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基于高通量测序的虾夷扇贝基因组微卫星特征分析
倪守胜1,2,3, 杨 钰1,2,4, 柳淑芳1,2, 庄志猛1
1.农业部海洋渔业可持续发展重点实验室 中国水产科学研究院黄海水产研究所 青岛 266071;2.青岛海洋科学与技术国家实验室 海洋渔业科学与食物产出过程功能实验室 青岛 266071;3.上海海洋大学水产与生命学院 上海 201306;4.大连海洋大学水产与生命学院 大连 116023
摘要:
为全面了解虾夷扇贝(Patinopecten yessoensis)微卫星分布频率和数量,深化对虾夷扇贝基因组的认识,本研究运用第二代高通量测序技术,进行虾夷扇贝简化基因组测序(RAD-seq),从基因组水平阐明虾夷扇贝基因组微卫星特征。结果显示,简化基因组测序共获得序列总长为92,551,435 bp,经过滤筛选,获得259,535个contig,其中,包含微卫星序列3618条,经引物设计共获得3460对微卫星引物。统计微卫星序列的重复类型,其中,三核苷酸重复单元数量最多(1587个,45.87%),其次是二核苷酸重复(1282个,37.05%),六核苷酸重复单元数量最少(20个,0.58%)。在三核苷酸重复中,以ATA重复类型所占比例最高(11.41%),共计181个。此外,虾夷扇贝同一重复类型的微卫星随着重复数增加其数量相对减少,而相同重复数的微卫星随着重复单元长度的增加其数量也呈下降趋势,可见微卫星长度与其数量呈负相关,表明长度较短的微卫星变异速率较快。本研究结果为认识虾夷扇贝基因组特征和在基因组水平开展种群遗传学研究提供了基础数据。
关键词:  虾夷扇贝  二代测序  基因组  微卫星
DOI:
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Microsatellite Analysis of Patinopecten yessoensis Using Next-Generation Sequencing Method
NI Shousheng1,2,3, YANG Yu1,2,4, LIU Shufang1,2, ZHUANG Zhimeng1
1.Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071;2.Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071;3.College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306;4.College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023
Abstract:
Microsatellite has become an important molecular marker for genetic diversity analysis and marker-assisted breeding as its unique advantages, such as high stability and repeatability, strong specificity and codominance. To understand the distribution and frequency of microsatellite of P. yessoensis genome, the current study analyzed the microsatellite sequences of P. yessoensis genome by establishing and sequencing a RAD library. The sequences were assembled, and SSRs were detected by bioinformatics method. The total length of the DNA sequences of P. yessoensis genome is 92,551,435 bp and 3,618 contigs from all filtered 259,535 contigs containing SSR sequences. The 3460 potential SSR loci were identified with the number of repeat motif from 2 to 6 using appropriate amplifying primers. A total of 1587 trinucleotide SSRs (45.87%) were the most common motif, and ATA (11.41% of whole trinucleotide motifs) was the richest motif. The dinucleotide and the tetranucleotide types ranked the second and the third with a proportion of 37.05%(1282) and 14.48%(501), respectively, while the pentanucleotide type accounted for 2.02%(70), and the hexanucleotide type was the least amount with a proportion of 0.58%(20). Interestingly, the abundance of microsatellites of the same repeat type decreased with the increase of copy number, and the abundance of microsatellites of the same copy number decreased with the increase of the repeat unit length. The variation of length distribution frequency, copy numbers and the abundance of the microsatellite suggested that the mutation rate of shorter repeats was larger than that of the longer repeats. These results provide basic information of microsatellite of P. yessoensis, which would be useful to study the genome and population genetics of P. yessoensis.
Key words:  Patinopecten yessoensis  Next-generation sequencing  Genomes  Microsatellite