4.7 Article

New molecular markers for fungal phylogenetics: Two genes for species-level systematics in the Sordariomycetes (Ascomycota)

期刊

MOLECULAR PHYLOGENETICS AND EVOLUTION
卷 64, 期 3, 页码 500-512

出版社

ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ympev.2012.05.005

关键词

Fungal phylogenetic markers; FG1093; Gnomoniaceae; MS204; Phylogenetic performance; Site rate evolution

资金

  1. National Science Foundation PEET [NSF PEET 03-28634]

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Although significant progress has been made resolving deep branches of the fungal tree of life, many fungal systematists are interested in species-level questions to both define species and assess fungal biodiversity. Fungal genome sequences are a useful resource to systematic biologists for developing new phylogenetic markers that better represent the whole genome. Here we report primers for two newly identified single-copy protein-coding genes. FG1093 and MS204, for use with ascomycetes. Although fungi were the focus of this study, this methodological approach could be easily applied to marker development for studies of other organisms. The tests used here to assess phylogenetic informativeness are computationally rapid, require only rudimentary datasets to evaluate existing or newly developed markers, and can be applied to other non-model organisms to assist in experimental design of phylogenetic studies. Phylogenetic utility of the markers was tested in two genera, Gnomoniopsis and Ophiognomonia (Gnomoniaceae, Diaporthales). The phylogenetic performance of beta-tubulin, ITS, and tef-1 alpha was compared with FG1093 and MS204. Phylogenies inferred from FG1093 and MS204 were largely in agreement with beta-tubulin, ITS, and tef-1 alpha although some topological conflict was observed. Resolution and support for branches differed based on the combination of markers used for each genus. Based on two independent tests of phylogenetic performance. FG1093 and MS204 were determined to be equal to or better than beta-tubulin, ITS, and tef-1 alpha in resolving species relationships. Differences were found in site-specific rate of evolution in all five markers. In addition, isolates from 15 orders and 22 families of Ascomycota were screened using primers for FG1093 and MS204 to demonstrate primer utility across a wide diversity of ascomycetes. The primer sets for the newly identified genes FG1093 and MS204 and methods used to develop them are useful additions to the ascomycete systematists' toolbox. (C) 2012 Elsevier Inc. All rights reserved.

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