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

• Published in: Molluscan Research
• Main Authors: Zhang, Linlin, Li, Li, Xu, Fei, Qi, Haigang, Wang, Xiaotong, Que, Huayong, Zhang, Guofan, Li, L
• Format: Article in Journal/Newspaper
• Language: English
• Published: 2013
• Subjects: Microsatellite; Bivalvia; Ostreidae; Genomics; Large Dna Insert Library; Marine & Freshwater Biology; Zoology; Science & Technology; Life Sciences & Biomedicine; ARTIFICIAL CHROMOSOME LIBRARIES; SCALLOP CHLAMYS-FARRERI; ZHIKONG SCALLOP; HUMAN GENOME; INITIAL ANALYSIS; REPEATS; DNA; MUTATIONS; GENES; Pacific; Crassostrea gigas; Pacific oyster
• Online Access: http://ir.qdio.ac.cn/handle/337002/16700; https://doi.org/10.1080/13235818.2012.754149

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) ...