Genome-scale transcriptome analysis of the desert poplar, Populus euphratica.
Identifieur interne : 002E64 ( Main/Exploration ); précédent : 002E63; suivant : 002E65Genome-scale transcriptome analysis of the desert poplar, Populus euphratica.
Auteurs : Qiang Qiu [République populaire de Chine] ; Tao Ma ; Quanjun Hu ; Bingbing Liu ; Yuxia Wu ; Haihong Zhou ; Qian Wang ; Juan Wang ; Jianquan LiuSource :
- Tree physiology [ 1758-4469 ] ; 2011.
Descripteurs français
- KwdFr :
- ARN des plantes (génétique), ARN messager (génétique), Annotation de séquence moléculaire (MeSH), Banque de gènes (MeSH), Chine (MeSH), Climat désertique (MeSH), Gènes de plante (génétique), Génome végétal (génétique), Modèles génétiques (MeSH), Populus (génétique), Populus (physiologie), Régulation de l'expression des gènes végétaux (MeSH), Régulation négative (MeSH), Régulation positive (MeSH), Spécificité d'espèce (MeSH), Stress physiologique (physiologie), Séquençage nucléotidique à haut débit (MeSH), Séquençage par oligonucléotides en batterie (MeSH), Transcriptome (MeSH), Étiquettes de séquences exprimées (MeSH).
- MESH :
- génétique : ARN des plantes, ARN messager, Gènes de plante, Génome végétal, Populus.
- physiologie : Populus, Stress physiologique.
- Annotation de séquence moléculaire, Banque de gènes, Chine, Climat désertique, Modèles génétiques, Régulation de l'expression des gènes végétaux, Régulation négative, Régulation positive, Spécificité d'espèce, Séquençage nucléotidique à haut débit, Séquençage par oligonucléotides en batterie, Transcriptome, Étiquettes de séquences exprimées.
- Wicri :
- geographic : République populaire de Chine.
English descriptors
- KwdEn :
- China (MeSH), Desert Climate (MeSH), Down-Regulation (MeSH), Expressed Sequence Tags (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Library (MeSH), Genes, Plant (genetics), Genome, Plant (genetics), High-Throughput Nucleotide Sequencing (MeSH), Models, Genetic (MeSH), Molecular Sequence Annotation (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Populus (genetics), Populus (physiology), RNA, Messenger (genetics), RNA, Plant (genetics), Species Specificity (MeSH), Stress, Physiological (physiology), Transcriptome (MeSH), Up-Regulation (MeSH).
- MESH :
- chemical , genetics : RNA, Messenger, RNA, Plant.
- geographic : China.
- genetics : Genes, Plant, Genome, Plant, Populus.
- physiology : Populus, Stress, Physiological.
- Desert Climate, Down-Regulation, Expressed Sequence Tags, Gene Expression Regulation, Plant, Gene Library, High-Throughput Nucleotide Sequencing, Models, Genetic, Molecular Sequence Annotation, Oligonucleotide Array Sequence Analysis, Species Specificity, Transcriptome, Up-Regulation.
Abstract
Populus euphratica is well-adapted to extreme desert environments and is an important model species for studying the effects of abiotic stresses on trees. Here we present the first deep transcriptomic analysis of this species. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of desert-grown trees and two types of callus (salt-stressed and unstressed). De novo assembly generated 86,777 Unigenes using Solexa sequence data. These sequences covered 92% of previously reported P. euphratica expressed sequence tags (ESTs) and 90% of the TIGR poplar ESTs, and a total of 58,499 high-quality unique sequences were annotated by BLAST similarity searches against public databases. We found that 27% of the total Unigenes were differentially expressed (up- or down-regulated) in response to salt stress in P. euphratica callus. These differentially expressed genes are mainly involved in transport, transcription, cellular communication and metabolism. In addition, we found that numerous putative genes involved in ABA regulation and biosynthesis were also differentially regulated. This study represents the deepest transcriptomic and gene-annotation analysis of P. euphratica to date. The genetic knowledge acquired should be very useful for future studies of the molecular adaptation of this tree species to abiotic stress and facilitate genetic manipulation of other poplar species.
DOI: 10.1093/treephys/tpr015
PubMed: 21427158
Affiliations:
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well-adapted to extreme desert environments and is an important model species for studying the effects of abiotic stresses on trees. Here we present the first deep transcriptomic analysis of this species. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of desert-grown trees and two types of callus (salt-stressed and unstressed). De novo assembly generated 86,777 Unigenes using Solexa sequence data. These sequences covered 92% of previously reported P. euphratica expressed sequence tags (ESTs) and 90% of the TIGR poplar ESTs, and a total of 58,499 high-quality unique sequences were annotated by BLAST similarity searches against public databases. We found that 27% of the total Unigenes were differentially expressed (up- or down-regulated) in response to salt stress in P. euphratica callus. These differentially expressed genes are mainly involved in transport, transcription, cellular communication and metabolism. In addition, we found that numerous putative genes involved in ABA regulation and biosynthesis were also differentially regulated. This study represents the deepest transcriptomic and gene-annotation analysis of P. euphratica to date. The genetic knowledge acquired should be very useful for future studies of the molecular adaptation of this tree species to abiotic stress and facilitate genetic manipulation of other poplar species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21427158</PMID><DateCompleted><Year>2012</Year><Month>06</Month><Day>28</Day></DateCompleted><DateRevised><Year>2011</Year><Month>05</Month><Day>09</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1758-4469</ISSN><JournalIssue CitedMedium="Internet"><Volume>31</Volume><Issue>4</Issue><PubDate><Year>2011</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Tree physiology</Title><ISOAbbreviation>Tree Physiol</ISOAbbreviation></Journal><ArticleTitle>Genome-scale transcriptome analysis of the desert poplar, Populus euphratica.</ArticleTitle><Pagination><MedlinePgn>452-61</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/treephys/tpr015</ELocationID><Abstract><AbstractText>Populus euphratica is well-adapted to extreme desert environments and is an important model species for studying the effects of abiotic stresses on trees. Here we present the first deep transcriptomic analysis of this species. To maximize representation of conditional transcripts, mRNA was obtained from living tissues of desert-grown trees and two types of callus (salt-stressed and unstressed). De novo assembly generated 86,777 Unigenes using Solexa sequence data. These sequences covered 92% of previously reported P. euphratica expressed sequence tags (ESTs) and 90% of the TIGR poplar ESTs, and a total of 58,499 high-quality unique sequences were annotated by BLAST similarity searches against public databases. We found that 27% of the total Unigenes were differentially expressed (up- or down-regulated) in response to salt stress in P. euphratica callus. These differentially expressed genes are mainly involved in transport, transcription, cellular communication and metabolism. In addition, we found that numerous putative genes involved in ABA regulation and biosynthesis were also differentially regulated. This study represents the deepest transcriptomic and gene-annotation analysis of P. euphratica to date. The genetic knowledge acquired should be very useful for future studies of the molecular adaptation of this tree species to abiotic stress and facilitate genetic manipulation of other poplar species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Qiu</LastName><ForeName>Qiang</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, Lanzhou University, Lanzhou 730000, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Tao</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Quanjun</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Bingbing</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Yuxia</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Haihong</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Qian</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Juan</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jianquan</ForeName><Initials>J</Initials></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>2011</Year><Month>03</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>Canada</Country><MedlineTA>Tree Physiol</MedlineTA><NlmUniqueID>100955338</NlmUniqueID><ISSNLinking>0829-318X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002681" MajorTopicYN="N" Type="Geographic">China</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003889" MajorTopicYN="N">Desert Climate</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015536" MajorTopicYN="N">Down-Regulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013312" MajorTopicYN="N">Stress, Physiological</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015854" MajorTopicYN="N">Up-Regulation</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>3</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>3</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2012</Year><Month>6</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">21427158</ArticleId><ArticleId IdType="pii">tpr015</ArticleId><ArticleId IdType="doi">10.1093/treephys/tpr015</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Hu, Quanjun" sort="Hu, Quanjun" uniqKey="Hu Q" first="Quanjun" last="Hu">Quanjun Hu</name><name sortKey="Liu, Bingbing" sort="Liu, Bingbing" uniqKey="Liu B" first="Bingbing" last="Liu">Bingbing Liu</name><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><name sortKey="Ma, Tao" sort="Ma, Tao" uniqKey="Ma T" first="Tao" last="Ma">Tao Ma</name><name sortKey="Wang, Juan" sort="Wang, Juan" uniqKey="Wang J" first="Juan" last="Wang">Juan Wang</name><name sortKey="Wang, Qian" sort="Wang, Qian" uniqKey="Wang Q" first="Qian" last="Wang">Qian Wang</name><name sortKey="Wu, Yuxia" sort="Wu, Yuxia" uniqKey="Wu Y" first="Yuxia" last="Wu">Yuxia Wu</name><name sortKey="Zhou, Haihong" sort="Zhou, Haihong" uniqKey="Zhou H" first="Haihong" last="Zhou">Haihong Zhou</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Qiu, Qiang" sort="Qiu, Qiang" uniqKey="Qiu Q" first="Qiang" last="Qiu">Qiang Qiu</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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