LSD 3.0: a comprehensive resource for the leaf senescence research community.
Identifieur interne : 000668 ( Main/Corpus ); précédent : 000667; suivant : 000669LSD 3.0: a comprehensive resource for the leaf senescence research community.
Auteurs : Zhonghai Li ; Yang Zhang ; Dong Zou ; Yi Zhao ; Hou-Ling Wang ; Yi Zhang ; Xinli Xia ; Jingchu Luo ; Hongwei Guo ; Zhang ZhangSource :
- Nucleic acids research [ 1362-4962 ] ; 2020.
English descriptors
- KwdEn :
- Aging (genetics), Arabidopsis (genetics), Computational Biology (methods), Databases, Genetic (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Molecular Sequence Annotation (MeSH), Mutation (MeSH), Phenotype (MeSH), Plant Leaves (genetics), Web Browser (MeSH).
- MESH :
Abstract
The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reliable services for the plant research community, LSD 3.0 (https://bigd.big.ac.cn/lsd/) has been moved to and maintained by the National Genomics Data Center at Beijing Institute of Genomics, Chinese Academy of Sciences. In the current release, we added some new features: (i) Transcriptome data of leaf senescence in poplar were integrated; (ii) Leaf senescence-associated transcriptome data information in Arabidopsis, rice and soybean were included; (iii) Senescence-differentially expressed small RNAs (Sen-smRNA) in Arabidopsis were identified; (iv) Interaction pairs between Sen-smRNAs and senescence-associated transcription factors (Sen-TF) were established; (v) Senescence phenotypes of 90 natural accessions (ecotypes) and 42 images of ecotypes in Arabidopsis were incorporated; (vi) Mutant seed information of SAGs in rice obtained from Kitbase was integrated; (vii) New options of search engines for ecotypes and transcriptome data were implemented. Together, the updated database bears great utility to continue to provide users with useful resources for studies of leaf senescence.
DOI: 10.1093/nar/gkz898
PubMed: 31599330
PubMed Central: PMC6943054
Links to Exploration step
pubmed:31599330Le document en format XML
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Beijing Forestry University, Beijing 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Yang" sort="Zhang, Yang" uniqKey="Zhang Y" first="Yang" last="Zhang">Yang Zhang</name><affiliation><nlm:affiliation>National Genomics Data Center, Beijing 100101, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>University of Chinese Academy of Sciences, Beijing 100049, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zou, Dong" sort="Zou, Dong" uniqKey="Zou D" first="Dong" last="Zou">Dong Zou</name><affiliation><nlm:affiliation>National Genomics Data Center, Beijing 100101, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhao, Yi" sort="Zhao, Yi" uniqKey="Zhao Y" first="Yi" last="Zhao">Yi Zhao</name><affiliation><nlm:affiliation>College of Life Sciences, Peking University, Beijing 100871, China.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Hou Ling" sort="Wang, Hou Ling" uniqKey="Wang H" first="Hou-Ling" last="Wang">Hou-Ling Wang</name><affiliation><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Yi" sort="Zhang, Yi" uniqKey="Zhang Y" first="Yi" last="Zhang">Yi Zhang</name><affiliation><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Xia, Xinli" sort="Xia, Xinli" uniqKey="Xia X" first="Xinli" last="Xia">Xinli Xia</name><affiliation><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China.</nlm:affiliation></affiliation></author><author><name sortKey="Luo, Jingchu" sort="Luo, Jingchu" uniqKey="Luo J" first="Jingchu" last="Luo">Jingchu Luo</name><affiliation><nlm:affiliation>College of Life Sciences, Peking University, Beijing 100871, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Center for Bioinformatics, Peking University, Beijing 100871, China.</nlm:affiliation></affiliation></author><author><name sortKey="Guo, Hongwei" sort="Guo, Hongwei" uniqKey="Guo H" first="Hongwei" last="Guo">Hongwei Guo</name><affiliation><nlm:affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China.</nlm:affiliation></affiliation></author><author><name sortKey="Zhang, Zhang" sort="Zhang, Zhang" uniqKey="Zhang Z" first="Zhang" last="Zhang">Zhang Zhang</name><affiliation><nlm:affiliation>National Genomics Data Center, Beijing 100101, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>University of Chinese Academy of Sciences, Beijing 100049, China.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Nucleic acids research</title><idno type="eISSN">1362-4962</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Aging (genetics)</term><term>Arabidopsis (genetics)</term><term>Computational Biology (methods)</term><term>Databases, Genetic (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Mutation (MeSH)</term><term>Phenotype (MeSH)</term><term>Plant Leaves (genetics)</term><term>Web Browser (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Aging</term><term>Arabidopsis</term><term>Plant Leaves</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Molecular Sequence Annotation</term><term>Mutation</term><term>Phenotype</term><term>Web Browser</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reliable services for the plant research community, LSD 3.0 (https://bigd.big.ac.cn/lsd/) has been moved to and maintained by the National Genomics Data Center at Beijing Institute of Genomics, Chinese Academy of Sciences. In the current release, we added some new features: (i) Transcriptome data of leaf senescence in poplar were integrated; (ii) Leaf senescence-associated transcriptome data information in Arabidopsis, rice and soybean were included; (iii) Senescence-differentially expressed small RNAs (Sen-smRNA) in Arabidopsis were identified; (iv) Interaction pairs between Sen-smRNAs and senescence-associated transcription factors (Sen-TF) were established; (v) Senescence phenotypes of 90 natural accessions (ecotypes) and 42 images of ecotypes in Arabidopsis were incorporated; (vi) Mutant seed information of SAGs in rice obtained from Kitbase was integrated; (vii) New options of search engines for ecotypes and transcriptome data were implemented. Together, the updated database bears great utility to continue to provide users with useful resources for studies of leaf senescence.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31599330</PMID><DateCompleted><Year>2020</Year><Month>05</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>05</Month><Day>18</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1362-4962</ISSN><JournalIssue CitedMedium="Internet"><Volume>48</Volume><Issue>D1</Issue><PubDate><Year>2020</Year><Month>01</Month><Day>08</Day></PubDate></JournalIssue><Title>Nucleic acids research</Title><ISOAbbreviation>Nucleic Acids Res</ISOAbbreviation></Journal><ArticleTitle>LSD 3.0: a comprehensive resource for the leaf senescence research community.</ArticleTitle><Pagination><MedlinePgn>D1069-D1075</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/nar/gkz898</ELocationID><Abstract><AbstractText>The leaf senescence database (LSD) is a comprehensive resource of senescence-associated genes (SAGs) and their corresponding mutants. Through manual curation and extensive annotation, we updated the LSD to a new version LSD 3.0, which contains 5853 genes and 617 mutants from 68 species. To provide sustainable and reliable services for the plant research community, LSD 3.0 (https://bigd.big.ac.cn/lsd/) has been moved to and maintained by the National Genomics Data Center at Beijing Institute of Genomics, Chinese Academy of Sciences. In the current release, we added some new features: (i) Transcriptome data of leaf senescence in poplar were integrated; (ii) Leaf senescence-associated transcriptome data information in Arabidopsis, rice and soybean were included; (iii) Senescence-differentially expressed small RNAs (Sen-smRNA) in Arabidopsis were identified; (iv) Interaction pairs between Sen-smRNAs and senescence-associated transcription factors (Sen-TF) were established; (v) Senescence phenotypes of 90 natural accessions (ecotypes) and 42 images of ecotypes in Arabidopsis were incorporated; (vi) Mutant seed information of SAGs in rice obtained from Kitbase was integrated; (vii) New options of search engines for ecotypes and transcriptome data were implemented. Together, the updated database bears great utility to continue to provide users with useful resources for studies of leaf senescence.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Zhonghai</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>National Genomics Data Center, Beijing 100101, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>University of Chinese Academy of Sciences, Beijing 100049, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zou</LastName><ForeName>Dong</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>National Genomics Data Center, Beijing 100101, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhao</LastName><ForeName>Yi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Peking University, Beijing 100871, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Hou-Ling</ForeName><Initials>HL</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Yi</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xia</LastName><ForeName>Xinli</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Jingchu</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Peking University, Beijing 100871, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Center for Bioinformatics, Peking University, Beijing 100871, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>Hongwei</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Zhang</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>National Genomics Data Center, Beijing 100101, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>University of Chinese Academy of Sciences, Beijing 100049, China.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Nucleic Acids Res</MedlineTA><NlmUniqueID>0411011</NlmUniqueID><ISSNLinking>0305-1048</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000375" MajorTopicYN="N">Aging</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="Y">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName><QualifierName UI="Q000235" 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