SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing

doi:10.1371/journal.pone.0087218

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	SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing
	Yu, Yang1,2 ; Wei, Jiankai1,2 ; Zhang, Xiaojun 1; Liu, Jingwen1,2 ; Liu, Chengzhang 1; Li, Fuhua 1; Xiang, Jianhai1 ; Li, FH (reprint author), Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Peoples R China.
	2014-01-30
发表期刊	PLOS ONE
卷号	9 期号:1 页码:e87218
文章类型	Article
摘要	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.
学科领域	Science & Technology - Other Topics
DOI	10.1371/journal.pone.0087218
收录类别	SCI
语种	英语
WOS记录号	WOS:000330617100062
引用统计	被引频次：40[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/24169
专题	实验海洋生物学重点实验室
通讯作者	Li, FH (reprint author), Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Peoples R China.
作者单位	1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China
第一作者单位	中国科学院海洋研究所
推荐引用方式 GB/T 7714	Yu, Yang,Wei, Jiankai,Zhang, Xiaojun,et al. SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing[J]. PLOS ONE,2014,9(1):e87218.
APA	Yu, Yang.,Wei, Jiankai.,Zhang, Xiaojun.,Liu, Jingwen.,Liu, Chengzhang.,...&Li, FH .(2014).SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing.PLOS ONE,9(1),e87218.
MLA	Yu, Yang,et al."SNP Discovery in the Transcriptome of White Pacific Shrimp Litopenaeus vannamei by Next Generation Sequencing".PLOS ONE 9.1(2014):e87218.

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