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

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	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
刊名	CHINESE JOURNAL OF OCEANOLOGY AND LIMNOLOGY
	2012-05-01
卷号	30 期号:3 页码:456-470
关键词	Litopenaeus vannamei BES repetitive sequences SSR genome survey
ISSN号	0254-4059
通讯作者	Zhang, XJ (reprint author), Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China.
英文摘要	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.
学科主题	Limnology ; Oceanography
收录类别	SCI
原文出处	10.1007/s00343-012-1159-y
语种	英语
WOS记录号	WOS:000303680400013
公开日期	2013-09-24
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/12289]
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 266071, Peoples R China 2.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China
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.,...&Huang Chao.(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.