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

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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, Jingwen 1,2; Liu, Chengzhang 1; Li, Fuhua 1; Xiang, Jianhai1
刊名	PLOS ONE
	2014-01-30
卷号	9 期号:1 页码:e87218
通讯作者	Li, FH (reprint author), Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Peoples R China.
英文摘要	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.
学科主题	Science & Technology - Other Topics
收录类别	SCI
语种	英语
WOS记录号	WOS:000330617100062
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/24169]
专题	海洋研究所_实验海洋生物学重点实验室
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
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.,...&Xiang, Jianhai.(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.