Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica.
Identifieur interne : 002300 ( Main/Exploration ); précédent : 002299; suivant : 002301Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica.
Auteurs : Jinhuan Chen ; Qianqian Tian ; Tao Pang ; Libo Jiang ; Rongling Wu ; Xinli Xia [République populaire de Chine] ; Weilun YinSource :
- BMC genomics [ 1471-2164 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Populus.
- métabolisme : Facteurs de transcription.
- physiologie : Populus.
- Basse température, Données de séquences moléculaires, Gènes de plante, Séquençage nucléotidique à haut débit, Transcriptome.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Transcription Factors.
- genetics : Populus.
- physiology : Populus.
- Cold Temperature, Genes, Plant, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Transcriptome.
Abstract
BACKGROUND
Compared with other Populus species, Populus euphratica Oliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signaling pathways involved in low temperature stress responses in this species. Recent development of Illumina/Solexa-based deep-sequencing technologies has accelerated the study of global transcription profiling under specific conditions. To understand the gene network controlling low temperature perception in P. euphratica, we performed transcriptome sequencing using Solexa sequence analysis to generate a leaf transcriptome at a depth of 10 gigabases for each sample.
RESULTS
Using the Trinity method, 52,081,238 high-quality trimmed reads were assembled into a non-redundant set and 108,502 unigenes with an average length of 1,047 bp were generated. After performing functional annotations by aligning all-unigenes with public protein databases, 85,584 unigenes were annotated. Differentially expressed genes were investigated using the FPKM method by applying the Benjamini and Hochberg corrections. Overall, 2,858 transcripts were identified as differentially expressed unigenes in at least two samples and 131 were assigned as unigenes expressed differently in all three samples. In 4 °C-treated sample and -4 °C-treated sample, 1,661 and 866 differently expressed unigenes were detected at an estimated absolute log2-fold change of > 1, respectively. Among them, the respective number of up-regulated unigenes in C4 and F4 sample was 1,113 and 630, while the respective number of down-regulated ungenes is 548 and 236. To increase our understanding of these differentially expressed genes, we performed gene ontology enrichment and metabolic pathway enrichment analyses. A large number of early cold (below or above freezing temperature)-responsive genes were identified, suggesting that a multitude of transcriptional cascades function in cold perception. Analyses of multiple cold-responsive genes, transcription factors, and some key transduction components involved in ABA and calcium signaling revealed their potential function in low temperature responses in P. euphratica.
CONCLUSIONS
Our results provide a global transcriptome picture of P. euphratica under low temperature stress. The potential cold stress related transcripts identified in this study provide valuable information for further understanding the molecular mechanisms of low temperature perception in P. euphratica.
DOI: 10.1186/1471-2164-15-326
PubMed: 24884892
PubMed Central: PMC4035058
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Laboratory for Tree Breeding, Beijing 100083, China. xiaxl@bjfu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24884892</idno><idno type="pmid">24884892</idno><idno type="doi">10.1186/1471-2164-15-326</idno><idno type="pmc">PMC4035058</idno><idno type="wicri:Area/Main/Corpus">002166</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">002166</idno><idno type="wicri:Area/Main/Curation">002166</idno><idno type="wicri:explorRef" wicri:stream="Main" 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last="Xia">Xinli Xia</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, Beijing 100083, China. xiaxl@bjfu.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Yin, Weilun" sort="Yin, Weilun" uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name></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>Cold Temperature (MeSH)</term><term>Genes, Plant (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Populus (genetics)</term><term>Populus (physiology)</term><term>Transcription Factors (metabolism)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Basse température (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Facteurs de transcription (métabolisme)</term><term>Gènes de plante (MeSH)</term><term>Populus (génétique)</term><term>Populus (physiologie)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</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>Cold Temperature</term><term>Genes, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Molecular Sequence Data</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Basse température</term><term>Données de séquences moléculaires</term><term>Gènes de plante</term><term>Séquençage nucléotidique à haut débit</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Compared with other Populus species, Populus euphratica Oliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signaling pathways involved in low temperature stress responses in this species. Recent development of Illumina/Solexa-based deep-sequencing technologies has accelerated the study of global transcription profiling under specific conditions. To understand the gene network controlling low temperature perception in P. euphratica, we performed transcriptome sequencing using Solexa sequence analysis to generate a leaf transcriptome at a depth of 10 gigabases for each sample.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Using the Trinity method, 52,081,238 high-quality trimmed reads were assembled into a non-redundant set and 108,502 unigenes with an average length of 1,047 bp were generated. After performing functional annotations by aligning all-unigenes with public protein databases, 85,584 unigenes were annotated. Differentially expressed genes were investigated using the FPKM method by applying the Benjamini and Hochberg corrections. Overall, 2,858 transcripts were identified as differentially expressed unigenes in at least two samples and 131 were assigned as unigenes expressed differently in all three samples. In 4 °C-treated sample and -4 °C-treated sample, 1,661 and 866 differently expressed unigenes were detected at an estimated absolute log2-fold change of > 1, respectively. Among them, the respective number of up-regulated unigenes in C4 and F4 sample was 1,113 and 630, while the respective number of down-regulated ungenes is 548 and 236. To increase our understanding of these differentially expressed genes, we performed gene ontology enrichment and metabolic pathway enrichment analyses. A large number of early cold (below or above freezing temperature)-responsive genes were identified, suggesting that a multitude of transcriptional cascades function in cold perception. Analyses of multiple cold-responsive genes, transcription factors, and some key transduction components involved in ABA and calcium signaling revealed their potential function in low temperature responses in P. euphratica.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Our results provide a global transcriptome picture of P. euphratica under low temperature stress. The potential cold stress related transcripts identified in this study provide valuable information for further understanding the molecular mechanisms of low temperature perception in P. euphratica.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24884892</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>01</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Deep-sequencing transcriptome analysis of low temperature perception in a desert tree, Populus euphratica.</ArticleTitle><Pagination><MedlinePgn>326</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-15-326</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Compared with other Populus species, Populus euphratica Oliv. exhibits better tolerance to abiotic stress, especially those involving extreme temperatures. However, little is known about gene regulation and signaling pathways involved in low temperature stress responses in this species. Recent development of Illumina/Solexa-based deep-sequencing technologies has accelerated the study of global transcription profiling under specific conditions. To understand the gene network controlling low temperature perception in P. euphratica, we performed transcriptome sequencing using Solexa sequence analysis to generate a leaf transcriptome at a depth of 10 gigabases for each sample.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Using the Trinity method, 52,081,238 high-quality trimmed reads were assembled into a non-redundant set and 108,502 unigenes with an average length of 1,047 bp were generated. After performing functional annotations by aligning all-unigenes with public protein databases, 85,584 unigenes were annotated. Differentially expressed genes were investigated using the FPKM method by applying the Benjamini and Hochberg corrections. Overall, 2,858 transcripts were identified as differentially expressed unigenes in at least two samples and 131 were assigned as unigenes expressed differently in all three samples. In 4 °C-treated sample and -4 °C-treated sample, 1,661 and 866 differently expressed unigenes were detected at an estimated absolute log2-fold change of > 1, respectively. Among them, the respective number of up-regulated unigenes in C4 and F4 sample was 1,113 and 630, while the respective number of down-regulated ungenes is 548 and 236. To increase our understanding of these differentially expressed genes, we performed gene ontology enrichment and metabolic pathway enrichment analyses. A large number of early cold (below or above freezing temperature)-responsive genes were identified, suggesting that a multitude of transcriptional cascades function in cold perception. Analyses of multiple cold-responsive genes, transcription factors, and some key transduction components involved in ABA and calcium signaling revealed their potential function in low temperature responses in P. euphratica.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our results provide a global transcriptome picture of P. euphratica under low temperature stress. The potential cold stress related transcripts identified in this study provide valuable information for further understanding the molecular mechanisms of low temperature perception in P. euphratica.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Jinhuan</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Tian</LastName><ForeName>Qianqian</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Pang</LastName><ForeName>Tao</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Libo</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Rongling</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Xia</LastName><ForeName>Xinli</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, Beijing 100083, China. 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uniqKey="Yin W" first="Weilun" last="Yin">Weilun Yin</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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