Tags

Type your tag names separated by a space and hit enter

A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales.
Genome Biol Evol. 2016 Apr 21; 8(4):1150-64.GB

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 (ρ), sigma (σ), and tau (τ), 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.

Authors+Show Affiliations

Donald Danforth Plant Science Center, St. Louis, Missouri Department of Plant Biology, University of Georgia mrmckain@gmail.com.Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China School of Plant Sciences, iPlant Collaborative, University of Arizona.Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University Department of Plant Biology, University of Georgia.Department of Plant Biology, University of Georgia.L. H. Bailey Hortorium and Department of Plant Biology, Cornell University.Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, Pennsylvania.Department of Botany, University of Wisconsin-Madison.Division of Biological Sciences, University of Missouri, Columbia.New York Botanical Garden, Bronx, New York.Department of Plant Biology, University of Georgia.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

26988252

Citation

McKain, Michael R., et al. "A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution Across the Poales." Genome Biology and Evolution, vol. 8, no. 4, 2016, pp. 1150-64.
McKain MR, Tang H, McNeal JR, et al. A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales. Genome Biol Evol. 2016;8(4):1150-64.
McKain, M. R., Tang, H., McNeal, J. R., Ayyampalayam, S., Davis, J. I., dePamphilis, C. W., Givnish, T. J., Pires, J. C., Stevenson, D. W., & Leebens-Mack, J. H. (2016). A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales. Genome Biology and Evolution, 8(4), 1150-64. https://doi.org/10.1093/gbe/evw060
McKain MR, et al. A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution Across the Poales. Genome Biol Evol. 2016 Apr 21;8(4):1150-64. PubMed PMID: 26988252.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales. 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, AU - Pires,J Chris, AU - Stevenson,Dennis Wm, AU - Leebens-Mack,James H, Y1 - 2016/04/21/ PY - 2016/3/19/entrez PY - 2016/3/19/pubmed PY - 2017/3/14/medline KW - GC content KW - grasses KW - monocots KW - whole-genome duplication SP - 1150 EP - 64 JF - Genome biology and evolution JO - Genome Biol Evol VL - 8 IS - 4 N2 - 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 (ρ), sigma (σ), and tau (τ), 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. SN - 1759-6653 UR - https://www.unboundmedicine.com/medline/citation/26988252/A_Phylogenomic_Assessment_of_Ancient_Polyploidy_and_Genome_Evolution_across_the_Poales_ L2 - https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/evw060 DB - PRIME DP - Unbound Medicine ER -