Fosmid library construction and end sequences analysis of the Pacific oyster, Crassostrea gigas

doi:10.1080/13235818.2012.754149

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	Fosmid library construction and end sequences analysis of the Pacific oyster, Crassostrea gigas
	Zhang, Linlin; Li, Li; Xu, Fei; Qi, Haigang; Wang, Xiaotong; Que, Huayong; Zhang, Guofan; Li, L
	2013
发表期刊	MOLLUSCAN RESEARCH
ISSN	1323-5818
卷号	33 期号:1 页码:65-73
文章类型	Article
摘要	The Pacific oyster (Crassostrea gigas) is globally distributed and is one of the most commercially and ecologically important marine organisms. However, little is known about the genome of this species. In this study, a C. gigas fosmid library was constructed that contains 459,936 clones with an average insert size of approximately 40 kb, representing 22.34-fold haploid genome equivalents. End sequencing generated 90,240 fosmid end sequences (FESs) with an average length of 384.27 base pairs (bp), covering approximately 2.58% of the Pacific oyster genome. The FESs were subsequently assembled and annotated, resulting in 6332 sequences with predicted open reading frames >= 300 and 1,189,100 bp repeats. Furthermore, a total of 3200 microsatellite repeats were identified, and dinucleotide repeats were found to occur most abundantly, with AG and AAT being the most abundant repeat class of dinucleotides and trinucleotides. We also found that the repeat number was generally negatively proportional to the repeat element length. Microsatellites composition between the transcribed sequences and genomic sequences was shown to be different. Point mutations of microsatellite were non-random and underwent strong selection stress. Overall, a comprehensive sequence resource for the Pacific oyster was created, including annotated transposable elements, tandem repeats, protein coding sequences and microsatellites. These initial findings will serve as resources for further in-depth studies of physical mapping, gene discovery, microsatellite marker developing and evolution studies.; The Pacific oyster (Crassostrea gigas) is globally distributed and is one of the most commercially and ecologically important marine organisms. However, little is known about the genome of this species. In this study, a C. gigas fosmid library was constructed that contains 459,936 clones with an average insert size of approximately 40 kb, representing 22.34-fold haploid genome equivalents. End sequencing generated 90,240 fosmid end sequences (FESs) with an average length of 384.27 base pairs (bp), covering approximately 2.58% of the Pacific oyster genome. The FESs were subsequently assembled and annotated, resulting in 6332 sequences with predicted open reading frames >= 300 and 1,189,100 bp repeats. Furthermore, a total of 3200 microsatellite repeats were identified, and dinucleotide repeats were found to occur most abundantly, with AG and AAT being the most abundant repeat class of dinucleotides and trinucleotides. We also found that the repeat number was generally negatively proportional to the repeat element length. Microsatellites composition between the transcribed sequences and genomic sequences was shown to be different. Point mutations of microsatellite were non-random and underwent strong selection stress. Overall, a comprehensive sequence resource for the Pacific oyster was created, including annotated transposable elements, tandem repeats, protein coding sequences and microsatellites. These initial findings will serve as resources for further in-depth studies of physical mapping, gene discovery, microsatellite marker developing and evolution studies.
关键词	Microsatellite Bivalvia Ostreidae Genomics Large Dna Insert Library
学科领域	Marine & Freshwater Biology ; Zoology
DOI	10.1080/13235818.2012.754149
URL	查看原文
收录类别	SCI
语种	英语
WOS研究方向	Marine & Freshwater Biology ; Zoology
WOS类目	Marine & Freshwater Biology ; Zoology
WOS记录号	WOS:000318168800008
WOS关键词	ARTIFICIAL CHROMOSOME LIBRARIES ; SCALLOP CHLAMYS-FARRERI ; ZHIKONG SCALLOP ; HUMAN GENOME ; INITIAL ANALYSIS ; REPEATS ; MICROSATELLITE ; DNA ; MUTATIONS ; GENES
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
引用统计
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/16700
专题	海洋生物技术研发中心
通讯作者	Li, L
作者单位	Chinese Acad Sci, Inst Oceanol, Qingdao 266071, Shandong, 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	Zhang, Linlin,Li, Li,Xu, Fei,et al. Fosmid library construction and end sequences analysis of the Pacific oyster, Crassostrea gigas[J]. MOLLUSCAN RESEARCH,2013,33(1):65-73.
APA	Zhang, Linlin.,Li, Li.,Xu, Fei.,Qi, Haigang.,Wang, Xiaotong.,...&Li, L.(2013).Fosmid library construction and end sequences analysis of the Pacific oyster, Crassostrea gigas.MOLLUSCAN RESEARCH,33(1),65-73.
MLA	Zhang, Linlin,et al."Fosmid library construction and end sequences analysis of the Pacific oyster, Crassostrea gigas".MOLLUSCAN RESEARCH 33.1(2013):65-73.

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