ArticlePloS one2014
SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 22 citations in OpenAlex.
- Comparative Analysis of the Transcriptome and Distribution of Putative SNPs in Two Rainbow Trout (Genes · 2020Article
- Large-scale SNP screenings identify markers linked with GCRV resistant traits through transcriptomes of individuals and cell lines in Ctenopharyngodon idella.Scientific reports · 2017Article
- Genome-wide identification and functional analysis of S-RNase involved in the self-incompatibility of citrus.Molecular genetics and genomics : MGG · 2017Article
- Transcriptome assembly and identification of genes and SNPs associated with growth traits in largemouth bass (Micropterus salmoides).Genetica · 2017Article
- Transcriptome Analysis and Differential Gene Expression on the Testis of Orange Mud Crab, Scylla olivacea, during Sexual Maturation.PloS one · 2017Article
- Identification of Immune-Related Genes and Development of SSR/SNP Markers from the Spleen Transcriptome of Schizothorax prenanti.PloS one · 2016Article
- Transcriptional Profiling Reveals Differential Gene Expression of Amur Ide (Leuciscus waleckii) during Spawning Migration.International journal of molecular sciences · 2015Article
- RNA sequencing to study gene expression and SNP variations associated with growth in zebrafish fed a plant protein-based diet.Marine biotechnology (New York, N.Y.) · 2015Article
- Article
- Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation sequencing.PloS one · 2015Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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