Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars.
Identifieur interne : 000936 ( Main/Exploration ); précédent : 000935; suivant : 000937Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars.
Auteurs : Jianchao Ma [République populaire de Chine] ; Xiaotao Bai [République populaire de Chine] ; Wenchun Luo [République populaire de Chine] ; Yannan Feng [République populaire de Chine] ; Xuemin Shao [République populaire de Chine] ; Qiuxian Bai [République populaire de Chine] ; Shujiao Sun [République populaire de Chine] ; Qiming Long [République populaire de Chine] ; Dongshi Wan [République populaire de Chine]Source :
- Frontiers in genetics [ 1664-8021 ] ; 2019.
Abstract
Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (Populus euphratica and Populus alba var. pyramidalis), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in P. euphratica but not in P. alba var. pyramidalis and 3,425 lncRNAs were identified to be species-specific in P. euphratica in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included Aux/IAA, NAC, MYB, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.
DOI: 10.3389/fgene.2019.00777
PubMed: 31543901
PubMed Central: PMC6739720
Affiliations:
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Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng</wicri:regionArea><wicri:noRegion>Kaifeng</wicri:noRegion></affiliation></author><author><name sortKey="Bai, Xiaotao" sort="Bai, Xiaotao" uniqKey="Bai X" first="Xiaotao" last="Bai">Xiaotao Bai</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Luo, Wenchun" sort="Luo, Wenchun" uniqKey="Luo W" first="Wenchun" last="Luo">Wenchun Luo</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Feng, Yannan" sort="Feng, Yannan" uniqKey="Feng Y" first="Yannan" last="Feng">Yannan Feng</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Shao, Xuemin" sort="Shao, Xuemin" uniqKey="Shao X" first="Xuemin" last="Shao">Xuemin Shao</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Bai, Qiuxian" sort="Bai, Qiuxian" uniqKey="Bai Q" first="Qiuxian" last="Bai">Qiuxian Bai</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Sun, Shujiao" sort="Sun, Shujiao" uniqKey="Sun S" first="Shujiao" last="Sun">Shujiao Sun</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Long, Qiming" sort="Long, Qiming" uniqKey="Long Q" first="Qiming" last="Long">Qiming Long</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author><author><name sortKey="Wan, Dongshi" sort="Wan, Dongshi" uniqKey="Wan D" first="Dongshi" last="Wan">Dongshi Wan</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou</wicri:regionArea><wicri:noRegion>Lanzhou</wicri:noRegion></affiliation></author></analytic><series><title level="j">Frontiers in genetics</title><idno type="ISSN">1664-8021</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (<i>Populus euphratica</i> and <i>Populus alba</i> var. <i>pyramidalis</i>), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in <i>P. euphratica</i> but not in <i>P. alba</i> var. <i>pyramidalis</i> and 3,425 lncRNAs were identified to be species-specific in <i>P. euphratica</i> in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included <i>Aux/IAA</i>, <i>NAC</i>, <i>MYB</i>, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">31543901</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-8021</ISSN><JournalIssue CitedMedium="Print"><Volume>10</Volume><PubDate><Year>2019</Year></PubDate></JournalIssue><Title>Frontiers in genetics</Title><ISOAbbreviation>Front Genet</ISOAbbreviation></Journal><ArticleTitle>Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars.</ArticleTitle><Pagination><MedlinePgn>777</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fgene.2019.00777</ELocationID><Abstract><AbstractText>Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (<i>Populus euphratica</i> and <i>Populus alba</i> var. <i>pyramidalis</i>), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in <i>P. euphratica</i> but not in <i>P. alba</i> var. <i>pyramidalis</i> and 3,425 lncRNAs were identified to be species-specific in <i>P. euphratica</i> in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included <i>Aux/IAA</i>, <i>NAC</i>, <i>MYB</i>, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Jianchao</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bai</LastName><ForeName>Xiaotao</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Wenchun</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Yannan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shao</LastName><ForeName>Xuemin</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bai</LastName><ForeName>Qiuxian</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Shujiao</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Long</LastName><ForeName>Qiming</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wan</LastName><ForeName>Dongshi</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>09</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Genet</MedlineTA><NlmUniqueID>101560621</NlmUniqueID><ISSNLinking>1664-8021</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">long noncoding RNAs</Keyword><Keyword MajorTopicYN="N">plant growth</Keyword><Keyword MajorTopicYN="N">poplars</Keyword><Keyword MajorTopicYN="N">salt response</Keyword><Keyword MajorTopicYN="N">tissue-specific expression</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>11</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>07</Month><Day>23</Day></PubMedPubDate><PubMedPubDate 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IdType="pubmed">30044051</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Ma, Jianchao" sort="Ma, Jianchao" uniqKey="Ma J" first="Jianchao" last="Ma">Jianchao Ma</name></noRegion><name sortKey="Bai, Qiuxian" sort="Bai, Qiuxian" uniqKey="Bai Q" first="Qiuxian" last="Bai">Qiuxian Bai</name><name sortKey="Bai, Xiaotao" sort="Bai, Xiaotao" uniqKey="Bai X" first="Xiaotao" last="Bai">Xiaotao Bai</name><name sortKey="Feng, Yannan" sort="Feng, Yannan" uniqKey="Feng Y" first="Yannan" last="Feng">Yannan Feng</name><name sortKey="Long, Qiming" sort="Long, Qiming" uniqKey="Long Q" first="Qiming" last="Long">Qiming Long</name><name sortKey="Luo, Wenchun" sort="Luo, Wenchun" uniqKey="Luo W" first="Wenchun" last="Luo">Wenchun Luo</name><name sortKey="Ma, Jianchao" sort="Ma, Jianchao" uniqKey="Ma J" first="Jianchao" last="Ma">Jianchao Ma</name><name sortKey="Shao, Xuemin" sort="Shao, Xuemin" uniqKey="Shao X" first="Xuemin" last="Shao">Xuemin Shao</name><name sortKey="Sun, Shujiao" sort="Sun, Shujiao" uniqKey="Sun S" first="Shujiao" last="Sun">Shujiao Sun</name><name sortKey="Wan, Dongshi" sort="Wan, Dongshi" uniqKey="Wan D" first="Dongshi" last="Wan">Dongshi Wan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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