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Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex

Allopolyploidy combines two progenitor genomes in the same nucleus. It is a common speciation process, especially in plants. Deciphering the origins of polyploid species is a complex problem due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid popu...

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Detalles Bibliográficos
Autores principales: Bombarely, Aureliano, Coate, Jeremy E., Doyle, Jeff J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034613/
https://www.ncbi.nlm.nih.gov/pubmed/24883252
http://dx.doi.org/10.7717/peerj.391
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author Bombarely, Aureliano
Coate, Jeremy E.
Doyle, Jeff J.
author_facet Bombarely, Aureliano
Coate, Jeremy E.
Doyle, Jeff J.
author_sort Bombarely, Aureliano
collection PubMed
description Allopolyploidy combines two progenitor genomes in the same nucleus. It is a common speciation process, especially in plants. Deciphering the origins of polyploid species is a complex problem due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid populations, and loss of parental contributions through gene or chromosome loss. Among the perennial species of Glycine, the plant genus that includes the cultivated soybean (G. max), are eight allopolyploid species, three of which are studied here. Previous crossing studies and molecular systematic results from two nuclear gene sequences led to hypotheses of origin for these species from among extant diploid species. We use several phylogenetic and population genomics approaches to clarify the origins of the genomes of three of these allopolyploid species using single nucleotide polymorphism data and a guided transcriptome assembly. The results support the hypothesis that all three polyploid species are fixed hybrids combining the genomes of the two putative parents hypothesized on the basis of previous work. Based on mapping to the soybean reference genome, there appear to be no large regions for which one homoeologous contribution is missing. Phylogenetic analyses of 27 selected transcripts using a coalescent approach also are consistent with multiple origins for these allopolyploid species, and suggest that origins occurred within the last several hundred thousand years.
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spelling pubmed-40346132014-05-30 Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex Bombarely, Aureliano Coate, Jeremy E. Doyle, Jeff J. PeerJ Evolutionary Studies Allopolyploidy combines two progenitor genomes in the same nucleus. It is a common speciation process, especially in plants. Deciphering the origins of polyploid species is a complex problem due to, among other things, extinct progenitors, multiple origins, gene flow between different polyploid populations, and loss of parental contributions through gene or chromosome loss. Among the perennial species of Glycine, the plant genus that includes the cultivated soybean (G. max), are eight allopolyploid species, three of which are studied here. Previous crossing studies and molecular systematic results from two nuclear gene sequences led to hypotheses of origin for these species from among extant diploid species. We use several phylogenetic and population genomics approaches to clarify the origins of the genomes of three of these allopolyploid species using single nucleotide polymorphism data and a guided transcriptome assembly. The results support the hypothesis that all three polyploid species are fixed hybrids combining the genomes of the two putative parents hypothesized on the basis of previous work. Based on mapping to the soybean reference genome, there appear to be no large regions for which one homoeologous contribution is missing. Phylogenetic analyses of 27 selected transcripts using a coalescent approach also are consistent with multiple origins for these allopolyploid species, and suggest that origins occurred within the last several hundred thousand years. PeerJ Inc. 2014-05-20 /pmc/articles/PMC4034613/ /pubmed/24883252 http://dx.doi.org/10.7717/peerj.391 Text en © 2014 Bombarely et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Evolutionary Studies
Bombarely, Aureliano
Coate, Jeremy E.
Doyle, Jeff J.
Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
title Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
title_full Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
title_fullStr Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
title_full_unstemmed Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
title_short Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
title_sort mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex
topic Evolutionary Studies
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034613/
https://www.ncbi.nlm.nih.gov/pubmed/24883252
http://dx.doi.org/10.7717/peerj.391
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