PoplarV1, Main, Exploration, bibRecord, 001852

Genome-wide analysis of lectin receptor-like kinases in Populus.

Identifieur interne : 001852 ( Main/Exploration ); précédent : 001851; suivant : 001853

Genome-wide analysis of lectin receptor-like kinases in Populus.

Auteurs : Yongil Yang [États-Unis] ; Jessy Labbé [États-Unis] ; Wellington Muchero [États-Unis] ; Xiaohan Yang [États-Unis] ; Sara S. Jawdy [États-Unis] ; Megan Kennedy [États-Unis] ; Jenifer Johnson [États-Unis] ; Avinash Sreedasyam [États-Unis] ; Jeremy Schmutz [États-Unis] ; Gerald A. Tuskan [États-Unis] ; Jin-Gui Chen [États-Unis]

Source :

BMC genomics [ 1471-2164 ] ; 2016.

RBID : pubmed:27580945

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Motifs (MeSH), Arabidopsis (genetics), Chromosome Mapping (MeSH), Cluster Analysis (MeSH), Gene Expression Regulation, Plant (MeSH), Genome, Plant (MeSH), Genome-Wide Association Study (MeSH), Genomics (methods), Phylogeny (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (classification), Populus (genetics), Populus (metabolism), Protein Interaction Domains and Motifs (MeSH), Sequence Homology, Amino Acid (MeSH), Tandem Repeat Sequences (MeSH).
MESH :
- chemical , chemistry : Plant Proteins.
- classification : Populus.
- genetics : Arabidopsis, Plant Proteins, Populus.
- chemical , metabolism : Plant Proteins, Populus.
- methods : Genomics.
- Amino Acid Motifs, Chromosome Mapping, Cluster Analysis, Gene Expression Regulation, Plant, Genome, Plant, Genome-Wide Association Study, Phylogeny, Protein Interaction Domains and Motifs, Sequence Homology, Amino Acid, Tandem Repeat Sequences.

Abstract

BACKGROUND

Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants.

RESULTS

Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs.

CONCLUSIONS

This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.

DOI: 10.1186/s12864-016-3026-2
PubMed: 27580945
PubMed Central: PMC5007699

Affiliations:

États-Unis

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Le document en format XML

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<author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name>
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<author><name sortKey="Chen, Jin Gui" sort="Chen, Jin Gui" uniqKey="Chen J" first="Jin-Gui" last="Chen">Jin-Gui Chen</name>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Motifs (MeSH)</term>
<term>Arabidopsis (genetics)</term>
<term>Chromosome Mapping (MeSH)</term>
<term>Cluster Analysis (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Genome, Plant (MeSH)</term>
<term>Genome-Wide Association Study (MeSH)</term>
<term>Genomics (methods)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Proteins (chemistry)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Populus (classification)</term>
<term>Populus (genetics)</term>
<term>Populus (metabolism)</term>
<term>Protein Interaction Domains and Motifs (MeSH)</term>
<term>Sequence Homology, Amino Acid (MeSH)</term>
<term>Tandem Repeat Sequences (MeSH)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de regroupements (MeSH)</term>
<term>Arabidopsis (génétique)</term>
<term>Cartographie chromosomique (MeSH)</term>
<term>Génome végétal (MeSH)</term>
<term>Génomique (méthodes)</term>
<term>Motifs d'acides aminés (MeSH)</term>
<term>Motifs et domaines d'intéraction protéique (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Populus (classification)</term>
<term>Populus (génétique)</term>
<term>Populus (métabolisme)</term>
<term>Protéines végétales (composition chimique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Similitude de séquences d'acides aminés (MeSH)</term>
<term>Séquences répétées en tandem (MeSH)</term>
<term>Étude d'association pangénomique (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plant Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Populus</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term>
<term>Plant Proteins</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term>
<term>Populus</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Populus</term>
<term>Protéines végétales</term>
</keywords>
<keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Génomique</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Motifs</term>
<term>Chromosome Mapping</term>
<term>Cluster Analysis</term>
<term>Gene Expression Regulation, Plant</term>
<term>Genome, Plant</term>
<term>Genome-Wide Association Study</term>
<term>Phylogeny</term>
<term>Protein Interaction Domains and Motifs</term>
<term>Sequence Homology, Amino Acid</term>
<term>Tandem Repeat Sequences</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de regroupements</term>
<term>Cartographie chromosomique</term>
<term>Génome végétal</term>
<term>Motifs d'acides aminés</term>
<term>Motifs et domaines d'intéraction protéique</term>
<term>Phylogenèse</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Similitude de séquences d'acides aminés</term>
<term>Séquences répétées en tandem</term>
<term>Étude d'association pangénomique</term>
</keywords>
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<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b>
</p>
<p>This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.</p>
</div>
</front>
</TEI>
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<DateCompleted><Year>2017</Year>
<Month>09</Month>
<Day>01</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>17</Volume>
<PubDate><Year>2016</Year>
<Month>09</Month>
<Day>01</Day>
</PubDate>
</JournalIssue>
<Title>BMC genomics</Title>
<ISOAbbreviation>BMC Genomics</ISOAbbreviation>
</Journal>
<ArticleTitle>Genome-wide analysis of lectin receptor-like kinases in Populus.</ArticleTitle>
<Pagination><MedlinePgn>699</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-016-3026-2</ELocationID>
<Abstract><AbstractText Label="BACKGROUND">Receptor-like kinases (RLKs) belong to a large protein family with over 600 members in Arabidopsis and over 1000 in rice. Among RLKs, the lectin receptor-like kinases (LecRLKs) possess a characteristic extracellular carbohydrate-binding lectin domain and play important roles in plant development and innate immunity. There are 75 and 173 LecRLKs in Arabidopsis and rice, respectively. However, little is known about LecRLKs in perennial woody plants.</AbstractText>
<AbstractText Label="RESULTS">Here we report the genome-wide analysis of classification, domain architecture and expression of LecRLKs in the perennial woody model plant Populus. We found that the LecRLK family has expanded in Populus to a total of 231, including 180 G-type, 50 L-type and 1 C-type LecRLKs. Expansion of the Populus LecRLKs (PtLecRLKs) occurred partially through tandem duplication. Based on domain architecture and orientation features, we classified PtLecRLKs into eight different classes. RNA-seq-based transcriptomics analysis revealed diverse expression patterns of PtLecRLK genes among leaves, stems, roots, buds and reproductive tissues and organs.</AbstractText>
<AbstractText Label="CONCLUSIONS">This study offers a comprehensive view of LecRLKs in the perennial woody model plant Populus and provides a foundation for functional characterization of this important family of receptor-like kinases.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yang</LastName>
<ForeName>Yongil</ForeName>
<Initials>Y</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Labbé</LastName>
<ForeName>Jessy</ForeName>
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Genome-wide analysis of lectin receptor-like kinases in Populus.

Genome-wide analysis of lectin receptor-like kinases in Populus.

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