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Single-copy genes as molecular markers for phylogenomic studies in seed plants

Zhen Li UGent, Amanda R De La Torre, Lieven Sterck UGent, Francisco M Cánovas, Concepción Avila, Irene Merino, Jose Antonio Cabezas, María Teresa Cervera, Par K Ingvarsson and Yves Van de Peer UGent (2017) GENOME BIOLOGY AND EVOLUTION. 9(5). p.1130-1147
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
CODON-SUBSTITUTION MODELS, PICEA-GLAUCA GENOME, NUCLEAR GENES, LAND, PLANTS, CHLOROPLAST PHYLOGENOMICS, EXTANT GYMNOSPERMS, SEQUENCE, EVOLUTION, SOFTWARE PACKAGE, TREE SELECTION, LARGE SETS, single-copy genes, gymnosperms, angiosperms, seed plants, phylogenomics
journal title
GENOME BIOLOGY AND EVOLUTION
Genome Biol. Evol.
volume
9
issue
5
pages
1130 - 1147
Web of Science type
Article
Web of Science id
000406760400002
ISSN
1759-6653
DOI
10.1093/gbe/evx070
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
id
8529693
handle
http://hdl.handle.net/1854/LU-8529693
date created
2017-08-28 08:15:32
date last changed
2017-10-23 09:56:31
@article{8529693,
  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.},
  author       = {Li, Zhen and De La Torre, Amanda R and Sterck, Lieven and C{\'a}novas, Francisco M and Avila, Concepci{\'o}n and Merino, Irene and Cabezas, Jose Antonio and Cervera, Mar{\'i}a Teresa and Ingvarsson, Par K and Van de Peer, Yves},
  issn         = {1759-6653},
  journal      = {GENOME BIOLOGY AND EVOLUTION},
  keyword      = {CODON-SUBSTITUTION MODELS,PICEA-GLAUCA GENOME,NUCLEAR GENES,LAND,PLANTS,CHLOROPLAST PHYLOGENOMICS,EXTANT GYMNOSPERMS,SEQUENCE,EVOLUTION,SOFTWARE PACKAGE,TREE SELECTION,LARGE SETS,single-copy genes,gymnosperms,angiosperms,seed plants,phylogenomics},
  language     = {eng},
  number       = {5},
  pages        = {1130--1147},
  title        = {Single-copy genes as molecular markers for phylogenomic studies in seed plants},
  url          = {http://dx.doi.org/10.1093/gbe/evx070},
  volume       = {9},
  year         = {2017},
}

Chicago
Li, Zhen, Amanda R De La Torre, Lieven Sterck, Francisco M Cánovas, Concepción Avila, Irene Merino, Jose Antonio Cabezas, María Teresa Cervera, Par K Ingvarsson, and Yves Van de Peer. 2017. “Single-copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants.” Genome Biology and Evolution 9 (5): 1130–1147.
APA
Li, Zhen, De La Torre, A. R., Sterck, L., Cánovas, F. M., Avila, C., Merino, I., Cabezas, J. A., et al. (2017). Single-copy genes as molecular markers for phylogenomic studies in seed plants. GENOME BIOLOGY AND EVOLUTION, 9(5), 1130–1147.
Vancouver
1.
Li Z, De La Torre AR, Sterck L, Cánovas FM, Avila C, Merino I, et al. Single-copy genes as molecular markers for phylogenomic studies in seed plants. GENOME BIOLOGY AND EVOLUTION. 2017;9(5):1130–47.
MLA
Li, Zhen, Amanda R De La Torre, Lieven Sterck, et al. “Single-copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants.” GENOME BIOLOGY AND EVOLUTION 9.5 (2017): 1130–1147. Print.