De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.

Detalhes bibliográficos
Autor(a) principal: SILVA, G. T.
Data de Publicação: 2013
Outros Autores: SILVA, C. B. C., JANK, L., SOUZA, A. P.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
Texto Completo: http://www.alice.cnptia.embrapa.br/alice/handle/doc/981465
Resumo: Guinea grass (Panicum maximum Jacq.) is a tropical African grass often used to feed beef cattle, which is an important economic activity in Brazil. Brazil is the leader in global meat exportation because of its exclusively pasture-raised bovine herds. Guinea grass also has potential uses in bioenergy production due to its elevated biomass generation through the C4 photosynthesis pathway. We generated approximately 13 Gb of data from Illumina sequencing of P. maximum leaves. Four different genotypes were sequenced, and the combined reads were assembled de novo into 38,192 unigenes and annotated; approximately 63% of the unigenes had homology to other proteins in the NCBI non-redundant protein database. Functional classification through COG (Clusters of Orthologous Groups), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses showed that the unigenes from Guinea grass leaves are involved in a wide range of biological processes and metabolic pathways, including C4 photosynthesis and lignocellulose generation, which are important for cattle grazing and bioenergy production. The most abundant transcripts were involved in carbon fixation, photosynthesis, RNA translation and heavy metal cellular homeostasis. Finally, we identified a number of potential molecular markers, including 5,035 microsatellites (SSRs) and 346,456 single nucleotide polymorphisms (SNPs). To the best of our knowledge, this is the first study to characterize the complete leaf transcriptome of P. maximum using highthroughput sequencing. The biological information provided here will aid in gene expression studies and marker-assisted selection-based breeding research in tropical grasses.
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spelling De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.Panicum maximumAlimento animalGraminea tropicalCarneBeef cattleMegathyrsus maximusGuinea grass (Panicum maximum Jacq.) is a tropical African grass often used to feed beef cattle, which is an important economic activity in Brazil. Brazil is the leader in global meat exportation because of its exclusively pasture-raised bovine herds. Guinea grass also has potential uses in bioenergy production due to its elevated biomass generation through the C4 photosynthesis pathway. We generated approximately 13 Gb of data from Illumina sequencing of P. maximum leaves. Four different genotypes were sequenced, and the combined reads were assembled de novo into 38,192 unigenes and annotated; approximately 63% of the unigenes had homology to other proteins in the NCBI non-redundant protein database. Functional classification through COG (Clusters of Orthologous Groups), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses showed that the unigenes from Guinea grass leaves are involved in a wide range of biological processes and metabolic pathways, including C4 photosynthesis and lignocellulose generation, which are important for cattle grazing and bioenergy production. The most abundant transcripts were involved in carbon fixation, photosynthesis, RNA translation and heavy metal cellular homeostasis. Finally, we identified a number of potential molecular markers, including 5,035 microsatellites (SSRs) and 346,456 single nucleotide polymorphisms (SNPs). To the best of our knowledge, this is the first study to characterize the complete leaf transcriptome of P. maximum using highthroughput sequencing. The biological information provided here will aid in gene expression studies and marker-assisted selection-based breeding research in tropical grasses.GUILHERME TOLEDO-SILVA, Molecular Biology Center and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.CLAUDIO BENICIO CARDOSO-SILVA, Molecular Biology Center and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, BrazilLIANA JANK, CNPGCANETE PEREIRA SOUZA, Molecular Biology Center and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, BrazilDepartment of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, São Paulo, BraziL.SILVA, G. T.SILVA, C. B. C.JANK, L.SOUZA, A. P.2014-02-27T11:11:11Z2014-02-27T11:11:11Z2014-02-2720132018-02-21T11:11:11Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePLOS ONE, v. 8, n. 7, p. 1-10, july 2013http://www.alice.cnptia.embrapa.br/alice/handle/doc/981465enginfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)instacron:EMBRAPA2017-08-16T00:55:33Zoai:www.alice.cnptia.embrapa.br:doc/981465Repositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestopendoar:21542017-08-16T00:55:33falseRepositório InstitucionalPUBhttps://www.alice.cnptia.embrapa.br/oai/requestcg-riaa@embrapa.bropendoar:21542017-08-16T00:55:33Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice) - Empresa Brasileira de Pesquisa Agropecuária (Embrapa)false
dc.title.none.fl_str_mv De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.
title De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.
spellingShingle De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.
SILVA, G. T.
Panicum maximum
Alimento animal
Graminea tropical
Carne
Beef cattle
Megathyrsus maximus
title_short De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.
title_full De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.
title_fullStr De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.
title_full_unstemmed De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.
title_sort De novo transcriptome assembly for the tropical grass Panicum maximum Jacq.
author SILVA, G. T.
author_facet SILVA, G. T.
SILVA, C. B. C.
JANK, L.
SOUZA, A. P.
author_role author
author2 SILVA, C. B. C.
JANK, L.
SOUZA, A. P.
author2_role author
author
author
dc.contributor.none.fl_str_mv GUILHERME TOLEDO-SILVA, Molecular Biology Center and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
CLAUDIO BENICIO CARDOSO-SILVA, Molecular Biology Center and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
LIANA JANK, CNPGC
ANETE PEREIRA SOUZA, Molecular Biology Center and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, São Paulo, BraziL.
dc.contributor.author.fl_str_mv SILVA, G. T.
SILVA, C. B. C.
JANK, L.
SOUZA, A. P.
dc.subject.por.fl_str_mv Panicum maximum
Alimento animal
Graminea tropical
Carne
Beef cattle
Megathyrsus maximus
topic Panicum maximum
Alimento animal
Graminea tropical
Carne
Beef cattle
Megathyrsus maximus
description Guinea grass (Panicum maximum Jacq.) is a tropical African grass often used to feed beef cattle, which is an important economic activity in Brazil. Brazil is the leader in global meat exportation because of its exclusively pasture-raised bovine herds. Guinea grass also has potential uses in bioenergy production due to its elevated biomass generation through the C4 photosynthesis pathway. We generated approximately 13 Gb of data from Illumina sequencing of P. maximum leaves. Four different genotypes were sequenced, and the combined reads were assembled de novo into 38,192 unigenes and annotated; approximately 63% of the unigenes had homology to other proteins in the NCBI non-redundant protein database. Functional classification through COG (Clusters of Orthologous Groups), GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses showed that the unigenes from Guinea grass leaves are involved in a wide range of biological processes and metabolic pathways, including C4 photosynthesis and lignocellulose generation, which are important for cattle grazing and bioenergy production. The most abundant transcripts were involved in carbon fixation, photosynthesis, RNA translation and heavy metal cellular homeostasis. Finally, we identified a number of potential molecular markers, including 5,035 microsatellites (SSRs) and 346,456 single nucleotide polymorphisms (SNPs). To the best of our knowledge, this is the first study to characterize the complete leaf transcriptome of P. maximum using highthroughput sequencing. The biological information provided here will aid in gene expression studies and marker-assisted selection-based breeding research in tropical grasses.
publishDate 2013
dc.date.none.fl_str_mv 2013
2014-02-27T11:11:11Z
2014-02-27T11:11:11Z
2014-02-27
2018-02-21T11:11:11Z
dc.type.driver.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv PLOS ONE, v. 8, n. 7, p. 1-10, july 2013
http://www.alice.cnptia.embrapa.br/alice/handle/doc/981465
identifier_str_mv PLOS ONE, v. 8, n. 7, p. 1-10, july 2013
url http://www.alice.cnptia.embrapa.br/alice/handle/doc/981465
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
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dc.source.none.fl_str_mv reponame:Repositório Institucional da EMBRAPA (Repository Open Access to Scientific Information from EMBRAPA - Alice)
instname:Empresa Brasileira de Pesquisa Agropecuária (Embrapa)
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