SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies in many species. High-throughput sequencing of RNA was developed primarily to analyze global gene expression, while it is an efficient way to discover SNPs from the expressed genes. In this st...

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Autores principales:	Jun Cui, Hongdi Wang, Shikai Liu, Lifu Zhu, Xuemei Qiu, Zhiqiang Jiang, Xiuli Wang, Zhanjiang Liu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/ac4643fec78f4ffda5b859682ea46247
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spelling	oai:doaj.org-article:ac4643fec78f4ffda5b859682ea462472021-11-18T08:26:59ZSNP discovery from transcriptome of the swimbladder of Takifugu rubripes.1932-620310.1371/journal.pone.0092502https://doaj.org/article/ac4643fec78f4ffda5b859682ea462472014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24651578/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies in many species. High-throughput sequencing of RNA was developed primarily to analyze global gene expression, while it is an efficient way to discover SNPs from the expressed genes. In this study, we conducted transcriptome sequencing of the swimbladder of Takifugu rubripes using Illumina HiSeq2000 platform to identify gene-associated SNPs in the swimbladder. A total of 30,312,181 unique-mapped-reads were obtained from 44,736,850 raw reads. A total of 62,270 putative SNPs were discovered, which were located in 11,306 expressed genes and 2,246 scaffolds. The average minor allele frequency (MAF) of the SNPs was 0.26. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Validation of selected SNPs revealed that 54% of SNPs (26/48) were true SNPs. The results suggest that RNA-Seq is an efficient and cost-effective approach to discover gene-associated SNPs. In this study, a large number of SNPs were identified and these data will be useful resources for population genetic study, evolution analysis, resource assessment, genetic linkage analysis and genome-wide association studies.Jun CuiHongdi WangShikai LiuLifu ZhuXuemei QiuZhiqiang JiangXiuli WangZhanjiang LiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 3, p e92502 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jun Cui Hongdi Wang Shikai Liu Lifu Zhu Xuemei Qiu Zhiqiang Jiang Xiuli Wang Zhanjiang Liu SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.
description	Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies in many species. High-throughput sequencing of RNA was developed primarily to analyze global gene expression, while it is an efficient way to discover SNPs from the expressed genes. In this study, we conducted transcriptome sequencing of the swimbladder of Takifugu rubripes using Illumina HiSeq2000 platform to identify gene-associated SNPs in the swimbladder. A total of 30,312,181 unique-mapped-reads were obtained from 44,736,850 raw reads. A total of 62,270 putative SNPs were discovered, which were located in 11,306 expressed genes and 2,246 scaffolds. The average minor allele frequency (MAF) of the SNPs was 0.26. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Validation of selected SNPs revealed that 54% of SNPs (26/48) were true SNPs. The results suggest that RNA-Seq is an efficient and cost-effective approach to discover gene-associated SNPs. In this study, a large number of SNPs were identified and these data will be useful resources for population genetic study, evolution analysis, resource assessment, genetic linkage analysis and genome-wide association studies.
format	article
author	Jun Cui Hongdi Wang Shikai Liu Lifu Zhu Xuemei Qiu Zhiqiang Jiang Xiuli Wang Zhanjiang Liu
author_facet	Jun Cui Hongdi Wang Shikai Liu Lifu Zhu Xuemei Qiu Zhiqiang Jiang Xiuli Wang Zhanjiang Liu
author_sort	Jun Cui
title	SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.
title_short	SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.
title_full	SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.
title_fullStr	SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.
title_full_unstemmed	SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.
title_sort	snp discovery from transcriptome of the swimbladder of takifugu rubripes.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/ac4643fec78f4ffda5b859682ea46247
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SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.

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