NJ cluster analysis of the SnRK2, PYR/PYL/RCAR, and ABF genes in Tibetan hulless barley.
Identifieur interne : 001758 ( Main/Exploration ); précédent : 001757; suivant : 001759NJ cluster analysis of the SnRK2, PYR/PYL/RCAR, and ABF genes in Tibetan hulless barley.
Auteurs : H J Yuan [République populaire de Chine] ; Y L Wang [République populaire de Chine] ; Z X Wei [République populaire de Chine] ; Q J Xu [République populaire de Chine] ; X Q Zeng [République populaire de Chine] ; Y W Tang [République populaire de Chine] ; T S Nyima [Oman]Source :
- Genetics and molecular research : GMR [ 1676-5680 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Hordeum, Protéines végétales.
- métabolisme : Protéines végétales.
- Analyse de regroupements, Gènes de plante, Phylogenèse.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Hordeum.
- chemical , metabolism : Plant Proteins.
- Cluster Analysis, Genes, Plant, Phylogeny.
Abstract
The abscisic acid (ABA) signaling pathway is known as one of the most important signaling pathways in plants and is mediated by multiple regulators. The genes SnRK2, PYR/PYL/RCAR, and ABF are relevant to both ABA-dependent and -independent signaling pathways. To elucidate the profile of these genes from Tibetan hulless barley (Hordeum vulgare L. var. nudum Hook. f.), we collected available sequences from RNA-Seq data, together with NCBI data from five other model plant species (Arabidopsis thaliana, Brachypodium distachyon, Oryza sativa, Populus trichocarpa, and Sorghum bicolor). Gene trees of SnRK2, PYR/PYL/RCAR, and ABF were constructed using a neighbor joining (NJ) method. For all genes, we identified a dominant group in which all six species were represented. Three, four, and five groups were found in the NJ trees of SnRK2, PYR/PYL/RCAR, and ABF, respectively. For each gene, Tibetan hulless barley was divided into three groups. Our analyses indicated that Tibetan hulless barley was associated with B. distachyon. The NJ cluster analysis also suggested that Tibetan hulless barley was affiliated with S. bicolor (SnRK2), A. thaliana (PYR/PYL/RCAR), and O. sativa (ABF). These results illustrate a diverse expression of genes SnRK2, PYR/PYL/RCAR, and ABF, and suggest a relationship among the six species studied. Collectively, our characterization of the three components of the ABA signaling pathway may contribute to improve stress tolerance in Tibetan hulless barley.
DOI: 10.4238/gmr15048840
PubMed: 27819745
Affiliations:
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Chine</country><wicri:regionArea>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Y L" sort="Wang, Y L" uniqKey="Wang Y" first="Y L" last="Wang">Y L Wang</name><affiliation wicri:level="1"><nlm:affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Tibet Academy of Agricultural and Animal Husbandry Sciences, 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Q" first="Q J" last="Xu">Q J Xu</name><affiliation wicri:level="1"><nlm:affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation></author><author><name sortKey="Zeng, X Q" sort="Zeng, X Q" uniqKey="Zeng X" first="X Q" last="Zeng">X Q Zeng</name><affiliation wicri:level="1"><nlm:affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation></author><author><name sortKey="Tang, Y W" sort="Tang, Y W" uniqKey="Tang Y" first="Y W" last="Tang">Y W Tang</name><affiliation wicri:level="1"><nlm:affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation></author><author><name sortKey="Nyima, T S" sort="Nyima, T S" uniqKey="Nyima T" first="T S" last="Nyima">T S Nyima</name><affiliation wicri:level="1"><nlm:affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China nima_zhaxi@sina.com.</nlm:affiliation><country wicri:rule="url">Oman</country><wicri:regionArea>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China nima_zhaxi@sina.com.</nlm:affiliation><country wicri:rule="url">Oman</country><wicri:regionArea>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa</wicri:regionArea><wicri:noRegion>Lhasa</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genetics and molecular research : GMR</title><idno type="eISSN">1676-5680</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cluster Analysis (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Hordeum (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Hordeum (génétique)</term><term>Phylogenèse (MeSH)</term><term>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Hordeum</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Hordeum</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Cluster Analysis</term><term>Genes, Plant</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term><term>Gènes de plante</term><term>Phylogenèse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The abscisic acid (ABA) signaling pathway is known as one of the most important signaling pathways in plants and is mediated by multiple regulators. The genes SnRK2, PYR/PYL/RCAR, and ABF are relevant to both ABA-dependent and -independent signaling pathways. To elucidate the profile of these genes from Tibetan hulless barley (Hordeum vulgare L. var. nudum Hook. f.), we collected available sequences from RNA-Seq data, together with NCBI data from five other model plant species (Arabidopsis thaliana, Brachypodium distachyon, Oryza sativa, Populus trichocarpa, and Sorghum bicolor). Gene trees of SnRK2, PYR/PYL/RCAR, and ABF were constructed using a neighbor joining (NJ) method. For all genes, we identified a dominant group in which all six species were represented. Three, four, and five groups were found in the NJ trees of SnRK2, PYR/PYL/RCAR, and ABF, respectively. For each gene, Tibetan hulless barley was divided into three groups. Our analyses indicated that Tibetan hulless barley was associated with B. distachyon. The NJ cluster analysis also suggested that Tibetan hulless barley was affiliated with S. bicolor (SnRK2), A. thaliana (PYR/PYL/RCAR), and O. sativa (ABF). These results illustrate a diverse expression of genes SnRK2, PYR/PYL/RCAR, and ABF, and suggest a relationship among the six species studied. Collectively, our characterization of the three components of the ABA signaling pathway may contribute to improve stress tolerance in Tibetan hulless barley.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27819745</PMID><DateCompleted><Year>2017</Year><Month>02</Month><Day>28</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>28</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1676-5680</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><Issue>4</Issue><PubDate><Year>2016</Year><Month>Nov</Month><Day>03</Day></PubDate></JournalIssue><Title>Genetics and molecular research : GMR</Title><ISOAbbreviation>Genet Mol Res</ISOAbbreviation></Journal><ArticleTitle>NJ cluster analysis of the SnRK2, PYR/PYL/RCAR, and ABF genes in Tibetan hulless barley.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.4238/gmr15048840</ELocationID><Abstract><AbstractText>The abscisic acid (ABA) signaling pathway is known as one of the most important signaling pathways in plants and is mediated by multiple regulators. The genes SnRK2, PYR/PYL/RCAR, and ABF are relevant to both ABA-dependent and -independent signaling pathways. To elucidate the profile of these genes from Tibetan hulless barley (Hordeum vulgare L. var. nudum Hook. f.), we collected available sequences from RNA-Seq data, together with NCBI data from five other model plant species (Arabidopsis thaliana, Brachypodium distachyon, Oryza sativa, Populus trichocarpa, and Sorghum bicolor). Gene trees of SnRK2, PYR/PYL/RCAR, and ABF were constructed using a neighbor joining (NJ) method. For all genes, we identified a dominant group in which all six species were represented. Three, four, and five groups were found in the NJ trees of SnRK2, PYR/PYL/RCAR, and ABF, respectively. For each gene, Tibetan hulless barley was divided into three groups. Our analyses indicated that Tibetan hulless barley was associated with B. distachyon. The NJ cluster analysis also suggested that Tibetan hulless barley was affiliated with S. bicolor (SnRK2), A. thaliana (PYR/PYL/RCAR), and O. sativa (ABF). These results illustrate a diverse expression of genes SnRK2, PYR/PYL/RCAR, and ABF, and suggest a relationship among the six species studied. Collectively, our characterization of the three components of the ABA signaling pathway may contribute to improve stress tolerance in Tibetan hulless barley.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yuan</LastName><ForeName>H J</ForeName><Initials>HJ</Initials><AffiliationInfo><Affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Y L</ForeName><Initials>YL</Initials><AffiliationInfo><Affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Z X</ForeName><Initials>ZX</Initials><AffiliationInfo><Affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Q J</ForeName><Initials>QJ</Initials><AffiliationInfo><Affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zeng</LastName><ForeName>X Q</ForeName><Initials>XQ</Initials><AffiliationInfo><Affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Y W</ForeName><Initials>YW</Initials><AffiliationInfo><Affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nyima</LastName><ForeName>T S</ForeName><Initials>TS</Initials><AffiliationInfo><Affiliation>Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China nima_zhaxi@sina.com.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Barley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa, China nima_zhaxi@sina.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>11</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>Brazil</Country><MedlineTA>Genet Mol Res</MedlineTA><NlmUniqueID>101169387</NlmUniqueID><ISSNLinking>1676-5680</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001467" MajorTopicYN="N">Hordeum</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" 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IdType="doi">10.4238/gmr15048840</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Oman</li><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Yuan, H J" sort="Yuan, H J" uniqKey="Yuan H" first="H J" last="Yuan">H J Yuan</name></noRegion><name sortKey="Tang, Y W" sort="Tang, Y W" uniqKey="Tang Y" first="Y W" last="Tang">Y W Tang</name><name sortKey="Tang, Y W" sort="Tang, Y W" uniqKey="Tang Y" first="Y W" last="Tang">Y W Tang</name><name sortKey="Wang, Y L" sort="Wang, Y L" uniqKey="Wang Y" first="Y L" last="Wang">Y L Wang</name><name sortKey="Wang, Y L" sort="Wang, Y L" uniqKey="Wang Y" first="Y L" last="Wang">Y L Wang</name><name sortKey="Wei, Z X" sort="Wei, Z X" uniqKey="Wei Z" first="Z X" last="Wei">Z X Wei</name><name sortKey="Xu, Q J" sort="Xu, Q J" uniqKey="Xu Q" first="Q J" last="Xu">Q J Xu</name><name sortKey="Xu, Q J" sort="Xu, Q J" uniqKey="Xu Q" first="Q J" last="Xu">Q J Xu</name><name sortKey="Yuan, H J" sort="Yuan, H J" uniqKey="Yuan H" first="H J" last="Yuan">H J Yuan</name><name sortKey="Zeng, X Q" sort="Zeng, X Q" uniqKey="Zeng X" first="X Q" last="Zeng">X Q Zeng</name><name sortKey="Zeng, X Q" sort="Zeng, X Q" uniqKey="Zeng X" first="X Q" last="Zeng">X Q Zeng</name></country><country name="Oman"><noRegion><name sortKey="Nyima, T S" sort="Nyima, T S" uniqKey="Nyima T" first="T S" last="Nyima">T S Nyima</name></noRegion><name sortKey="Nyima, T S" sort="Nyima, T S" uniqKey="Nyima T" first="T S" last="Nyima">T S Nyima</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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