A phylogenomic assessment of ancient polyploidy and genome evolution across the poales

Michael R. McKain, Haibao Tang, Joel R. McNeal, Saravanaraj Ayyampalayam, Jerrold I. Davis, Claude W. Depamphilis, Thomas J. Givnish, J. Chris Pires, Dennis W. Stevenson, James H. Leebens-Mack

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (r), sigma (s), and tau (t), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification.

Original languageEnglish (US)
Pages (from-to)1150-1164
Number of pages15
JournalGenome biology and evolution
Volume8
Issue number4
DOIs
StatePublished - Jan 1 2016

Fingerprint

Poales
polyploidy
Polyploidy
genome
Genome
Poaceae
gene
Base Composition
Transcriptome
Liliopsida
transcriptome
Duplicate Genes
genes
Genes
divergence
Asparagales
Plant Genome
grass
grasses
duplicate genes

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

Cite this

McKain, M. R., Tang, H., McNeal, J. R., Ayyampalayam, S., Davis, J. I., Depamphilis, C. W., ... Leebens-Mack, J. H. (2016). A phylogenomic assessment of ancient polyploidy and genome evolution across the poales. Genome biology and evolution, 8(4), 1150-1164. https://doi.org/10.1093/gbe/evw060
McKain, Michael R. ; Tang, Haibao ; McNeal, Joel R. ; Ayyampalayam, Saravanaraj ; Davis, Jerrold I. ; Depamphilis, Claude W. ; Givnish, Thomas J. ; Chris Pires, J. ; Stevenson, Dennis W. ; Leebens-Mack, James H. / A phylogenomic assessment of ancient polyploidy and genome evolution across the poales. In: Genome biology and evolution. 2016 ; Vol. 8, No. 4. pp. 1150-1164.
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McKain, MR, Tang, H, McNeal, JR, Ayyampalayam, S, Davis, JI, Depamphilis, CW, Givnish, TJ, Chris Pires, J, Stevenson, DW & Leebens-Mack, JH 2016, 'A phylogenomic assessment of ancient polyploidy and genome evolution across the poales', Genome biology and evolution, vol. 8, no. 4, pp. 1150-1164. https://doi.org/10.1093/gbe/evw060

A phylogenomic assessment of ancient polyploidy and genome evolution across the poales. / McKain, Michael R.; Tang, Haibao; McNeal, Joel R.; Ayyampalayam, Saravanaraj; Davis, Jerrold I.; Depamphilis, Claude W.; Givnish, Thomas J.; Chris Pires, J.; Stevenson, Dennis W.; Leebens-Mack, James H.

In: Genome biology and evolution, Vol. 8, No. 4, 01.01.2016, p. 1150-1164.

Research output: Contribution to journalArticle

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AU - McKain, Michael R.

AU - Tang, Haibao

AU - McNeal, Joel R.

AU - Ayyampalayam, Saravanaraj

AU - Davis, Jerrold I.

AU - Depamphilis, Claude W.

AU - Givnish, Thomas J.

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AU - Stevenson, Dennis W.

AU - Leebens-Mack, James H.

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