...Continue Reading

References

Nov 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·S Henikoff, J G Henikoff
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Mar 11, 1988·Nucleic Acids Research·H S Bilofsky, C Burks
Apr 1, 1994·Computer Applications in the Biosciences : CABIOS·S KumarM Nei
Jul 1, 1993·Nucleic Acids Research·D BensonJ Ostell
Oct 1, 1996·Epidemiology and Infection·M S JohnstonD J Hampson
Feb 28, 1998·Nucleic Acids Research·S L SalzbergO White
Sep 2, 1998·Trends in Genetics : TIG·M Y Galperin, S E Brenner
Dec 10, 1998·Nucleic Acids Research·H OgataM Kanehisa
May 15, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Nov 11, 1999·Nucleic Acids Research·A L DelcherS L Salzberg
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Dec 11, 1999·Nucleic Acids Research·R L TatusovE V Koonin
Dec 11, 1999·Nucleic Acids Research·A BatemanE L Sonnhammer
May 30, 2002·Nucleic Acids Research·Arthur L DelcherSteven L Salzberg
Mar 1, 1990·Genomics·D BensonJ Ostell
Jul 24, 2002·Nucleic Acids Research·Kazutaka KatohTakashi Miyata
Jan 10, 2003·Nucleic Acids Research·Daniel H HaftOwen White
Feb 5, 2003·Genome Research·David T PrideMartin J Blaser
Feb 14, 2003·Bioinformatics·William HsiaoFiona S L Brinkman
Sep 13, 2003·BMC Bioinformatics·Roman L TatusovDarren A Natale
Sep 25, 2003·Evolution; International Journal of Organic Evolution·Eric Haywood-Farmer, Sarah P Otto
Oct 8, 2003·Systematic Biology·Stéphane Guindon, Olivier Gascuel
Dec 19, 2003·Nucleic Acids Research·Raphaël LeplaeAriane Toussaint
Dec 19, 2003·Nucleic Acids Research·Minoru KanehisaMasahiro Hattori
Feb 5, 2004·Genome Biology·Stefan KurtzSteven L Salzberg
Apr 29, 2004·BMC Bioinformatics·Rainer Merkl
May 25, 2004·Science·Eric Cascales, Peter J Christie
Jul 3, 2004·Genome Research·Aaron C E DarlingNicole T Perna
Aug 13, 2004·Environmental Microbiology·Hanno TeelingFrank Oliver Glöckner
Feb 11, 2005·Proceedings of the National Academy of Sciences of the United States of America·Konstantinos T Konstantinidis, James M Tiedje
Sep 3, 2005·Nature Reviews. Microbiology·Laura S FrostAriane Toussaint
Sep 3, 2005·Nature Reviews. Microbiology·Dirk GeversJean Swings
Sep 20, 2005·Genome Research·Belinda GiardineAnton Nekrutenko
Oct 4, 2005·EMBO Reports·Konrad U FoerstnerPeer Bork
Oct 17, 2006·BMC Evolutionary Biology·Mark W J van PasselTeun Boekhout

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Datasets Mentioned

BETA
WAC3373
CP015515.1

Methods Mentioned

BETA
glycosylation
electrophoresis
phosphotransferase
PanSeq
PCR

Software Mentioned

HMM
REALPHY
BLAST +
MicroScope
MAFFT
SecReT4
HMMER3
HGAP
PHAST Search Tool
IslandPath

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