Incongruence between multi-locus sequence analysis ( MLSA) and whole-genome-based phylogenies: Pseudomonas syringae pathovar pisi as a cautionary tale

被引：20

作者：

Baltrus, David A. ^{[1
]}

Dougherty, Kevin ^{[1
]}

Beckstrom-Sternberg, Stephen M. ^{[2
]}

Beckstrom-Sternberg, James S. ^{[2
]}

Foster, Jeffrey T. ^{[2
]}

机构：

[1] Univ Arizona, Sch Plant Sci, Tucson, AZ 85721 USA

[2] No Arizona Univ, Ctr Microbial Genet & Genom, Flagstaff, AZ 86011 USA

来源：

MOLECULAR PLANT PATHOLOGY | 2014年 / 15卷 / 05期

关键词：

VIRULENCE; FRAMEWORK; EVOLUTION;

D O I：

10.1111/mpp.12103

中图分类号：

Q94 [植物学];

学科分类号：

071001 ;

摘要：

Previous phylogenies, built using a subset of genomic loci, split Pseudomonas syringae pv. pisi into two well-supported clades and implied convergence in host range for these lineages. The analysis of phenotypic and genotypic data within the context of this phylogenetic relationship implied further convergence at the level of virulence gene loss and acquisition. We generate draft genome assemblies for two additional P.syringae strains, isolated from diseased pea plants, and demonstrate incongruence between phylogenies created from a subset of the data compared with the whole genomes. Our whole-genome analysis demonstrates that strains classified as pv. pisi actually form a coherent monophyletic clade, so that apparent convergence is actually the product of shared ancestry. We use this example to urge caution when making evolutionary inferences across closely related strains of P.syringae.

引用

页码：461 / 465

页数：5

共 22 条

[1]

[Anonymous], 2002, PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods). Version 4

[2]

[Anonymous], 2005, PHYLIP (phylogeny inference package) version 3.6

[3] Molecular characterization of avrPphD, a widely-distributed gene from Pseudomonas syringae pv. phaseolicola involved in non-host recognition by pea (Pisum sativum) [J].

Arnold, DL ;

Gibbon, MJ ;

Jackson, RW ;

Wood, JR ;

Brown, J ;

Mansfield, JW ;

Taylor, JD ;

Vivian, A .

PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY, 2001, 58 (02) :55-62

[4] The Molecular Basis of Host Specialization in Bean Pathovars of Pseudomonas syringae [J].

Baltrus, David A. ;

Nishimura, Marc T. ;

Dougherty, Kevin M. ;

Biswas, Surojit ;

Mukhtar, M. Shahid ;

Vicente, Joana ;

Holub, Eric B. ;

Dangl, Jeffery L. .

MOLECULAR PLANT-MICROBE INTERACTIONS, 2012, 25 (07) :877-888

[5] Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates [J].

Baltrus, David A. ;

Nishimura, Marc T. ;

Romanchuk, Artur ;

Chang, Jeff H. ;

Mukhtar, M. Shahid ;

Cherkis, Karen ;

Roach, Jeff ;

Grant, Sarah R. ;

Jones, Corbin D. ;

Dangl, Jeffery L. .

PLOS PATHOGENS, 2011, 7 (07)

[6] SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing [J].

Bankevich, Anton ;

Nurk, Sergey ;

Antipov, Dmitry ;

Gurevich, Alexey A. ;

Dvorkin, Mikhail ;

Kulikov, Alexander S. ;

Lesin, Valery M. ;

Nikolenko, Sergey I. ;

Son Pham ;

Prjibelski, Andrey D. ;

Pyshkin, Alexey V. ;

Sirotkin, Alexander V. ;

Vyahhi, Nikolay ;

Tesler, Glenn ;

Alekseyev, Max A. ;

Pevzner, Pavel A. .

JOURNAL OF COMPUTATIONAL BIOLOGY, 2012, 19 (05) :455-477

[7] GenBank [J].

Benson, Dennis A. ;

Karsch-Mizrachi, Ilene ;

Lipman, David J. ;

Ostell, James ;

Wheeler, David L. .

NUCLEIC ACIDS RESEARCH, 2008, 36 :D25-D30

[8] A framework for variation discovery and genotyping using next-generation DNA sequencing data [J].

DePristo, Mark A. ;

Banks, Eric ;

Poplin, Ryan ;

Garimella, Kiran V. ;

Maguire, Jared R. ;

Hartl, Christopher ;

Philippakis, Anthony A. ;

del Angel, Guillermo ;

Rivas, Manuel A. ;

Hanna, Matt ;

McKenna, Aaron ;

Fennell, Tim J. ;

Kernytsky, Andrew M. ;

Sivachenko, Andrey Y. ;

Cibulskis, Kristian ;

Gabriel, Stacey B. ;

Altshuler, David ;

Daly, Mark J. .

NATURE GENETICS, 2011, 43 (05) :491-+

[9] Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000 [J].

Feil, H ;

Feil, WS ;

Chain, P ;

Larimer, F ;

DiBartolo, G ;

Copeland, A ;

Lykidis, A ;

Trong, S ;

Nolan, M ;

Goltsman, E ;

Thiel, J ;

Malfatti, S ;

Loper, JE ;

Lapidus, A ;

Detter, JC ;

Land, M ;

Richardson, PM ;

Kyrpides, NC ;

Ivanova, N ;

Lindow, SE .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (31) :11064-11069

[10] Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae [J].

Hwang, MSH ;

Morgan, RL ;

Sarkar, SF ;

Wang, PW ;

Guttman, DS .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2005, 71 (09) :5182-5191

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