Two plastid DNA lineages--Rapa/Oleracea and Nigra--within the tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: evidence from divergence times of the plastid genomes and R-block genes of the A and B genomes of Brassica juncea.
Identifieur interne : 001F81 ( Main/Exploration ); précédent : 001F80; suivant : 001F82Two plastid DNA lineages--Rapa/Oleracea and Nigra--within the tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: evidence from divergence times of the plastid genomes and R-block genes of the A and B genomes of Brassica juncea.
Auteurs : Sarita Sharma [Inde] ; K Lakshmi Padmaja [Inde] ; Vibha Gupta [Inde] ; Kumar Paritosh [Inde] ; Akshay K. Pradhan [Inde] ; Deepak Pental [Inde]Source :
- PloS one [ 1932-6203 ] ; 2014.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (MeSH), Biologie informatique (MeSH), Brassicaceae (classification), Brassicaceae (génétique), Cartographie chromosomique (MeSH), Croisements génétiques (MeSH), Gènes de plante (MeSH), Génome plastidique (MeSH), Modèles génétiques (MeSH), Phylogenèse (MeSH), Plastes (génétique), Polyploïdie (MeSH), Populus (génétique), Portulaca (génétique), Variation génétique (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : Brassicaceae, Plastes, Populus, Portulaca.
- classification : Analyse de séquence d'ADN, Biologie informatique, Brassicaceae, Cartographie chromosomique, Croisements génétiques, Gènes de plante, Génome plastidique, Modèles génétiques, Phylogenèse, Polyploïdie, Variation génétique, Évolution moléculaire.
English descriptors
- KwdEn :
- Brassicaceae (classification), Brassicaceae (genetics), Chromosome Mapping (MeSH), Computational Biology (MeSH), Crosses, Genetic (MeSH), Evolution, Molecular (MeSH), Genes, Plant (MeSH), Genetic Variation (MeSH), Genome, Plastid (MeSH), Models, Genetic (MeSH), Phylogeny (MeSH), Plastids (genetics), Polyploidy (MeSH), Populus (genetics), Portulaca (genetics), Sequence Analysis, DNA (MeSH).
- MESH :
- classification : Brassicaceae.
- genetics : Brassicaceae, Plastids, Populus, Portulaca.
- Chromosome Mapping, Computational Biology, Crosses, Genetic, Evolution, Molecular, Genes, Plant, Genetic Variation, Genome, Plastid, Models, Genetic, Phylogeny, Polyploidy, Sequence Analysis, DNA.
Abstract
Brassica species (tribe Brassiceae) belonging to U's triangle--B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. juncea (AABB), B. napus (AACC) and B. carinata (BBCC)--originated via two polyploidization rounds: a U event producing the three allopolyploids, and a more ancient b genome-triplication event giving rise to the A-, B-, and C-genome diploid species. Molecular mapping studies, in situ hybridization, and genome sequencing of B. rapa support the genome triplication origin of tribe Brassiceae, and suggest that these three diploid species diversified from a common hexaploid ancestor. Analysis of plastid DNA has revealed two distinct lineages--Rapa/Oleracea and Nigra--that conflict with hexaploidization as a single event defining the tribe Brassiceae. We analysed an R-block region of A. thaliana present in six copies in B. juncea (AABB), three copies each on A- and B-genomes to study gene fractionation pattern and synonymous base substitution rates (Ks values). Divergence time of paralogues within the A and B genomes and homoeologues between the A and B genomes was estimated. Homoeologous R blocks of the A and B genomes exhibited high gene collinearity and a conserved gene fractionation pattern. The three progenitors of diploid Brassicas were estimated to have diverged approximately 12 mya. Divergence of B. rapa and B. nigra, calculated from plastid gene sequences, was estimated to have occurred approximately 12 mya, coinciding with the divergence of the three genomes participating in the b event. Divergence of B. juncea A and B genome homoeologues was estimated to have taken place around 7 mya. Based on divergence time estimates and the presence of distinct plastid lineages in tribe Brassiceae, it is concluded that at least two independent triplication events involving reciprocal crosses at the time of the b event have given rise to Rapa/Oleracea and Nigra lineages.
DOI: 10.1371/journal.pone.0093260
PubMed: 24691069
PubMed Central: PMC3972200
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Two plastid DNA lineages--Rapa/Oleracea and Nigra--within the tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: evidence from divergence times of the plastid genomes and R-block genes of the A and B genomes of Brassica juncea.</title><author><name sortKey="Sharma, Sarita" sort="Sharma, Sarita" uniqKey="Sharma S" first="Sarita" last="Sharma">Sarita Sharma</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Padmaja, K Lakshmi" sort="Padmaja, K Lakshmi" uniqKey="Padmaja K" first="K Lakshmi" last="Padmaja">K Lakshmi Padmaja</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Gupta, Vibha" sort="Gupta, Vibha" uniqKey="Gupta V" first="Vibha" last="Gupta">Vibha Gupta</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Paritosh, Kumar" sort="Paritosh, Kumar" uniqKey="Paritosh K" first="Kumar" last="Paritosh">Kumar Paritosh</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Pradhan, Akshay K" sort="Pradhan, Akshay K" uniqKey="Pradhan A" first="Akshay K" last="Pradhan">Akshay K. 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Pradhan</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India; Department of Genetics, University of Delhi South Campus, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India; Department of Genetics, University of Delhi South Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Pental, Deepak" sort="Pental, Deepak" uniqKey="Pental D" first="Deepak" last="Pental">Deepak Pental</name><affiliation wicri:level="1"><nlm:affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India; Department of Genetics, University of Delhi South Campus, New Delhi, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India; Department of Genetics, University of Delhi South Campus, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Brassicaceae (classification)</term><term>Brassicaceae (genetics)</term><term>Chromosome Mapping (MeSH)</term><term>Computational Biology (MeSH)</term><term>Crosses, Genetic (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Plastid (MeSH)</term><term>Models, Genetic (MeSH)</term><term>Phylogeny (MeSH)</term><term>Plastids (genetics)</term><term>Polyploidy (MeSH)</term><term>Populus (genetics)</term><term>Portulaca (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Biologie informatique (MeSH)</term><term>Brassicaceae (classification)</term><term>Brassicaceae (génétique)</term><term>Cartographie chromosomique (MeSH)</term><term>Croisements génétiques (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Génome plastidique (MeSH)</term><term>Modèles génétiques (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Plastes (génétique)</term><term>Polyploïdie (MeSH)</term><term>Populus (génétique)</term><term>Portulaca (génétique)</term><term>Variation génétique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Brassicaceae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Brassicaceae</term><term>Plastids</term><term>Populus</term><term>Portulaca</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Brassicaceae</term><term>Plastes</term><term>Populus</term><term>Portulaca</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Computational Biology</term><term>Crosses, Genetic</term><term>Evolution, Molecular</term><term>Genes, Plant</term><term>Genetic Variation</term><term>Genome, Plastid</term><term>Models, Genetic</term><term>Phylogeny</term><term>Polyploidy</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Brassicaceae</term><term>Cartographie chromosomique</term><term>Croisements génétiques</term><term>Gènes de plante</term><term>Génome plastidique</term><term>Modèles génétiques</term><term>Phylogenèse</term><term>Polyploïdie</term><term>Variation génétique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Brassica species (tribe Brassiceae) belonging to U's triangle--B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. juncea (AABB), B. napus (AACC) and B. carinata (BBCC)--originated via two polyploidization rounds: a U event producing the three allopolyploids, and a more ancient b genome-triplication event giving rise to the A-, B-, and C-genome diploid species. Molecular mapping studies, in situ hybridization, and genome sequencing of B. rapa support the genome triplication origin of tribe Brassiceae, and suggest that these three diploid species diversified from a common hexaploid ancestor. Analysis of plastid DNA has revealed two distinct lineages--Rapa/Oleracea and Nigra--that conflict with hexaploidization as a single event defining the tribe Brassiceae. We analysed an R-block region of A. thaliana present in six copies in B. juncea (AABB), three copies each on A- and B-genomes to study gene fractionation pattern and synonymous base substitution rates (Ks values). Divergence time of paralogues within the A and B genomes and homoeologues between the A and B genomes was estimated. Homoeologous R blocks of the A and B genomes exhibited high gene collinearity and a conserved gene fractionation pattern. The three progenitors of diploid Brassicas were estimated to have diverged approximately 12 mya. Divergence of B. rapa and B. nigra, calculated from plastid gene sequences, was estimated to have occurred approximately 12 mya, coinciding with the divergence of the three genomes participating in the b event. Divergence of B. juncea A and B genome homoeologues was estimated to have taken place around 7 mya. Based on divergence time estimates and the presence of distinct plastid lineages in tribe Brassiceae, it is concluded that at least two independent triplication events involving reciprocal crosses at the time of the b event have given rise to Rapa/Oleracea and Nigra lineages.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24691069</PMID><DateCompleted><Year>2015</Year><Month>12</Month><Day>17</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>4</Issue><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Two plastid DNA lineages--Rapa/Oleracea and Nigra--within the tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: evidence from divergence times of the plastid genomes and R-block genes of the A and B genomes of Brassica juncea.</ArticleTitle><Pagination><MedlinePgn>e93260</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0093260</ELocationID><Abstract><AbstractText>Brassica species (tribe Brassiceae) belonging to U's triangle--B. rapa (AA), B. nigra (BB), B. oleracea (CC), B. juncea (AABB), B. napus (AACC) and B. carinata (BBCC)--originated via two polyploidization rounds: a U event producing the three allopolyploids, and a more ancient b genome-triplication event giving rise to the A-, B-, and C-genome diploid species. Molecular mapping studies, in situ hybridization, and genome sequencing of B. rapa support the genome triplication origin of tribe Brassiceae, and suggest that these three diploid species diversified from a common hexaploid ancestor. Analysis of plastid DNA has revealed two distinct lineages--Rapa/Oleracea and Nigra--that conflict with hexaploidization as a single event defining the tribe Brassiceae. We analysed an R-block region of A. thaliana present in six copies in B. juncea (AABB), three copies each on A- and B-genomes to study gene fractionation pattern and synonymous base substitution rates (Ks values). Divergence time of paralogues within the A and B genomes and homoeologues between the A and B genomes was estimated. Homoeologous R blocks of the A and B genomes exhibited high gene collinearity and a conserved gene fractionation pattern. The three progenitors of diploid Brassicas were estimated to have diverged approximately 12 mya. Divergence of B. rapa and B. nigra, calculated from plastid gene sequences, was estimated to have occurred approximately 12 mya, coinciding with the divergence of the three genomes participating in the b event. Divergence of B. juncea A and B genome homoeologues was estimated to have taken place around 7 mya. Based on divergence time estimates and the presence of distinct plastid lineages in tribe Brassiceae, it is concluded that at least two independent triplication events involving reciprocal crosses at the time of the b event have given rise to Rapa/Oleracea and Nigra lineages.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sharma</LastName><ForeName>Sarita</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Padmaja</LastName><ForeName>K Lakshmi</ForeName><Initials>KL</Initials><AffiliationInfo><Affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gupta</LastName><ForeName>Vibha</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Paritosh</LastName><ForeName>Kumar</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pradhan</LastName><ForeName>Akshay K</ForeName><Initials>AK</Initials><AffiliationInfo><Affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India; Department of Genetics, University of Delhi South Campus, New Delhi, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pental</LastName><ForeName>Deepak</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, India; Department of Genetics, University of Delhi South Campus, New Delhi, India.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>04</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D019607" MajorTopicYN="N">Brassicaceae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003433" MajorTopicYN="Y">Crosses, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054627" MajorTopicYN="N">Genome, Plastid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018087" MajorTopicYN="N">Plastids</DescriptorName><QualifierName UI="Q000235" 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last="Paritosh">Kumar Paritosh</name><name sortKey="Pental, Deepak" sort="Pental, Deepak" uniqKey="Pental D" first="Deepak" last="Pental">Deepak Pental</name><name sortKey="Pradhan, Akshay K" sort="Pradhan, Akshay K" uniqKey="Pradhan A" first="Akshay K" last="Pradhan">Akshay K. 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|texte= Two plastid DNA lineages--Rapa/Oleracea and Nigra--within the tribe Brassiceae can be best explained by reciprocal crosses at hexaploidy: evidence from divergence times of the plastid genomes and R-block genes of the A and B genomes of Brassica juncea.
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