Transcriptome differences between two sister desert poplar species under salt stress.
Identifieur interne : 001F92 ( Main/Exploration ); précédent : 001F91; suivant : 001F93Transcriptome differences between two sister desert poplar species under salt stress.
Auteurs : Jian Zhang ; Jianju Feng ; Jing Lu ; Yongzhi Yang ; Xu Zhang ; Dongshi Wan ; Jianquan Liu [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2014.
Descripteurs français
- KwdFr :
- ARN messager (génétique), Allèles (MeSH), Chlorure de sodium (MeSH), Gènes de plante (MeSH), Populus (génétique), Populus (physiologie), Réaction de polymérisation en chaîne (MeSH), Régulation positive (MeSH), Spécificité d'espèce (MeSH), Stress physiologique (MeSH), Transcriptome (MeSH), Épissage alternatif (MeSH).
- MESH :
- génétique : ARN messager, Populus.
- physiologie : Populus.
- Allèles, Chlorure de sodium, Gènes de plante, Réaction de polymérisation en chaîne, Régulation positive, Spécificité d'espèce, Stress physiologique, Transcriptome, Épissage alternatif.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Messenger.
- genetics : Populus.
- physiology : Populus.
- Alleles, Alternative Splicing, Genes, Plant, Polymerase Chain Reaction, Sodium Chloride, Species Specificity, Stress, Physiological, Transcriptome, Up-Regulation.
Abstract
BACKGROUND
Populus euphratica Oliv and P. pruinosa Schrenk (Salicaceae) both grow in dry desert areas with high summer temperatures. However, P. euphratica is distributed in dry deserts with deep underground water whereas P. pruinosa occurs in deserts in which there is underground water close to the surface. We therefore hypothesized that these two sister species may have evolved divergent regulatory and metabolic pathways during their interaction with different salt habitats and other stresses. To test this hypothesis, we compared transcriptomes from callus exposed to 24 h of salt stress and control callus samples from both species and identified differentially expressed genes (DEGs) and alternative splicing (AS) events that had occurred under salt stress.
RESULTS
A total of 36,144 transcripts were identified and 1430 genes were found to be differentially expressed in at least one species in response to salt stress. Of these DEGs, 884 and 860 were identified in P. euphratica and P. pruinosa, respectively, while 314 DEGs were common to both species. On the basis of parametric analysis of gene set enrichment, GO enrichment in P. euphratica was found to be significantly different from that in P. pruinosa. Numerous genes involved in hormone biosynthesis, transporters and transcription factors showed clear differences between the two species in response to salt stress. We also identified 26,560 AS events which were mapped to 8380 poplar genomic loci from four libraries. GO enrichments for genes undergoing AS events in P. euphratica differed significantly from those in P. pruinosa.
CONCLUSIONS
A number of salt-responsive genes in both P. euphratica and P. pruinosa were identified and candidate genes with potential roles in the salinity adaptation were proposed. Transcriptome comparisons of two sister desert poplar species under salt stress suggest that these two species may have developed different genetic pathways in order to adapt to different desert salt habitats. The DEGs that were found to be common to both species under salt stress may be especially important for future genetic improvement of cultivated poplars or other crops through transgenic approaches in order to increase tolerance of saline soil conditions.
DOI: 10.1186/1471-2164-15-337
PubMed: 24886148
PubMed Central: PMC4035067
Affiliations:
Links toward previous steps (curation, corpus...)
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last="Liu">Jianquan Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China. liujq@nwipb.ac.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu</wicri:regionArea><wicri:noRegion>Gansu</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24886148</idno><idno type="pmid">24886148</idno><idno type="doi">10.1186/1471-2164-15-337</idno><idno type="pmc">PMC4035067</idno><idno type="wicri:Area/Main/Corpus">002164</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002164</idno><idno type="wicri:Area/Main/Curation">002164</idno><idno 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last="Wan">Dongshi Wan</name></author><author><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" last="Liu">Jianquan Liu</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, China. liujq@nwipb.ac.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Grassland and Agro-Ecosystems, School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu</wicri:regionArea><wicri:noRegion>Gansu</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term><term>Alternative Splicing (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Polymerase Chain Reaction (MeSH)</term><term>Populus (genetics)</term><term>Populus (physiology)</term><term>RNA, Messenger (genetics)</term><term>Sodium Chloride (MeSH)</term><term>Species Specificity (MeSH)</term><term>Stress, Physiological (MeSH)</term><term>Transcriptome (MeSH)</term><term>Up-Regulation (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term><term>Allèles (MeSH)</term><term>Chlorure de sodium (MeSH)</term><term>Gènes de plante (MeSH)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Réaction de polymérisation en chaîne (MeSH)</term><term>Régulation positive (MeSH)</term><term>Spécificité d'espèce (MeSH)</term><term>Stress physiologique (MeSH)</term><term>Transcriptome (MeSH)</term><term>Épissage alternatif (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Alternative Splicing</term><term>Genes, Plant</term><term>Polymerase Chain Reaction</term><term>Sodium Chloride</term><term>Species Specificity</term><term>Stress, Physiological</term><term>Transcriptome</term><term>Up-Regulation</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Chlorure de sodium</term><term>Gènes de plante</term><term>Réaction de polymérisation en chaîne</term><term>Régulation positive</term><term>Spécificité d'espèce</term><term>Stress physiologique</term><term>Transcriptome</term><term>Épissage alternatif</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Populus euphratica Oliv and P. pruinosa Schrenk (Salicaceae) both grow in dry desert areas with high summer temperatures. However, P. euphratica is distributed in dry deserts with deep underground water whereas P. pruinosa occurs in deserts in which there is underground water close to the surface. We therefore hypothesized that these two sister species may have evolved divergent regulatory and metabolic pathways during their interaction with different salt habitats and other stresses. To test this hypothesis, we compared transcriptomes from callus exposed to 24 h of salt stress and control callus samples from both species and identified differentially expressed genes (DEGs) and alternative splicing (AS) events that had occurred under salt stress.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>A total of 36,144 transcripts were identified and 1430 genes were found to be differentially expressed in at least one species in response to salt stress. Of these DEGs, 884 and 860 were identified in P. euphratica and P. pruinosa, respectively, while 314 DEGs were common to both species. On the basis of parametric analysis of gene set enrichment, GO enrichment in P. euphratica was found to be significantly different from that in P. pruinosa. Numerous genes involved in hormone biosynthesis, transporters and transcription factors showed clear differences between the two species in response to salt stress. We also identified 26,560 AS events which were mapped to 8380 poplar genomic loci from four libraries. GO enrichments for genes undergoing AS events in P. euphratica differed significantly from those in P. pruinosa.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>A number of salt-responsive genes in both P. euphratica and P. pruinosa were identified and candidate genes with potential roles in the salinity adaptation were proposed. Transcriptome comparisons of two sister desert poplar species under salt stress suggest that these two species may have developed different genetic pathways in order to adapt to different desert salt habitats. The DEGs that were found to be common to both species under salt stress may be especially important for future genetic improvement of cultivated poplars or other crops through transgenic approaches in order to increase tolerance of saline soil conditions.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24886148</PMID><DateCompleted><Year>2015</Year><Month>02</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>15</Volume><PubDate><Year>2014</Year><Month>May</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Transcriptome differences between two sister desert poplar species under salt stress.</ArticleTitle><Pagination><MedlinePgn>337</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-15-337</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Populus euphratica Oliv and P. pruinosa Schrenk (Salicaceae) both grow in dry desert areas with high summer temperatures. However, P. euphratica is distributed in dry deserts with deep underground water whereas P. pruinosa occurs in deserts in which there is underground water close to the surface. We therefore hypothesized that these two sister species may have evolved divergent regulatory and metabolic pathways during their interaction with different salt habitats and other stresses. To test this hypothesis, we compared transcriptomes from callus exposed to 24 h of salt stress and control callus samples from both species and identified differentially expressed genes (DEGs) and alternative splicing (AS) events that had occurred under salt stress.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">A total of 36,144 transcripts were identified and 1430 genes were found to be differentially expressed in at least one species in response to salt stress. Of these DEGs, 884 and 860 were identified in P. euphratica and P. pruinosa, respectively, while 314 DEGs were common to both species. On the basis of parametric analysis of gene set enrichment, GO enrichment in P. euphratica was found to be significantly different from that in P. pruinosa. Numerous genes involved in hormone biosynthesis, transporters and transcription factors showed clear differences between the two species in response to salt stress. We also identified 26,560 AS events which were mapped to 8380 poplar genomic loci from four libraries. GO enrichments for genes undergoing AS events in P. euphratica differed significantly from those in P. pruinosa.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">A number of salt-responsive genes in both P. euphratica and P. pruinosa were identified and candidate genes with potential roles in the salinity adaptation were proposed. Transcriptome comparisons of two sister desert poplar species under salt stress suggest that these two species may have developed different genetic pathways in order to adapt to different desert salt habitats. The DEGs that were found to be common to both species under salt stress may be especially important for future genetic improvement of cultivated poplars or other crops through transgenic approaches in order to increase tolerance of saline soil conditions.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jian</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Feng</LastName><ForeName>Jianju</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Lu</LastName><ForeName>Jing</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Yongzhi</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Xu</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Wan</LastName><ForeName>Dongshi</ForeName><Initials>D</Initials></Author><Author 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IdType="pubmed">23776666</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><noCountry><name sortKey="Feng, Jianju" sort="Feng, Jianju" uniqKey="Feng J" first="Jianju" last="Feng">Jianju Feng</name><name sortKey="Lu, Jing" sort="Lu, Jing" uniqKey="Lu J" first="Jing" last="Lu">Jing Lu</name><name sortKey="Wan, Dongshi" sort="Wan, Dongshi" uniqKey="Wan D" first="Dongshi" last="Wan">Dongshi Wan</name><name sortKey="Yang, Yongzhi" sort="Yang, Yongzhi" uniqKey="Yang Y" first="Yongzhi" last="Yang">Yongzhi Yang</name><name sortKey="Zhang, Jian" sort="Zhang, Jian" uniqKey="Zhang J" first="Jian" last="Zhang">Jian Zhang</name><name sortKey="Zhang, Xu" sort="Zhang, Xu" uniqKey="Zhang X" first="Xu" last="Zhang">Xu Zhang</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Liu, Jianquan" sort="Liu, Jianquan" uniqKey="Liu J" first="Jianquan" 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