Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads.
Identifieur interne : 002306 ( Main/Exploration ); précédent : 002305; suivant : 002307Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads.
Auteurs : Dayana E. Salas-Leiva [États-Unis] ; Alan W. Meerow ; Javier Francisco-Ortega ; Michael Calonje ; M Patrick Griffith ; Dennis W. Stevenson ; Kyoko NakamuraSource :
- Molecular ecology resources [ 1755-0998 ] ; 2014.
Descripteurs français
- KwdFr :
- ADN des plantes (composition chimique), ADN des plantes (génétique), Analyse de séquence d'ADN (MeSH), Caraïbe (MeSH), Cycadopsida (classification), Cycadopsida (génétique), Données de séquences moléculaires (MeSH), Marqueurs génétiques (MeSH), Phylogéographie (MeSH), Séquence conservée (MeSH), Variation génétique (MeSH).
- MESH :
- composition chimique : ADN des plantes, Cycadopsida.
- génétique : ADN des plantes, Cycadopsida.
- Analyse de séquence d'ADN, Caraïbe, Données de séquences moléculaires, Marqueurs génétiques, Phylogéographie, Séquence conservée, Variation génétique.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Plant.
- classification : Cycadopsida.
- genetics : Cycadopsida, DNA, Plant.
- Caribbean Region, Conserved Sequence, Genetic Markers, Genetic Variation, Molecular Sequence Data, Phylogeography, Sequence Analysis, DNA.
Abstract
Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera.
DOI: 10.1111/1755-0998.12228
PubMed: 24444413
Affiliations:
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Salas-Leiva</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA; USDA-ARS-SHRS, National Germplasm Repository, Miami, FL, 33158, USA; Montgomery Botanical Center, Miami, FL, 33156, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA; USDA-ARS-SHRS, National Germplasm Repository, Miami, FL, 33158, USA; Montgomery Botanical Center, Miami, FL, 33156</wicri:regionArea><wicri:noRegion>33156</wicri:noRegion></affiliation></author><author><name sortKey="Meerow, Alan W" sort="Meerow, Alan W" uniqKey="Meerow A" first="Alan W" last="Meerow">Alan W. 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Stevenson</name></author><author><name sortKey="Nakamura, Kyoko" sort="Nakamura, Kyoko" uniqKey="Nakamura K" first="Kyoko" last="Nakamura">Kyoko Nakamura</name></author></analytic><series><title level="j">Molecular ecology resources</title><idno type="eISSN">1755-0998</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Caribbean Region (MeSH)</term><term>Conserved Sequence (MeSH)</term><term>Cycadopsida (classification)</term><term>Cycadopsida (genetics)</term><term>DNA, Plant (chemistry)</term><term>DNA, Plant (genetics)</term><term>Genetic Markers (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeography (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (composition chimique)</term><term>ADN des plantes (génétique)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Caraïbe (MeSH)</term><term>Cycadopsida (classification)</term><term>Cycadopsida (génétique)</term><term>Données de séquences moléculaires (MeSH)</term><term>Marqueurs génétiques (MeSH)</term><term>Phylogéographie (MeSH)</term><term>Séquence conservée (MeSH)</term><term>Variation génétique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Cycadopsida</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>ADN des plantes</term><term>Cycadopsida</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cycadopsida</term><term>DNA, Plant</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Cycadopsida</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Caribbean Region</term><term>Conserved Sequence</term><term>Genetic Markers</term><term>Genetic Variation</term><term>Molecular Sequence Data</term><term>Phylogeography</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Caraïbe</term><term>Données de séquences moléculaires</term><term>Marqueurs génétiques</term><term>Phylogéographie</term><term>Séquence conservée</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24444413</PMID><DateCompleted><Year>2015</Year><Month>01</Month><Day>26</Day></DateCompleted><DateRevised><Year>2017</Year><Month>11</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1755-0998</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><Issue>4</Issue><PubDate><Year>2014</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Molecular ecology resources</Title><ISOAbbreviation>Mol Ecol Resour</ISOAbbreviation></Journal><ArticleTitle>Conserved genetic regions across angiosperms as tools to develop single-copy nuclear markers in gymnosperms: an example using cycads.</ArticleTitle><Pagination><MedlinePgn>831-45</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/1755-0998.12228</ELocationID><Abstract><AbstractText>Several individuals of the Caribbean Zamia clade and other cycad genera were used to identify single-copy nuclear genes for phylogeographic and phylogenetic studies in Cycadales. Two strategies were employed to select target loci: (i) a tblastX search of Arabidopsis conserved ortholog sequence (COS) set and (ii) a tblastX search of Arabidopsis-Populus-Vitis-Oryza Shared Single-Copy genes (APVO SSC) against the EST Zamia databases in GenBank. From the first strategy, 30 loci were selected, and from the second, 16 loci. In both cases, the matching GenBank accessions of Zamia were used as a query for retrieving highly similar sequences from Cycas, Picea, Pinus species or Ginkgo biloba. After retrieving and aligning all the sequences in each locus, intron predictions were completed to assist in primer design. PCR was carried out in three rounds to detect paralogous loci. A total of 29 loci were successfully amplified as a single band of which 20 were likely single-copy loci. These loci showed different diversity and divergence levels. A preliminary screening allowed us to select 8 promising loci (40S, ATG2, BG, GroES, GTP, LiSH, PEX4 and TR) for the Zamia pumila complex and 4 loci (COS26, GroES, GTP and HTS) for all other cycad genera. </AbstractText><CopyrightInformation>Published 2014. This article is a U.S. Government work and is in the public domain in the U.S.A.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Salas-Leiva</LastName><ForeName>Dayana E</ForeName><Initials>DE</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA; USDA-ARS-SHRS, National Germplasm Repository, Miami, FL, 33158, USA; Montgomery Botanical Center, Miami, FL, 33156, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Meerow</LastName><ForeName>Alan W</ForeName><Initials>AW</Initials></Author><Author ValidYN="Y"><LastName>Francisco-Ortega</LastName><ForeName>Javier</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Calonje</LastName><ForeName>Michael</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Griffith</LastName><ForeName>M Patrick</ForeName><Initials>MP</Initials></Author><Author ValidYN="Y"><LastName>Stevenson</LastName><ForeName>Dennis W</ForeName><Initials>DW</Initials></Author><Author ValidYN="Y"><LastName>Nakamura</LastName><ForeName>Kyoko</ForeName><Initials>K</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>03</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Ecol Resour</MedlineTA><NlmUniqueID>101465604</NlmUniqueID><ISSNLinking>1755-098X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017691" MajorTopicYN="N">Caribbean Region</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032462" MajorTopicYN="N">Cycadopsida</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="Y">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058974" 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PubStatus="pubmed"><Year>2014</Year><Month>1</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>1</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24444413</ArticleId><ArticleId IdType="doi">10.1111/1755-0998.12228</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Calonje, Michael" sort="Calonje, Michael" uniqKey="Calonje M" first="Michael" last="Calonje">Michael Calonje</name><name sortKey="Francisco Ortega, Javier" sort="Francisco Ortega, Javier" uniqKey="Francisco Ortega J" first="Javier" last="Francisco-Ortega">Javier Francisco-Ortega</name><name sortKey="Griffith, M Patrick" sort="Griffith, M Patrick" uniqKey="Griffith M" first="M Patrick" last="Griffith">M Patrick Griffith</name><name sortKey="Meerow, Alan W" sort="Meerow, Alan W" uniqKey="Meerow A" first="Alan W" last="Meerow">Alan W. Meerow</name><name sortKey="Nakamura, Kyoko" sort="Nakamura, Kyoko" uniqKey="Nakamura K" first="Kyoko" last="Nakamura">Kyoko Nakamura</name><name sortKey="Stevenson, Dennis W" sort="Stevenson, Dennis W" uniqKey="Stevenson D" first="Dennis W" last="Stevenson">Dennis W. Stevenson</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Salas Leiva, Dayana E" sort="Salas Leiva, Dayana E" uniqKey="Salas Leiva D" first="Dayana E" last="Salas-Leiva">Dayana E. Salas-Leiva</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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