Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating Salix integra.
Identifieur interne : 000B02 ( Main/Corpus ); précédent : 000B01; suivant : 000B03Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating Salix integra.
Auteurs : Xiang Shi ; Haijing Sun ; Yitai Chen ; Hongwei Pan ; Shufeng WangSource :
- Frontiers in plant science [ 1664-462X ] ; 2016.
Abstract
Salix integra is a shrub willow native to northeastern China, Japan, Korea, and Primorsky Krai in the far southeast of Russia, and has been identified as cadmium (Cd)-accumulating trees in recent years. Although many physiological studies have been conducted with these plants, little is known about the molecular basis underlying Cd response in this plant, and this is confirmed by the very few number of gene sequences (only 39 nucleotide sequences) available in public databases. Advances in genomics for Salix are promising for future improvement in identification of new candidate genes involved in metal tolerance and accumulation. Thus, high-throughput transcriptome sequencing is essential for generating enormous transcript sequences from S. integra, especially for the purpose of Cd toxicity-responsive genes discovery. Using Illumina paired-end sequencing, approximately 60.05 million high-quality reads were obtained. De novo assembly yielded 80,105 unigenes with an average length of 703 bp, A total of 50,221 (63%) unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases. GO annotation reveals 1849 Cd responsive genes involving in Cd binding, transport, and detoxification and cellular Cd homeostasis, and these genes were highly enriched in plant response to Cd ion and Cd ion transport. By searching against the PlantCyc database, 509 unigenes were assigned to 14 PlantCyc pathways related to Cd transport and cellular detoxification, and many of them are genes encoding heavy metal ATPases (HMAs), nature resistance-associated with microphage proteins (NRAMPs), ATP-binding cassette (ABC) transporters, etc., Comprehensive RT-qPCR analysis of these selected genes in different tissues of S. integra under the control and Cd treatment revealed metallothionein-like protein (MT2A and MT2B), Metal tolerance protein (MTP1), ABCB25, NRAMP5, and ZIP1 may be involved in the Cd transport and detoxification in leaves, while NRAMP2, ZIP8, and NRAMP5 may be related to Cd transport in roots. Our study will enrich the sequence information of S. integra in public database, and would provide some new understanding of the molecular mechanisms of heavy metal tolerance and detoxification in willows.
DOI: 10.3389/fpls.2016.01577
PubMed: 27840630
PubMed Central: PMC5083712
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating <i>Salix integra</i>.</title><author><name sortKey="Shi, Xiang" sort="Shi, Xiang" uniqKey="Shi X" first="Xiang" last="Shi">Xiang Shi</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Haijing" sort="Sun, Haijing" uniqKey="Sun H" first="Haijing" last="Sun">Haijing Sun</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Yitai" sort="Chen, Yitai" uniqKey="Chen Y" first="Yitai" last="Chen">Yitai Chen</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of Forestry Hangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Pan, Hongwei" sort="Pan, Hongwei" uniqKey="Pan H" first="Hongwei" last="Pan">Hongwei Pan</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Shufeng" sort="Wang, Shufeng" uniqKey="Wang S" first="Shufeng" last="Wang">Shufeng Wang</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27840630</idno><idno type="pmid">27840630</idno><idno type="doi">10.3389/fpls.2016.01577</idno><idno type="pmc">PMC5083712</idno><idno type="wicri:Area/Main/Corpus">000B02</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000B02</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating <i>Salix integra</i>.</title><author><name sortKey="Shi, Xiang" sort="Shi, Xiang" uniqKey="Shi X" first="Xiang" last="Shi">Xiang Shi</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Sun, Haijing" sort="Sun, Haijing" uniqKey="Sun H" first="Haijing" last="Sun">Haijing Sun</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Chen, Yitai" sort="Chen, Yitai" uniqKey="Chen Y" first="Yitai" last="Chen">Yitai Chen</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of Forestry Hangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Pan, Hongwei" sort="Pan, Hongwei" uniqKey="Pan H" first="Hongwei" last="Pan">Hongwei Pan</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Shufeng" sort="Wang, Shufeng" uniqKey="Wang S" first="Shufeng" last="Wang">Shufeng Wang</name><affiliation><nlm:affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><i>Salix integra</i> is a shrub willow native to northeastern China, Japan, Korea, and Primorsky Krai in the far southeast of Russia, and has been identified as cadmium (Cd)-accumulating trees in recent years. Although many physiological studies have been conducted with these plants, little is known about the molecular basis underlying Cd response in this plant, and this is confirmed by the very few number of gene sequences (only 39 nucleotide sequences) available in public databases. Advances in genomics for <i>Salix</i> are promising for future improvement in identification of new candidate genes involved in metal tolerance and accumulation. Thus, high-throughput transcriptome sequencing is essential for generating enormous transcript sequences from <i>S. integra</i>, especially for the purpose of Cd toxicity-responsive genes discovery. Using Illumina paired-end sequencing, approximately 60.05 million high-quality reads were obtained. <i>De novo</i> assembly yielded 80,105 unigenes with an average length of 703 bp, A total of 50,221 (63%) unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases. GO annotation reveals 1849 Cd responsive genes involving in Cd binding, transport, and detoxification and cellular Cd homeostasis, and these genes were highly enriched in plant response to Cd ion and Cd ion transport. By searching against the PlantCyc database, 509 unigenes were assigned to 14 PlantCyc pathways related to Cd transport and cellular detoxification, and many of them are genes encoding heavy metal ATPases (<i>HMA</i>s), nature resistance-associated with microphage proteins (<i>NRAMP</i>s), ATP-binding cassette (ABC) transporters, etc., Comprehensive RT-qPCR analysis of these selected genes in different tissues of <i>S. integra</i> under the control and Cd treatment revealed metallothionein-like protein (<i>MT2A</i> and <i>MT2B</i>), Metal tolerance protein (<i>MTP1</i>), <i>ABCB25, NRAMP5</i>, and <i>ZIP1</i> may be involved in the Cd transport and detoxification in leaves, while <i>NRAMP2, ZIP8</i>, and <i>NRAMP5</i> may be related to Cd transport in roots. Our study will enrich the sequence information of <i>S. integra</i> in public database, and would provide some new understanding of the molecular mechanisms of heavy metal tolerance and detoxification in willows.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27840630</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Transcriptome Sequencing and Expression Analysis of Cadmium (Cd) Transport and Detoxification Related Genes in Cd-Accumulating <i>Salix integra</i>.</ArticleTitle><Pagination><MedlinePgn>1577</MedlinePgn></Pagination><Abstract><AbstractText><i>Salix integra</i> is a shrub willow native to northeastern China, Japan, Korea, and Primorsky Krai in the far southeast of Russia, and has been identified as cadmium (Cd)-accumulating trees in recent years. Although many physiological studies have been conducted with these plants, little is known about the molecular basis underlying Cd response in this plant, and this is confirmed by the very few number of gene sequences (only 39 nucleotide sequences) available in public databases. Advances in genomics for <i>Salix</i> are promising for future improvement in identification of new candidate genes involved in metal tolerance and accumulation. Thus, high-throughput transcriptome sequencing is essential for generating enormous transcript sequences from <i>S. integra</i>, especially for the purpose of Cd toxicity-responsive genes discovery. Using Illumina paired-end sequencing, approximately 60.05 million high-quality reads were obtained. <i>De novo</i> assembly yielded 80,105 unigenes with an average length of 703 bp, A total of 50,221 (63%) unigenes were further functionally annotated by comparing their sequences to different proteins and functional domain databases. GO annotation reveals 1849 Cd responsive genes involving in Cd binding, transport, and detoxification and cellular Cd homeostasis, and these genes were highly enriched in plant response to Cd ion and Cd ion transport. By searching against the PlantCyc database, 509 unigenes were assigned to 14 PlantCyc pathways related to Cd transport and cellular detoxification, and many of them are genes encoding heavy metal ATPases (<i>HMA</i>s), nature resistance-associated with microphage proteins (<i>NRAMP</i>s), ATP-binding cassette (ABC) transporters, etc., Comprehensive RT-qPCR analysis of these selected genes in different tissues of <i>S. integra</i> under the control and Cd treatment revealed metallothionein-like protein (<i>MT2A</i> and <i>MT2B</i>), Metal tolerance protein (<i>MTP1</i>), <i>ABCB25, NRAMP5</i>, and <i>ZIP1</i> may be involved in the Cd transport and detoxification in leaves, while <i>NRAMP2, ZIP8</i>, and <i>NRAMP5</i> may be related to Cd transport in roots. Our study will enrich the sequence information of <i>S. integra</i> in public database, and would provide some new understanding of the molecular mechanisms of heavy metal tolerance and detoxification in willows.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Xiang</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Haijing</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Yitai</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Research Institute of Subtropical Forestry, Chinese Academy of Forestry Hangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pan</LastName><ForeName>Hongwei</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Shufeng</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Research Institute of Subtropical Forestry, Chinese Academy of ForestryHangzhou, China; Key Laboratory of Tree Breeding of Zhejiang ProvinceHangzhou, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>10</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Plant Sci</MedlineTA><NlmUniqueID>101568200</NlmUniqueID><ISSNLinking>1664-462X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Cd stress</Keyword><Keyword MajorTopicYN="N">Cd transportation</Keyword><Keyword MajorTopicYN="N">Salix integra</Keyword><Keyword MajorTopicYN="N">de novo assembly</Keyword><Keyword MajorTopicYN="N">transcription factor</Keyword><Keyword MajorTopicYN="N">willow</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>07</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>10</Month><Day>06</Day></PubMedPubDate><PubMedPubDate 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