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

	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
刊名	MOLLUSCAN RESEARCH
	2013
卷号	33 期号:1 页码:65-73
关键词	microsatellite Bivalvia Ostreidae genomics large DNA insert library
ISSN号	1323-5818
通讯作者	Li, L
中文摘要	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.
英文摘要	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.
学科主题	Marine & Freshwater Biology ; Zoology
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Marine & Freshwater Biology ; Zoology
研究领域[WOS]	Marine & Freshwater Biology ; Zoology
关键词[WOS]	ARTIFICIAL CHROMOSOME LIBRARIES ; SCALLOP CHLAMYS-FARRERI ; ZHIKONG SCALLOP ; HUMAN GENOME ; INITIAL ANALYSIS ; REPEATS ; MICROSATELLITE ; DNA ; MUTATIONS ; GENES
收录类别	SCI
原文出处	10.1080/13235818.2012.754149
语种	英语
WOS记录号	WOS:000318168800008
公开日期	2014-07-17
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/16700]
专题	海洋研究所_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
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.