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Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants

Li, Zhen and De La Torre, Amanda R. and Sterck, Lieven and Canovas, Francisco and Avila, Concepción and Merino Sierra, Irene and Cabezas, José Antonio and Cervera, María Teresa and Ingvarsson, Pär and Van de Peer, Yves (2017). Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants. Genome Biology and Evolution. 9:4, 1130-1147
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Official URL: http://dx.doi.org/10.1093/gbe/evx070

Abstract

Phylogenetic relationships among seed plant taxa, especially within the gymnosperms, remain contested. In contrast to angio-sperms, for which several genomic, transcriptomic and phylogenetic resources are available, there are few, if any, molecular markers that allow broad comparisons among gymnosperm species. With few gymnosperm genomes available, recently obtained transcriptomes in gymnosperms are a great addition to identifying single-copy gene families as molecular markers for phylogenomic analysis in seed plants. Taking advantage of an increasing number of available genomes and transcriptomes, we identified single-copy genes in a broad collection of seed plants and used these to infer phylogenetic relationships between major seed plant taxa. This study aims at extending the current phylogenetic toolkit for seed plants, assessing its ability for resolving seed plant phylogeny, and discussing potential factors affecting phylogenetic reconstruction. In total, we identified 3,072 single-copy genes in 31 gymnosperms and 2,156 single-copy genes in 34 angiosperms. All studied seed plants shared 1,469 single-copy genes, which are generally involved in functions like DNA metabolism, cell cycle, and photosynthesis. A selected set of 106 single-copy genes provided good resolution for the seed plant phylogeny except for gnetophytes. Although some of our analyses support a sister relationship between gnetophytes and other gymnosperms, phylogenetic trees from concatenated alignments without 3rd codon positions and amino acid alignments under the CAT + GTR model, support gnetophytes as a sister group to Pinaceae. Our phylogenomic analyses demonstrate that, in general, single-copy genes can uncover both recent and deep divergences of seed plant phylogeny.

Authors/Creators:Li, Zhen and De La Torre, Amanda R. and Sterck, Lieven and Canovas, Francisco and Avila, Concepción and Merino Sierra, Irene and Cabezas, José Antonio and Cervera, María Teresa and Ingvarsson, Pär and Van de Peer, Yves
Title:Single-Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants
Series/Journal:Genome Biology and Evolution (1759-6653)
Year of publishing :2017
Volume:9
Number:4
Page range:1130-1147
Number of Pages:18
Publisher:Oxford University Press
ISSN:1759-6653
Language:English
Publication Type:Journal article
Refereed:Yes
Article category:Scientific peer reviewed
Version:Published version
Full Text Status:Public
Agris subject categories.:F Plant production > F30 Plant genetics and breeding
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Bioinformatics and Systems Biology (methods development to be 10203)
Keywords:single-copy genes, gymnosperms, angiosperms, seed plants, phylogenomics
URN:NBN:urn:nbn:se:slu:epsilon-e-4392
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-e-4392
Additional ID:
Type of IDID
Web of Science (WoS)000406760400002
ID Code:14551
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Department of Plant Biology (from 140101)
Deposited By: SLUpub Connector
Deposited On:04 Oct 2017 08:13
Metadata Last Modified:04 Oct 2017 08:13

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