Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data
• Premise of the study: Single-copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50-75 species. The genus includes several polyploid species, some of which are considered noxious agricultura...
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description | • Premise of the study: Single-copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50-75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single-copy nuclear locus Salt Overly Sensitive 1 (SOS1) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors. • Methods: Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were first separated by plasmid-mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses. • Key results: Homeologous sequences of polyploid species were found in four clades, which we designate as A-D. Two distinct polyploid lineages were identified: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs. • Conclusions: We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum, was identified as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa, and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium, groups with American diploid species, which suggests a transoceanic dispersal. |
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Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50-75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single-copy nuclear locus Salt Overly Sensitive 1 (SOS1) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors. • Methods: Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were first separated by plasmid-mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses. • Key results: Homeologous sequences of polyploid species were found in four clades, which we designate as A-D. Two distinct polyploid lineages were identified: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs. • Conclusions: We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum, was identified as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa, and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium, groups with American diploid species, which suggests a transoceanic dispersal.</description><identifier>ISSN: 0002-9122</identifier><identifier>EISSN: 1537-2197</identifier><identifier>DOI: 10.3732/ajb.1400344</identifier><identifier>PMID: 25878087</identifier><identifier>CODEN: AJBOAA</identifier><language>eng</language><publisher>United States: Botanical Society of America, Inc</publisher><subject>allopolyploidy ; Amaranthaceae ; Botany ; Chenopodium ; Chenopodium - classification ; Chenopodium - genetics ; Chenopodium - metabolism ; Chenopodium berlandieri subsp. nuttalliae ; Chenopodium pallidicaule ; Chenopodium quinoa ; Dispersal ; domestication ; Evolution, Molecular ; Flowers & plants ; Genome, Plant ; Genomes ; homeologous loci ; Molecular Sequence Data ; Phylogenetics ; Phylogeny ; Plant Proteins - genetics ; Plant Proteins - metabolism ; Polyploidy ; Sequence Analysis, DNA ; single‐copy nuclear locus ; tetraploid</subject><ispartof>American journal of botany, 2015-04, Vol.102 (4), p.533-543</ispartof><rights>Copyright 2015 Botanical Society of America, Inc.</rights><rights>2015 Botanical Society of America</rights><rights>2015 Botanical Society of America, Inc.</rights><rights>Copyright Botanical Society of America, Inc. Apr 2015</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4473-6a9462931eec8d3e5590bb7b889ec91027b2dfbc3bd31596d9e7a7691c68cdc83</citedby><cites>FETCH-LOGICAL-c4473-6a9462931eec8d3e5590bb7b889ec91027b2dfbc3bd31596d9e7a7691c68cdc83</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/43826539$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/43826539$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>314,780,784,803,1417,1433,27924,27925,45574,45575,46409,46833,58017,58250</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25878087$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Walsh, Brian M.</creatorcontrib><creatorcontrib>Adhikary, Dinesh</creatorcontrib><creatorcontrib>Maughan, Peter J.</creatorcontrib><creatorcontrib>Emshwiller, Eve</creatorcontrib><creatorcontrib>Jellen, Eric N.</creatorcontrib><title>Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data</title><title>American journal of botany</title><addtitle>Am J Bot</addtitle><description>• Premise of the study: Single-copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50-75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single-copy nuclear locus Salt Overly Sensitive 1 (SOS1) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors. • Methods: Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were first separated by plasmid-mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses. • Key results: Homeologous sequences of polyploid species were found in four clades, which we designate as A-D. Two distinct polyploid lineages were identified: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs. • Conclusions: We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum, was identified as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa, and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium, groups with American diploid species, which suggests a transoceanic dispersal.</description><subject>allopolyploidy</subject><subject>Amaranthaceae</subject><subject>Botany</subject><subject>Chenopodium</subject><subject>Chenopodium - classification</subject><subject>Chenopodium - genetics</subject><subject>Chenopodium - metabolism</subject><subject>Chenopodium berlandieri subsp. nuttalliae</subject><subject>Chenopodium pallidicaule</subject><subject>Chenopodium quinoa</subject><subject>Dispersal</subject><subject>domestication</subject><subject>Evolution, Molecular</subject><subject>Flowers & plants</subject><subject>Genome, Plant</subject><subject>Genomes</subject><subject>homeologous loci</subject><subject>Molecular Sequence Data</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Plant Proteins - genetics</subject><subject>Plant Proteins - metabolism</subject><subject>Polyploidy</subject><subject>Sequence Analysis, DNA</subject><subject>single‐copy nuclear locus</subject><subject>tetraploid</subject><issn>0002-9122</issn><issn>1537-2197</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkc1P3DAQxa2qCLbAqeciS1yoqoC_EtvHZdVSENIeFs6RY0_UrJI4tROq_Pf1arccekCcRiP93hu9eQh9puSaS85uzLa6poIQLsQHtKA5lxmjWn5EC0IIyzRl7AR9inGbVi00O0YnLFdSESUX6GH1C3o_eNdMHR58Ow-tb9yMm76GAL2FiOvgO7wx7YjXLxDaGW-gj83YvACm-Gqz3tCv2JnRnKGj2rQRzg_zFD3_-P60-pk9ru_uV8vHzAoheVYYLQqmOQWwynHIc02qSlZKabCaEiYr5urK8spxmuvCaZBGFpraQllnFT9FV3vfIfjfE8Sx7JpooW1ND36KJS1SykKJIn8HKgVLfyA0oZf_oVs_hT4F2VGaMUXo7va3PWWDjzFAXQ6h6UyYS0rKXRtlaqM8tJHoi4PnVHXgXtl_708A3QN_mhbmt7zK5cMtIznnSfNlr9nG0YdXjeCKpcSa_wVezJsO</recordid><startdate>20150401</startdate><enddate>20150401</enddate><creator>Walsh, Brian M.</creator><creator>Adhikary, Dinesh</creator><creator>Maughan, Peter J.</creator><creator>Emshwiller, Eve</creator><creator>Jellen, Eric N.</creator><general>Botanical Society of America, Inc</general><general>Botanical Society of America</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>7SN</scope><scope>7SS</scope><scope>7ST</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>SOI</scope><scope>7X8</scope></search><sort><creationdate>20150401</creationdate><title>Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data</title><author>Walsh, Brian M. ; Adhikary, Dinesh ; Maughan, Peter J. ; Emshwiller, Eve ; Jellen, Eric N.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4473-6a9462931eec8d3e5590bb7b889ec91027b2dfbc3bd31596d9e7a7691c68cdc83</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>allopolyploidy</topic><topic>Amaranthaceae</topic><topic>Botany</topic><topic>Chenopodium</topic><topic>Chenopodium - classification</topic><topic>Chenopodium - genetics</topic><topic>Chenopodium - metabolism</topic><topic>Chenopodium berlandieri subsp. nuttalliae</topic><topic>Chenopodium pallidicaule</topic><topic>Chenopodium quinoa</topic><topic>Dispersal</topic><topic>domestication</topic><topic>Evolution, Molecular</topic><topic>Flowers & plants</topic><topic>Genome, Plant</topic><topic>Genomes</topic><topic>homeologous loci</topic><topic>Molecular Sequence Data</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant Proteins - genetics</topic><topic>Plant Proteins - metabolism</topic><topic>Polyploidy</topic><topic>Sequence Analysis, DNA</topic><topic>single‐copy nuclear locus</topic><topic>tetraploid</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Walsh, Brian M.</creatorcontrib><creatorcontrib>Adhikary, Dinesh</creatorcontrib><creatorcontrib>Maughan, Peter J.</creatorcontrib><creatorcontrib>Emshwiller, Eve</creatorcontrib><creatorcontrib>Jellen, Eric N.</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Environment Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>Environment Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>American journal of botany</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Walsh, Brian M.</au><au>Adhikary, Dinesh</au><au>Maughan, Peter J.</au><au>Emshwiller, Eve</au><au>Jellen, Eric N.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data</atitle><jtitle>American journal of botany</jtitle><addtitle>Am J Bot</addtitle><date>2015-04-01</date><risdate>2015</risdate><volume>102</volume><issue>4</issue><spage>533</spage><epage>543</epage><pages>533-543</pages><issn>0002-9122</issn><eissn>1537-2197</eissn><coden>AJBOAA</coden><abstract>• Premise of the study: Single-copy nuclear loci can provide powerful insights into polyploid evolution. Chenopodium (Amaranthaceae) is a globally distributed genus composed of approximately 50-75 species. The genus includes several polyploid species, some of which are considered noxious agricultural weeds, and a few are domesticated crops. Very little research has addressed their evolutionary origin to date. We construct a phylogeny for Chenopodium based on two introns of the single-copy nuclear locus Salt Overly Sensitive 1 (SOS1) to clarify the relationships among the genomes of the allotetraploid and allohexaploid species, and to help identify their genome donors. • Methods: Diploid species were sequenced directly, whereas homeologous sequences of polyploid genomes were first separated by plasmid-mediated cloning. Data were evaluated in maximum likelihood and Bayesian phylogenetic analyses. • Key results: Homeologous sequences of polyploid species were found in four clades, which we designate as A-D. Two distinct polyploid lineages were identified: one composed of American tetraploid species with A and B class homeologs and a second composed of Eastern Hemisphere hexaploid species with B, C, and D class homeologs. • Conclusions: We infer that the two polyploid lineages arose independently and that each lineage may have originated only once. The American diploid, C. standleyanum, was identified as the closest living diploid relative of the A genome donor for American tetraploids, including domesticated C. quinoa, and is of potential importance for quinoa breeding. The east Asian diploid species, C. bryoniifolium, groups with American diploid species, which suggests a transoceanic dispersal.</abstract><cop>United States</cop><pub>Botanical Society of America, Inc</pub><pmid>25878087</pmid><doi>10.3732/ajb.1400344</doi><tpages>11</tpages><oa>free_for_read</oa></addata></record> |
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subjects | allopolyploidy Amaranthaceae Botany Chenopodium Chenopodium - classification Chenopodium - genetics Chenopodium - metabolism Chenopodium berlandieri subsp. nuttalliae Chenopodium pallidicaule Chenopodium quinoa Dispersal domestication Evolution, Molecular Flowers & plants Genome, Plant Genomes homeologous loci Molecular Sequence Data Phylogenetics Phylogeny Plant Proteins - genetics Plant Proteins - metabolism Polyploidy Sequence Analysis, DNA single‐copy nuclear locus tetraploid |
title | Chenopodium polyploidy inferences from Salt Overly Sensitive 1 (SOS1) data |
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