PoplarV1, Main, Exploration, bibRecord, 003489

Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.

Identifieur interne : 003489 ( Main/Exploration ); précédent : 003488; suivant : 003490

Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.

Auteurs : Carol Soderlund [États-Unis] ; Anne Descour ; Dave Kudrna ; Matthew Bomhoff ; Lomax Boyd ; Jennifer Currie ; Angelina Angelova ; Kristi Collura ; Marina Wissotski ; Elizabeth Ashley ; Darren Morrow ; John Fernandes ; Virginia Walbot ; Yeisoo Yu

Source :

PLoS genetics [ 1553-7404 ] ; 2009.

RBID : pubmed:19936069

Descripteurs français

English descriptors

KwdEn :
- Arabidopsis (genetics), Base Sequence (MeSH), Chromosome Mapping (methods), Chromosomes, Plant (genetics), Contig Mapping (MeSH), DNA Transposable Elements (genetics), DNA, Complementary (genetics), Expressed Sequence Tags (MeSH), Genes, Plant (genetics), Internet (MeSH), Minisatellite Repeats (genetics), Molecular Sequence Data (MeSH), Oryza (genetics), Plant Proteins (metabolism), Poly A (genetics), Polymorphism, Single Nucleotide (genetics), Populus (genetics), Sequence Analysis, DNA (methods), Sequence Homology, Nucleic Acid (MeSH), Sorghum (genetics), Transcription Factors (genetics), Zea mays (genetics).
MESH :
- chemical , genetics : DNA Transposable Elements, DNA, Complementary, Poly A, Transcription Factors.
- genetics : Arabidopsis, Chromosomes, Plant, Genes, Plant, Minisatellite Repeats, Oryza, Polymorphism, Single Nucleotide, Populus, Sorghum, Zea mays.
- chemical , metabolism : Plant Proteins.
- methods : Chromosome Mapping, Sequence Analysis, DNA.
- Base Sequence, Contig Mapping, Expressed Sequence Tags, Internet, Molecular Sequence Data, Sequence Homology, Nucleic Acid.

Abstract

Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org).

DOI: 10.1371/journal.pgen.1000740
PubMed: 19936069
PubMed Central: PMC2774520

Affiliations:

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Le document en format XML

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<term>Base Sequence (MeSH)</term>
<term>Chromosome Mapping (methods)</term>
<term>Chromosomes, Plant (genetics)</term>
<term>Contig Mapping (MeSH)</term>
<term>DNA Transposable Elements (genetics)</term>
<term>DNA, Complementary (genetics)</term>
<term>Expressed Sequence Tags (MeSH)</term>
<term>Genes, Plant (genetics)</term>
<term>Internet (MeSH)</term>
<term>Minisatellite Repeats (genetics)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Oryza (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Poly A (genetics)</term>
<term>Polymorphism, Single Nucleotide (genetics)</term>
<term>Populus (genetics)</term>
<term>Sequence Analysis, DNA (methods)</term>
<term>Sequence Homology, Nucleic Acid (MeSH)</term>
<term>Sorghum (genetics)</term>
<term>Transcription Factors (genetics)</term>
<term>Zea mays (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN complémentaire (génétique)</term>
<term>Analyse de séquence d'ADN (méthodes)</term>
<term>Arabidopsis (génétique)</term>
<term>Cartographie chromosomique (méthodes)</term>
<term>Cartographie de contigs (MeSH)</term>
<term>Chromosomes de plante (génétique)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Gènes de plante (génétique)</term>
<term>Internet (MeSH)</term>
<term>Oryza (génétique)</term>
<term>Poly A (génétique)</term>
<term>Polymorphisme de nucléotide simple (génétique)</term>
<term>Populus (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Répétitions minisatellites (génétique)</term>
<term>Similitude de séquences d'acides nucléiques (MeSH)</term>
<term>Sorghum (génétique)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>Zea mays (génétique)</term>
<term>Éléments transposables d'ADN (génétique)</term>
<term>Étiquettes de séquences exprimées (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Transposable Elements</term>
<term>DNA, Complementary</term>
<term>Poly A</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term>
<term>Chromosomes, Plant</term>
<term>Genes, Plant</term>
<term>Minisatellite Repeats</term>
<term>Oryza</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Populus</term>
<term>Sorghum</term>
<term>Zea mays</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN complémentaire</term>
<term>Arabidopsis</term>
<term>Chromosomes de plante</term>
<term>Facteurs de transcription</term>
<term>Gènes de plante</term>
<term>Oryza</term>
<term>Poly A</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Populus</term>
<term>Répétitions minisatellites</term>
<term>Sorghum</term>
<term>Zea mays</term>
<term>Éléments transposables d'ADN</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Chromosome Mapping</term>
<term>Sequence Analysis, DNA</term>
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<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Cartographie chromosomique</term>
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<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
<term>Contig Mapping</term>
<term>Expressed Sequence Tags</term>
<term>Internet</term>
<term>Molecular Sequence Data</term>
<term>Sequence Homology, Nucleic Acid</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Cartographie de contigs</term>
<term>Données de séquences moléculaires</term>
<term>Internet</term>
<term>Similitude de séquences d'acides nucléiques</term>
<term>Séquence nucléotidique</term>
<term>Étiquettes de séquences exprimées</term>
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<front><div type="abstract" xml:lang="en">Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org).</div>
</front>
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<DateCompleted><Year>2010</Year>
<Month>03</Month>
<Day>02</Day>
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<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
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<JournalIssue CitedMedium="Internet"><Volume>5</Volume>
<Issue>11</Issue>
<PubDate><Year>2009</Year>
<Month>Nov</Month>
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<Title>PLoS genetics</Title>
<ISOAbbreviation>PLoS Genet</ISOAbbreviation>
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<ArticleTitle>Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.</ArticleTitle>
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<Abstract><AbstractText>Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5' and 3' UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org).</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Soderlund</LastName>
<ForeName>Carol</ForeName>
<Initials>C</Initials>
<AffiliationInfo><Affiliation>BIO5 Institute, University of Arizona, Tucson, Arizona, USA. cari@agcol.arizona.edu</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Descour</LastName>
<ForeName>Anne</ForeName>
<Initials>A</Initials>
</Author>
<Author ValidYN="Y"><LastName>Kudrna</LastName>
<ForeName>Dave</ForeName>
<Initials>D</Initials>
</Author>
<Author ValidYN="Y"><LastName>Bomhoff</LastName>
<ForeName>Matthew</ForeName>
<Initials>M</Initials>
</Author>
<Author ValidYN="Y"><LastName>Boyd</LastName>
<ForeName>Lomax</ForeName>
<Initials>L</Initials>
</Author>
<Author ValidYN="Y"><LastName>Currie</LastName>
<ForeName>Jennifer</ForeName>
<Initials>J</Initials>
</Author>
<Author ValidYN="Y"><LastName>Angelova</LastName>
<ForeName>Angelina</ForeName>
<Initials>A</Initials>
</Author>
<Author ValidYN="Y"><LastName>Collura</LastName>
<ForeName>Kristi</ForeName>
<Initials>K</Initials>
</Author>
<Author ValidYN="Y"><LastName>Wissotski</LastName>
<ForeName>Marina</ForeName>
<Initials>M</Initials>
</Author>
<Author ValidYN="Y"><LastName>Ashley</LastName>
<ForeName>Elizabeth</ForeName>
<Initials>E</Initials>
</Author>
<Author ValidYN="Y"><LastName>Morrow</LastName>
<ForeName>Darren</ForeName>
<Initials>D</Initials>
</Author>
<Author ValidYN="Y"><LastName>Fernandes</LastName>
<ForeName>John</ForeName>
<Initials>J</Initials>
</Author>
<Author ValidYN="Y"><LastName>Walbot</LastName>
<ForeName>Virginia</ForeName>
<Initials>V</Initials>
</Author>
<Author ValidYN="Y"><LastName>Yu</LastName>
<ForeName>Yeisoo</ForeName>
<Initials>Y</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2009</Year>
<Month>11</Month>
<Day>20</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>PLoS Genet</MedlineTA>
<NlmUniqueID>101239074</NlmUniqueID>
<ISSNLinking>1553-7390</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D004251">DNA Transposable Elements</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D018076">DNA, Complementary</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>24937-83-5</RegistryNumber>
<NameOfSubstance UI="D011061">Poly A</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032461" MajorTopicYN="N">Chromosomes, Plant</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020451" MajorTopicYN="N">Contig Mapping</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D004251" MajorTopicYN="N">DNA Transposable Elements</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018076" MajorTopicYN="N">DNA, Complementary</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018598" MajorTopicYN="N">Minisatellite Repeats</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D011061" MajorTopicYN="N">Poly A</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012689" MajorTopicYN="N">Sequence Homology, Nucleic Acid</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D045868" MajorTopicYN="N">Sorghum</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D003313" MajorTopicYN="N">Zea mays</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
</MeshHeadingList>
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Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.

Sequencing, mapping, and analysis of 27,455 maize full-length cDNAs.

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