ArticlePloS one2014
SNP discovery in the transcriptome of white Pacific shrimp Litopenaeus vannamei by next generation sequencing.
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 35 papers.
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Who cites it
35 citing papers in PubMed.
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- Identification of SNPs in theInternational journal of molecular sciences · 2026Article
- Integrated omic techniques and their genomic features for invasive weeds.Functional & integrative genomics · 2023Review
- Genomic signatures of artificial selection in fecundity of Pacific white shrimp,Frontiers in genetics · 2022Article
- Genomic variants from RNA-seq for goats resistant or susceptible to gastrointestinal nematode infection.PloS one · 2021Article
- Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize.International journal of molecular sciences · 2020Article
- Comparative Analysis of Root Transcriptome Reveals Candidate Genes and Expression Divergence of Homoeologous Genes in Response to Water Stress in Wheat.Plants (Basel, Switzerland) · 2020Article
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- A high-throughput SNP discovery strategy for RNA-seq data.BMC genomics · 2019Article
- Identification of Single Nucleotide Polymorphisms Related to the Resistance Against Acute Hepatopancreatic Necrosis Disease in the Pacific White ShrimpFrontiers in genetics · 2019Article
- Single-molecule long-read sequencing facilitates shrimp transcriptome research.Scientific reports · 2018Article
- De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome.Scientific reports · 2018Article
- Identification of SNPs potentially related to immune responses and growth performance inPeerJ · 2018Article
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- Transcriptome analysis of Macrobrachium rosenbergii intestines under the white spot syndrome virus and poly (I:C) challenges.PloS one · 2018Article
- The State of "Frontiers in genetics · 2018Review
- Article
- Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares.Scientific data · 2017Article
- A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei.Scientific reports · 2017Article
- Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis.Marine biotechnology (New York, N.Y.) · 2017Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The application of next generation sequencing technology has greatly facilitated high throughput single nucleotide polymorphism (SNP) discovery and genotyping in genetic research. In the present study, SNPs were discovered based on two transcriptomes of Litopenaeus vannamei (L. vannamei) generated from Illumina sequencing platform HiSeq 2000. One transcriptome of L. vannamei was obtained through sequencing on the RNA from larvae at mysis stage and its reference sequence was de novo assembled. The data from another transcriptome were downloaded from NCBI and the reads of the two transcriptomes were mapped separately to the assembled reference by BWA. SNP calling was performed using SAMtools. A total of 58,717 and 36,277 SNPs with high quality were predicted from the two transcriptomes, respectively. SNP calling was also performed using the reads of two transcriptomes together, and a total of 96,040 SNPs with high quality were predicted. Among these 96,040 SNPs, 5,242 and 29,129 were predicted as non-synonymous and synonymous SNPs respectively. Characterization analysis of the predicted SNPs in L. vannamei showed that the estimated SNP frequency was 0.21% (one SNP per 476 bp) and the estimated ratio for transition to transversion was 2.0. Fifty SNPs were randomly selected for validation by Sanger sequencing after PCR amplification and 76% of SNPs were confirmed, which indicated that the SNPs predicted in this study were reliable. These SNPs will be very useful for genetic study in L. vannamei, especially for the high density linkage map construction and genome-wide association studies.
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