SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis.
Identifieur interne : 001D21 ( Main/Corpus ); précédent : 001D20; suivant : 001D22SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis.
Auteurs : Luis Carlos Belarmino ; Roberta Lane De Oliveira Silva ; Nina Da Mota Soares Cavalcanti ; Nicolas Krezdorn ; Ederson Akio Kido ; Ralf Horres ; Peter Winter ; Günter Kahl ; Ana Maria Benko-IsepponSource :
- BMC bioinformatics [ 1471-2105 ] ; 2013.
English descriptors
- KwdEn :
- MESH :
Abstract
BACKGROUND
The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database.
METHODS
Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions.
RESULTS
We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found.
CONCLUSIONS
The knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops.
DOI: 10.1186/1471-2105-14-S1-S2
PubMed: 23368899
PubMed Central: PMC3548678
Links to Exploration step
pubmed:23368899Le document en format XML
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Lane De Oliveira" last="Silva">Roberta Lane De Oliveira Silva</name></author><author><name sortKey="Cavalcanti, Nina Da Mota Soares" sort="Cavalcanti, Nina Da Mota Soares" uniqKey="Cavalcanti N" first="Nina Da Mota Soares" last="Cavalcanti">Nina Da Mota Soares Cavalcanti</name></author><author><name sortKey="Krezdorn, Nicolas" sort="Krezdorn, Nicolas" uniqKey="Krezdorn N" first="Nicolas" last="Krezdorn">Nicolas Krezdorn</name></author><author><name sortKey="Kido, Ederson Akio" sort="Kido, Ederson Akio" uniqKey="Kido E" first="Ederson Akio" last="Kido">Ederson Akio Kido</name></author><author><name sortKey="Horres, Ralf" sort="Horres, Ralf" uniqKey="Horres R" first="Ralf" last="Horres">Ralf Horres</name></author><author><name sortKey="Winter, Peter" sort="Winter, Peter" uniqKey="Winter P" first="Peter" last="Winter">Peter Winter</name></author><author><name sortKey="Kahl, Gunter" sort="Kahl, Gunter" uniqKey="Kahl G" first="Günter" last="Kahl">Günter Kahl</name></author><author><name sortKey="Benko Iseppon, Ana Maria" sort="Benko Iseppon, Ana Maria" uniqKey="Benko Iseppon A" first="Ana Maria" last="Benko-Iseppon">Ana Maria Benko-Iseppon</name></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Genetic (MeSH)</term><term>Expressed Sequence Tags (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Mycorrhizae (genetics)</term><term>Root Nodules, Plant (genetics)</term><term>Saccharum (genetics)</term><term>Software (MeSH)</term><term>Symbiosis (genetics)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mycorrhizae</term><term>Root Nodules, Plant</term><term>Saccharum</term><term>Symbiosis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Expressed Sequence Tags</term><term>Genes, Plant</term><term>Software</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database.</p></div><div type="abstract" xml:lang="en"><p><b>METHODS</b></p><p>Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">23368899</PMID><DateCompleted><Year>2013</Year><Month>08</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>14 Suppl 1</Volume><PubDate><Year>2013</Year></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis.</ArticleTitle><Pagination><MedlinePgn>S2</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2105-14-S1-S2</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database.</AbstractText><AbstractText Label="METHODS" NlmCategory="METHODS">Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Belarmino</LastName><ForeName>Luis Carlos</ForeName><Initials>LC</Initials><AffiliationInfo><Affiliation>Universidade Federal de Pernambuco, Centro de Ciências Biológicas, Departamento de Genética, Recife, PE, Brazil. lucabellarmino@gmail.com</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Silva</LastName><ForeName>Roberta Lane de Oliveira</ForeName><Initials>RL</Initials></Author><Author ValidYN="Y"><LastName>Cavalcanti</LastName><ForeName>Nina da Mota Soares</ForeName><Initials>Nda M</Initials></Author><Author ValidYN="Y"><LastName>Krezdorn</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Kido</LastName><ForeName>Ederson Akio</ForeName><Initials>EA</Initials></Author><Author ValidYN="Y"><LastName>Horres</LastName><ForeName>Ralf</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Winter</LastName><ForeName>Peter</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Kahl</LastName><ForeName>Günter</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Benko-Iseppon</LastName><ForeName>Ana Maria</ForeName><Initials>AM</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>01</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC 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