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Multiple large-scale gene and genome duplications during the evolution of hexapods.
Proc Natl Acad Sci U S A. 2018 05 01; 115(18):4713-4718.PN

Abstract

Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals. Using gene age distributions and phylogenomics, we found evidence for 18 ancient WGDs and six other large-scale bursts of gene duplication during insect evolution. These bursts of gene duplication occurred in the history of lineages such as the Lepidoptera, Trichoptera, and Odonata. To further corroborate the nature of these duplications, we evaluated the pattern of gene retention from putative WGDs observed in the gene age distributions. We found a relatively strong signal of convergent gene retention across many of the putative insect WGDs. Considering the phylogenetic breadth and depth of the insect phylogeny, this observation is consistent with polyploidy as we expect dosage balance to drive the parallel retention of genes. Together with recent research on plant evolution, our hexapod results suggest that genome duplications contributed to the evolution of two of the most diverse lineages of eukaryotes on Earth.

Authors+Show Affiliations

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721.Department of Biology, University of Florida, Gainesville, FL 32611. Department of Biology, Duke University, Durham, NC 27708.Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721.Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721.Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721.Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721. Department of Environmental and Forest Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY 13210.Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721; msbarker@email.arizona.edu.

Pub Type(s)

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

Language

eng

PubMed ID

29674453

Citation

Li, Zheng, et al. "Multiple Large-scale Gene and Genome Duplications During the Evolution of Hexapods." Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 18, 2018, pp. 4713-4718.
Li Z, Tiley GP, Galuska SR, et al. Multiple large-scale gene and genome duplications during the evolution of hexapods. Proc Natl Acad Sci USA. 2018;115(18):4713-4718.
Li, Z., Tiley, G. P., Galuska, S. R., Reardon, C. R., Kidder, T. I., Rundell, R. J., & Barker, M. S. (2018). Multiple large-scale gene and genome duplications during the evolution of hexapods. Proceedings of the National Academy of Sciences of the United States of America, 115(18), 4713-4718. https://doi.org/10.1073/pnas.1710791115
Li Z, et al. Multiple Large-scale Gene and Genome Duplications During the Evolution of Hexapods. Proc Natl Acad Sci USA. 2018 05 1;115(18):4713-4718. PubMed PMID: 29674453.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Multiple large-scale gene and genome duplications during the evolution of hexapods. AU - Li,Zheng, AU - Tiley,George P, AU - Galuska,Sally R, AU - Reardon,Chris R, AU - Kidder,Thomas I, AU - Rundell,Rebecca J, AU - Barker,Michael S, Y1 - 2018/04/19/ PY - 2018/4/21/pubmed PY - 2018/8/15/medline PY - 2018/4/21/entrez KW - genome duplication KW - genomics KW - hexapods KW - insects KW - polyploidy SP - 4713 EP - 4718 JF - Proceedings of the National Academy of Sciences of the United States of America JO - Proc. Natl. Acad. Sci. U.S.A. VL - 115 IS - 18 N2 - Polyploidy or whole genome duplication (WGD) is a major contributor to genome evolution and diversity. Although polyploidy is recognized as an important component of plant evolution, it is generally considered to play a relatively minor role in animal evolution. Ancient polyploidy is found in the ancestry of some animals, especially fishes, but there is little evidence for ancient WGDs in other metazoan lineages. Here we use recently published transcriptomes and genomes from more than 150 species across the insect phylogeny to investigate whether ancient WGDs occurred during the evolution of Hexapoda, the most diverse clade of animals. Using gene age distributions and phylogenomics, we found evidence for 18 ancient WGDs and six other large-scale bursts of gene duplication during insect evolution. These bursts of gene duplication occurred in the history of lineages such as the Lepidoptera, Trichoptera, and Odonata. To further corroborate the nature of these duplications, we evaluated the pattern of gene retention from putative WGDs observed in the gene age distributions. We found a relatively strong signal of convergent gene retention across many of the putative insect WGDs. Considering the phylogenetic breadth and depth of the insect phylogeny, this observation is consistent with polyploidy as we expect dosage balance to drive the parallel retention of genes. Together with recent research on plant evolution, our hexapod results suggest that genome duplications contributed to the evolution of two of the most diverse lineages of eukaryotes on Earth. SN - 1091-6490 UR - https://www.unboundmedicine.com/medline/citation/29674453/Multiple_large_scale_gene_and_genome_duplications_during_the_evolution_of_hexapods_ L2 - http://www.pnas.org/cgi/pmidlookup?view=long&pmid=29674453 DB - PRIME DP - Unbound Medicine ER -