De novo assembly and transcriptome analysis of contrasting sugarcane varieties.

Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated...

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Autores principales:	Claudio Benicio Cardoso-Silva, Estela Araujo Costa, Melina Cristina Mancini, Thiago Willian Almeida Balsalobre, Lucas Eduardo Costa Canesin, Luciana Rossini Pinto, Monalisa Sampaio Carneiro, Antonio Augusto Franco Garcia, Anete Pereira de Souza, Renato Vicentini
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5c8d85cd424f4ca4a691435f2be63bd6
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spelling	oai:doaj.org-article:5c8d85cd424f4ca4a691435f2be63bd62021-11-18T08:32:59ZDe novo assembly and transcriptome analysis of contrasting sugarcane varieties.1932-620310.1371/journal.pone.0088462https://doaj.org/article/5c8d85cd424f4ca4a691435f2be63bd62014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24523899/?tool=EBIhttps://doaj.org/toc/1932-6203Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.Claudio Benicio Cardoso-SilvaEstela Araujo CostaMelina Cristina ManciniThiago Willian Almeida BalsalobreLucas Eduardo Costa CanesinLuciana Rossini PintoMonalisa Sampaio CarneiroAntonio Augusto Franco GarciaAnete Pereira de SouzaRenato VicentiniPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e88462 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Claudio Benicio Cardoso-Silva Estela Araujo Costa Melina Cristina Mancini Thiago Willian Almeida Balsalobre Lucas Eduardo Costa Canesin Luciana Rossini Pinto Monalisa Sampaio Carneiro Antonio Augusto Franco Garcia Anete Pereira de Souza Renato Vicentini De novo assembly and transcriptome analysis of contrasting sugarcane varieties.
description	Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.
format	article
author	Claudio Benicio Cardoso-Silva Estela Araujo Costa Melina Cristina Mancini Thiago Willian Almeida Balsalobre Lucas Eduardo Costa Canesin Luciana Rossini Pinto Monalisa Sampaio Carneiro Antonio Augusto Franco Garcia Anete Pereira de Souza Renato Vicentini
author_facet	Claudio Benicio Cardoso-Silva Estela Araujo Costa Melina Cristina Mancini Thiago Willian Almeida Balsalobre Lucas Eduardo Costa Canesin Luciana Rossini Pinto Monalisa Sampaio Carneiro Antonio Augusto Franco Garcia Anete Pereira de Souza Renato Vicentini
author_sort	Claudio Benicio Cardoso-Silva
title	De novo assembly and transcriptome analysis of contrasting sugarcane varieties.
title_short	De novo assembly and transcriptome analysis of contrasting sugarcane varieties.
title_full	De novo assembly and transcriptome analysis of contrasting sugarcane varieties.
title_fullStr	De novo assembly and transcriptome analysis of contrasting sugarcane varieties.
title_full_unstemmed	De novo assembly and transcriptome analysis of contrasting sugarcane varieties.
title_sort	de novo assembly and transcriptome analysis of contrasting sugarcane varieties.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/5c8d85cd424f4ca4a691435f2be63bd6
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De novo assembly and transcriptome analysis of contrasting sugarcane varieties.

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