Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene
The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a...
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description | The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of the Pgk1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. maroccana and A. murphyi, but did not show a close relationship with any extant diploid species. |
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A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of the Pgk1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. maroccana and A. murphyi, but did not show a close relationship with any extant diploid species.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0200047</identifier><identifier>PMID: 30408035</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Biology and Life Sciences ; Chromosomes ; Collaboration ; Computer and Information Sciences ; Diploids ; Divergence ; Evolution ; Gene deletion ; Genes ; Genetics ; Genomes ; Goat grass ; Haplotypes ; Hybridization ; Hypotheses ; Hypothesis testing ; Molecular biology ; Morphology ; Oats ; Phosphoglycerate kinase ; Phylogenetics ; Phylogeny ; Polyploidy ; R&D ; Research & development ; Research and Analysis Methods ; Species</subject><ispartof>PloS one, 2018-11, Vol.13 (11), p.e0200047-e0200047</ispartof><rights>2018 Peng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2018 Peng et al 2018 Peng et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c526t-bec90c7fb2d13ed1eb4788fde079022f8d9115a91e2129d8217ab8cf01a4c95d3</citedby><cites>FETCH-LOGICAL-c526t-bec90c7fb2d13ed1eb4788fde079022f8d9115a91e2129d8217ab8cf01a4c95d3</cites><orcidid>0000-0001-7360-0670</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224039/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6224039/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30408035$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Jellen, Eric</contributor><creatorcontrib>Peng, Yuanying</creatorcontrib><creatorcontrib>Zhou, Pingping</creatorcontrib><creatorcontrib>Zhao, Jun</creatorcontrib><creatorcontrib>Li, Junzhuo</creatorcontrib><creatorcontrib>Lai, Shikui</creatorcontrib><creatorcontrib>Tinker, Nicholas A</creatorcontrib><creatorcontrib>Liao, Shu</creatorcontrib><creatorcontrib>Yan, Honghai</creatorcontrib><title>Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of the Pgk1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. maroccana and A. murphyi, but did not show a close relationship with any extant diploid species.</description><subject>Biology and Life Sciences</subject><subject>Chromosomes</subject><subject>Collaboration</subject><subject>Computer and Information Sciences</subject><subject>Diploids</subject><subject>Divergence</subject><subject>Evolution</subject><subject>Gene deletion</subject><subject>Genes</subject><subject>Genetics</subject><subject>Genomes</subject><subject>Goat grass</subject><subject>Haplotypes</subject><subject>Hybridization</subject><subject>Hypotheses</subject><subject>Hypothesis testing</subject><subject>Molecular biology</subject><subject>Morphology</subject><subject>Oats</subject><subject>Phosphoglycerate kinase</subject><subject>Phylogenetics</subject><subject>Phylogeny</subject><subject>Polyploidy</subject><subject>R&D</subject><subject>Research & 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relationships in the genus Avena based on the nuclear Pgk1 gene</title><author>Peng, Yuanying ; Zhou, Pingping ; Zhao, Jun ; Li, Junzhuo ; Lai, Shikui ; Tinker, Nicholas A ; Liao, Shu ; Yan, Honghai</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-bec90c7fb2d13ed1eb4788fde079022f8d9115a91e2129d8217ab8cf01a4c95d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Biology and Life Sciences</topic><topic>Chromosomes</topic><topic>Collaboration</topic><topic>Computer and Information Sciences</topic><topic>Diploids</topic><topic>Divergence</topic><topic>Evolution</topic><topic>Gene deletion</topic><topic>Genes</topic><topic>Genetics</topic><topic>Genomes</topic><topic>Goat grass</topic><topic>Haplotypes</topic><topic>Hybridization</topic><topic>Hypotheses</topic><topic>Hypothesis testing</topic><topic>Molecular 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Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Peng, Yuanying</au><au>Zhou, Pingping</au><au>Zhao, Jun</au><au>Li, Junzhuo</au><au>Lai, Shikui</au><au>Tinker, Nicholas A</au><au>Liao, Shu</au><au>Yan, Honghai</au><au>Jellen, Eric</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2018-11-08</date><risdate>2018</risdate><volume>13</volume><issue>11</issue><spage>e0200047</spage><epage>e0200047</epage><pages>e0200047-e0200047</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The phylogenetic relationships among 76 Avena taxa, representing 14 diploids, eight tetraploids, and four hexaploids were investigated by using the nuclear plastid 3-phosphoglycerate kinase gene (Pgk1). A significant deletion (131 bp) was detected in all the C genome homoeologues which reconfirmed a major structural divergence between the A and C genomes. Phylogenetic analysis indicated the Cp genome is more closely related to the polyploid species than is the Cv genome. Two haplotypes of Pgk1 gene were obtained from most of the AB genome tetraploids. Both types of the barbata group showed a close relationship with the As genome diploid species, supporting the hypothesis that both the A and B genomes are derived from an As genome. Two haplotypes were also detected in A. agadiriana, which showed close relationships with the As genome diploid and the Ac genome diploid, respectively, emphasizing the important role of the Ac genome in the evolution of A. agadiriana. Three homoeologues of the Pgk1 gene were detected in five hexaploid accessions. The homoeologues that might represent the D genome were tightly clustered with the tetraploids A. maroccana and A. murphyi, but did not show a close relationship with any extant diploid species.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>30408035</pmid><doi>10.1371/journal.pone.0200047</doi><orcidid>https://orcid.org/0000-0001-7360-0670</orcidid><oa>free_for_read</oa></addata></record> |
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subjects | Biology and Life Sciences Chromosomes Collaboration Computer and Information Sciences Diploids Divergence Evolution Gene deletion Genes Genetics Genomes Goat grass Haplotypes Hybridization Hypotheses Hypothesis testing Molecular biology Morphology Oats Phosphoglycerate kinase Phylogenetics Phylogeny Polyploidy R&D Research & development Research and Analysis Methods Species |
title | Phylogenetic relationships in the genus Avena based on the nuclear Pgk1 gene |
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