Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração
Autor(a) principal: | |
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Data de Publicação: | 2015 |
Tipo de documento: | Tese |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFG |
Texto Completo: | http://repositorio.bc.ufg.br/tede/handle/tede/4783 |
Resumo: | The sugarcane is one of the most important crop species to provide sugar and renewable energy in the world. Due to the high amount of repetitive elements and the various polyploidization events suffer during its evolution, the Saccharum spp. genome has not yet been assembled and annotated, unlike other agronomic important species. So, the knowledge about sugarcane transcriptome become even more useful for supporting genomic analyzes studies. A draft assembly of sugarcane transcriptome was obtained from Illumina sequencing paired-ends libraries of five different plant organs, sampled from thirty elite clones. Analyzes of quality control and normalization was done in the RNA-seq data. Trinity package was used for de novo assembly. The scaffolds obtained and identified as complete ORFs were annotated according to Gene Ontology terms. The draft assembly was characterized by the identification of microsatellites and SNPs molecular markers and for assessing the contribution of different plant organs for transcriptome final assembly. The draft sugarcane transcriptome comprised 178 Mb, over 131,831 scaffolds, representing 61,225 genes. The transcripts average size was 1,350 bp and N50 value was 1,667 bp. A total of 1,250 transcripts identified as complete ORFs showed no similarity to sequences of the nr NCBI database, are considered new Transcript Active Regions (nTARs). The annotation performed using the KEGG database identified 234 transcripts coding for enzymes members of sucrose and starch metabolism, an important metabolic pathway for understanding the relationship between photosynthetic rate and sucrose accumulation in the stalk. The five plant organs used contributed equally for the draft sugarcane transcriptome. A total of 12,931 genomic regions were identified containing perfect microsatellites, with a predominance of di and tri nucleotide. On average, one SNP every 18 bp was identified, with more than four million SNPs identified with satisfactory values of haplotype and quality scores. The nucleotide diversity of thirty elite clones used in this study was high. The identification of these molecular markers, particularly SNPs markers, provides the possibility of using these polymorphisms in genomic and genetic studies of sugarcane, including the possibility of application of genome wide selection like breeding strategy. The sugarcane transcriptome draft assembly proposed in this study has data and analysis quality sufficient to be used in attempt to encompass a reference transcriptome for the species of Saccharum spp. |
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Coelho, Alexandre Siqueira Guedeshttp://lattes.cnpq.br/0840926305216925Coelho, Alexandre Siqueira GuedesPappas Júnior, Georgios JoannisBorba, Tereza Cristina de OliveiraBrondani , CláudioNovaes, Evandrohttp://lattes.cnpq.br/5898950331344200Melo, Arthur Tavares de Oliveira2015-10-27T14:08:47Z2015-01-22MELO, A. T. O. Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração. 2015. 102 f. Tese (Doutorado em Genetica e Melhoramento de Plantas) - Universidade Federal de Goiás, Goiânia, 2015.http://repositorio.bc.ufg.br/tede/handle/tede/4783The sugarcane is one of the most important crop species to provide sugar and renewable energy in the world. Due to the high amount of repetitive elements and the various polyploidization events suffer during its evolution, the Saccharum spp. genome has not yet been assembled and annotated, unlike other agronomic important species. So, the knowledge about sugarcane transcriptome become even more useful for supporting genomic analyzes studies. A draft assembly of sugarcane transcriptome was obtained from Illumina sequencing paired-ends libraries of five different plant organs, sampled from thirty elite clones. Analyzes of quality control and normalization was done in the RNA-seq data. Trinity package was used for de novo assembly. The scaffolds obtained and identified as complete ORFs were annotated according to Gene Ontology terms. The draft assembly was characterized by the identification of microsatellites and SNPs molecular markers and for assessing the contribution of different plant organs for transcriptome final assembly. The draft sugarcane transcriptome comprised 178 Mb, over 131,831 scaffolds, representing 61,225 genes. The transcripts average size was 1,350 bp and N50 value was 1,667 bp. A total of 1,250 transcripts identified as complete ORFs showed no similarity to sequences of the nr NCBI database, are considered new Transcript Active Regions (nTARs). The annotation performed using the KEGG database identified 234 transcripts coding for enzymes members of sucrose and starch metabolism, an important metabolic pathway for understanding the relationship between photosynthetic rate and sucrose accumulation in the stalk. The five plant organs used contributed equally for the draft sugarcane transcriptome. A total of 12,931 genomic regions were identified containing perfect microsatellites, with a predominance of di and tri nucleotide. On average, one SNP every 18 bp was identified, with more than four million SNPs identified with satisfactory values of haplotype and quality scores. The nucleotide diversity of thirty elite clones used in this study was high. The identification of these molecular markers, particularly SNPs markers, provides the possibility of using these polymorphisms in genomic and genetic studies of sugarcane, including the possibility of application of genome wide selection like breeding strategy. The sugarcane transcriptome draft assembly proposed in this study has data and analysis quality sufficient to be used in attempt to encompass a reference transcriptome for the species of Saccharum spp.A cana-de-açúcar é uma das principais espécies cultivadas para o fornecimento mundial de açúcar e energia renovável. Devido à elevada quantidade de elementos repetitivos e os vários eventos de poliploidização, o genoma da espécie ainda não foi montado e anotado, diferentemente de outras espécies de interesse agronômico. Assim, as informações do transcritoma da espécie se tornam ainda mais úteis por dar suporte ás iniciativas de análises genômicas. Um draft assembly do transcritoma de cana-de-açúcar foi montado a partir do sequenciamento Illumina de bibliotecas paired-ends de cinco órgãos distintos da planta, obtidos de uma amostra de trinta clones elite. Os dados de RNA-seq passaram por análises de controle de qualidade e normalização. O software Trinity foi utilizado para montagem de novo do transcritoma. Os scaffolds obtidos identificados como ORFs completas foram anotados conforme os termos do Gene Ontology. O draft assembly obtido para o transcritoma de cana-de-açúcar foi caracterizado pela identificação de marcadores moleculares do tipo microssatélites e SNPs e pela avaliação da contribuição dos diferentes órgãos vegetais para constituição final do transcritoma. O transcritoma obtido compreendeu 178 Mb, distribuídos em 131.831 scaffolds, representando 61.225 genes. O tamanho médio dos transcritos foi de 1.350 pb, com valor de N50 igual a 1.667 pb. Um total de 1.250 transcritos, identificados como ORFs completas, não apresentaram similaridade com sequências do banco de dados nr do NCBI, sendo considerados novas regiões transcricionalmente ativas (nTARs). A anotação realizada através do banco de dados do KEGG identificou 234 transcritos codificantes para enzimas integrantes do metabolismo de sacarose e amido, uma importante rota metabólica para compreensão da relação entre taxa fotossintética e o acúmulo de sacarose no colmo. Os cinco órgãos vegetais utilizados contribuíram igualmente para a constituição do draft do transcritoma de cana-de-açúcar. Foram identificadas 12.931 regiões genômicas contendo microssatélites perfeitos, com predomínio de di e tri nucleotídeos. Em média, identificou-se um SNP a cada 18 pares de bases, com mais de quatro milhões de SNPs identificados. A diversidade nucleotídica dos trinta clones elites utilizados é elevada. A identificação destes marcadores moleculares, principalmente os marcadores SNPs, fornece a possibilidade de utilização destes polimorfismos em estudos genéticos e genômicos de cana-de-açúcar, incluindo o emprego em abordagens como seleção genômica ampla no melhoramento da espécie. O draft assembly do transcritoma de cana-de-açúcar proposto neste estudo possui qualidade de dados e de análise suficiente para ser utilizado na tentativa de abranger um transcritoma de referência para as espécies de Saccharum spp.Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2015-10-27T13:50:34Z No. of bitstreams: 2 Tese - Arthur Tavares de Oliveira Melo - 2015.pdf: 5375267 bytes, checksum: 306e8d72c2977068f8f669824b83ca4b (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5)Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2015-10-27T14:08:47Z (GMT) No. of bitstreams: 2 Tese - Arthur Tavares de Oliveira Melo - 2015.pdf: 5375267 bytes, checksum: 306e8d72c2977068f8f669824b83ca4b (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5)Made available in DSpace on 2015-10-27T14:08:47Z (GMT). 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dc.title.por.fl_str_mv |
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração |
dc.title.alternative.eng.fl_str_mv |
Assembly and characterization of sugarcane (Saccharum spp.) transcriptome using next generation sequencing data |
title |
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração |
spellingShingle |
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração Melo, Arthur Tavares de Oliveira Saccharum spp. Transcritoma Trinity RNA-seq Saccharum spp. Transcriptome RNA-seq Trinity CIENCIAS AGRARIAS::AGRONOMIA |
title_short |
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração |
title_full |
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração |
title_fullStr |
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração |
title_full_unstemmed |
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração |
title_sort |
Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração |
author |
Melo, Arthur Tavares de Oliveira |
author_facet |
Melo, Arthur Tavares de Oliveira |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Coelho, Alexandre Siqueira Guedes |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/0840926305216925 |
dc.contributor.referee1.fl_str_mv |
Coelho, Alexandre Siqueira Guedes |
dc.contributor.referee2.fl_str_mv |
Pappas Júnior, Georgios Joannis |
dc.contributor.referee3.fl_str_mv |
Borba, Tereza Cristina de Oliveira |
dc.contributor.referee4.fl_str_mv |
Brondani , Cláudio |
dc.contributor.referee5.fl_str_mv |
Novaes, Evandro |
dc.contributor.authorLattes.fl_str_mv |
http://lattes.cnpq.br/5898950331344200 |
dc.contributor.author.fl_str_mv |
Melo, Arthur Tavares de Oliveira |
contributor_str_mv |
Coelho, Alexandre Siqueira Guedes Coelho, Alexandre Siqueira Guedes Pappas Júnior, Georgios Joannis Borba, Tereza Cristina de Oliveira Brondani , Cláudio Novaes, Evandro |
dc.subject.por.fl_str_mv |
Saccharum spp. Transcritoma Trinity RNA-seq |
topic |
Saccharum spp. Transcritoma Trinity RNA-seq Saccharum spp. Transcriptome RNA-seq Trinity CIENCIAS AGRARIAS::AGRONOMIA |
dc.subject.eng.fl_str_mv |
Saccharum spp. Transcriptome RNA-seq Trinity |
dc.subject.cnpq.fl_str_mv |
CIENCIAS AGRARIAS::AGRONOMIA |
description |
The sugarcane is one of the most important crop species to provide sugar and renewable energy in the world. Due to the high amount of repetitive elements and the various polyploidization events suffer during its evolution, the Saccharum spp. genome has not yet been assembled and annotated, unlike other agronomic important species. So, the knowledge about sugarcane transcriptome become even more useful for supporting genomic analyzes studies. A draft assembly of sugarcane transcriptome was obtained from Illumina sequencing paired-ends libraries of five different plant organs, sampled from thirty elite clones. Analyzes of quality control and normalization was done in the RNA-seq data. Trinity package was used for de novo assembly. The scaffolds obtained and identified as complete ORFs were annotated according to Gene Ontology terms. The draft assembly was characterized by the identification of microsatellites and SNPs molecular markers and for assessing the contribution of different plant organs for transcriptome final assembly. The draft sugarcane transcriptome comprised 178 Mb, over 131,831 scaffolds, representing 61,225 genes. The transcripts average size was 1,350 bp and N50 value was 1,667 bp. A total of 1,250 transcripts identified as complete ORFs showed no similarity to sequences of the nr NCBI database, are considered new Transcript Active Regions (nTARs). The annotation performed using the KEGG database identified 234 transcripts coding for enzymes members of sucrose and starch metabolism, an important metabolic pathway for understanding the relationship between photosynthetic rate and sucrose accumulation in the stalk. The five plant organs used contributed equally for the draft sugarcane transcriptome. A total of 12,931 genomic regions were identified containing perfect microsatellites, with a predominance of di and tri nucleotide. On average, one SNP every 18 bp was identified, with more than four million SNPs identified with satisfactory values of haplotype and quality scores. The nucleotide diversity of thirty elite clones used in this study was high. The identification of these molecular markers, particularly SNPs markers, provides the possibility of using these polymorphisms in genomic and genetic studies of sugarcane, including the possibility of application of genome wide selection like breeding strategy. The sugarcane transcriptome draft assembly proposed in this study has data and analysis quality sufficient to be used in attempt to encompass a reference transcriptome for the species of Saccharum spp. |
publishDate |
2015 |
dc.date.accessioned.fl_str_mv |
2015-10-27T14:08:47Z |
dc.date.issued.fl_str_mv |
2015-01-22 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.citation.fl_str_mv |
MELO, A. T. O. Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração. 2015. 102 f. Tese (Doutorado em Genetica e Melhoramento de Plantas) - Universidade Federal de Goiás, Goiânia, 2015. |
dc.identifier.uri.fl_str_mv |
http://repositorio.bc.ufg.br/tede/handle/tede/4783 |
identifier_str_mv |
MELO, A. T. O. Montagem e caracterização do transcritoma de cana-de-açúcar (saccharum spp.) utilizando dados de sequenciamento de nova geração. 2015. 102 f. Tese (Doutorado em Genetica e Melhoramento de Plantas) - Universidade Federal de Goiás, Goiânia, 2015. |
url |
http://repositorio.bc.ufg.br/tede/handle/tede/4783 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.relation.program.fl_str_mv |
1167494949003462214 |
dc.relation.confidence.fl_str_mv |
600 600 600 600 |
dc.relation.department.fl_str_mv |
4500684695727928426 |
dc.relation.cnpq.fl_str_mv |
-3091138714907603907 |
dc.relation.sponsorship.fl_str_mv |
2075167498588264571 |
dc.rights.driver.fl_str_mv |
http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
http://creativecommons.org/licenses/by-nc-nd/4.0/ |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Universidade Federal de Goiás |
dc.publisher.program.fl_str_mv |
Programa de Pós-graduação em Genetica e Melhoramentode Plantas |
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UFG |
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Brasil |
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Escola de Agronomia e Engenharia de Alimentos - EAEA (RG) |
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Universidade Federal de Goiás |
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