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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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2014-05-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/391.pdf |
| _version_ | 1797418807627612160 |
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| author | Aureliano Bombarely Jeremy E. Coate Jeff J. Doyle |
| author_facet | Aureliano Bombarely Jeremy E. Coate Jeff J. Doyle |
| author_sort | Aureliano Bombarely |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T06:39:19Z |
| format | Article |
| id | doaj.art-7720dc717ee94a1e9ec6bf75dd231b9a |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:39:19Z |
| publishDate | 2014-05-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
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| spelling | doaj.art-7720dc717ee94a1e9ec6bf75dd231b9a2023-12-03T10:54:05ZengPeerJ Inc.PeerJ2167-83592014-05-012e39110.7717/peerj.391391Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complexAureliano Bombarely0Jeremy E. Coate1Jeff J. Doyle2Department of Plant Biology, Cornell University, Ithaca, NY, USADepartment of Biology, Reed College, Portland, OR, USADepartment of Plant Biology, Cornell University, Ithaca, NY, USAAllopolyploidy 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.https://peerj.com/articles/391.pdfPolyploidyPhylogeneticsPopulation genomicsNGS |
| spellingShingle | Aureliano Bombarely Jeremy E. Coate Jeff J. Doyle Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex PeerJ Polyploidy Phylogenetics Population genomics NGS |
| 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 | Polyploidy Phylogenetics Population genomics NGS |
| url | https://peerj.com/articles/391.pdf |
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