BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp

doi:10.1007/s00343-012-1159-y

IOCAS-IR > 实验海洋生物学重点实验室

	BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp
	Zhao Cui 1,2; Zhang Xiaojun 1; Liu Chengzhang 1; Huan Pin 1; Li Fuhua 1; Xiang Jianhai1 ; Huang Chao1,2 ; Zhang, XJ (reprint author), Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China.
	2012-05-01
发表期刊	CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY
ISSN	0254-4059
卷号	30 期号:3 页码:456-470
文章类型	Article
摘要	Little is known about the genome of Pacific white shrimp (Litopenaeus vannamei). To address this, we conducted BAC (bacterial artificial chromosome) end sequencing of L. vannamei. We selected and sequenced 7 812 BAC clones from the BAC library LvHE from the two ends of the inserts by Sanger sequencing. After trimming and quality filtering, 11 279 BAC end sequences (BESs) including 4 609 pairedends BESs were obtained. The total length of the BESs was 4 340 753 bp, representing 0.18% of the L. vannamei haploid genome. The lengths of the BESs ranged from 100 bp to 660 bp with an average length of 385 bp. Analysis of the BESs indicated that the L. vannamei genome is AT-rich and that the primary repeats patterns were simple sequence repeats (SSRs) and low complexity sequences. Dinucleotide and hexanucleotide repeats were the most common SSR types in the BESs. The most abundant transposable element was gypsy, which may contribute to the generation of the large genome size of L. vannamei. We successfully annotated 4 519 BESs by BLAST searching, including genes involved in immunity and sex determination. Our results provide an important resource for functional gene studies, map construction and integration, and complete genome assembly for this species.
关键词	Litopenaeus Vannamei Bes Repetitive Sequences Ssr Genome Survey
学科领域	Limnology ; Oceanography
DOI	10.1007/s00343-012-1159-y
URL	查看原文
收录类别	SCI
语种	英语
WOS记录号	WOS:000303680400013
引用统计	被引频次：12[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/337002/12289
专题	实验海洋生物学重点实验室
通讯作者	Zhang, XJ (reprint author), Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China.
作者单位	1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
第一作者单位	实验海洋生物学重点实验室
推荐引用方式 GB/T 7714	Zhao Cui,Zhang Xiaojun,Liu Chengzhang,et al. BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp[J]. CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY,2012,30(3):456-470.
APA	Zhao Cui.,Zhang Xiaojun.,Liu Chengzhang.,Huan Pin.,Li Fuhua.,...&Zhang, XJ .(2012).BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp.CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY,30(3),456-470.
MLA	Zhao Cui,et al."BAC end sequencing of Pacific white shrimp Litopenaeus vannamei: a glimpse into the genome of Penaeid shrimp".CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY 30.3(2012):456-470.

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