紫石房蛤高通量转录组文库测序和分子标记开发
发布时间：2019-06-16 18:37
【摘要】：紫石房蛤,是一种海洋双壳贝类,分布在中国,日本和韩国的周边地区。由于它的高营养和经济价值,使它成为一种重要的经济海产品。近年来,由于过度捕捞和环境恶化,紫石房蛤的自然资源一直呈下降趋势,为了保护野生群体,开发和利用分子标记对紫石房蛤野生群体进行遗传分析是必要的。在本研究中,我们通过Illumina Hiseq 2500测序平台对紫石房蛤的鳃进行转录组文库测序,旨在获得转录组数据开发分子标记,为这个物种遗传多样性分析和分子标记辅助育种奠定基础。在测序报告中,我们获得了100,480,000条原始读段,去除低质量序列、rRNA和接头序列后,得到68,080,636条干净读段。利用这些读段进行组装,共获得到了5,115,494条重叠群,120,479条转录本和66,388条unigenes。通过与NCBI数据库进行比对,一共有26,781条unigenes被注释。利用生物信息学软件,从转录组数据库的66,388条unigene序列中进行筛选获得414个微卫星序列,其中二碱基重复135个,三碱基重复217个,四碱基重复58个,分别占微卫星序列总数的32.6%,52.4%和14%。随机选取35个微卫星序列设计引物,26个引物扩增出目的产物,利用30个紫石房蛤个体检测微卫星的多态性,其中13个证明有多态性位点。进一步结果分析显示等位基因从3到6不等,平均每个位点4.69个等位基因;观测杂合度和期望杂合度为0.4667-0.6667和0.5847-0.8322,没有观察到连锁不平衡位点(LD);2个位点显著偏离哈迪温伯格平衡(PHWE0.01)。转录组测序平台展示了对紫石房蛤物种快速开发分子资源的能力。这些新的多态性微卫星标记对进一步的种群研究和保护遗传学提供基础资料。
[Abstract]:Purple clam, a kind of marine bivalve shellfish, is distributed in the surrounding areas of China, Japan and South Korea. Because of its high nutrition and economic value, it has become an important economic seafood. In recent years, due to overfishing and environmental deterioration, the natural resources of clam have been declining. In order to protect the wild population, it is necessary to develop and use molecular markers to carry out genetic analysis of the wild population of clam. In this study, we sequenced the Gill of clam by Illumina Hiseq 2500 sequencing platform in order to obtain the data of transcriptional group and develop molecular markers, which laid a foundation for genetic diversity analysis and molecular marker assisted breeding of this species. In the sequencing report, 100480000 original reading segments were obtained, and 68080636 clean reading segments were obtained after removing low quality sequences, rRNA and connector sequences. Using these reading segments to assemble, a total of 5115494 overlapping groups, 120479 transcripts and 66388 unigenes. were obtained. Compared with the NCBI database, a total of 26781 unigenes have been commented on. Using bioinformatics software, 414 microsatellite sequences were screened from 66388 unigene sequences in the transcriptional group database, including two base repeats, three base repeats and 58 four base repeats, accounting for 32.6%, 52.4% and 14% of the total microsatellite sequences, respectively. Thirty-five microsatellite sequences were randomly selected to design primers, and 26 primers were used to amplify the target products. The microsatellite polymorphism was detected by 30 individuals of the clam, 13 of which proved to have polymorphism sites. The further results showed that the alleles varied from 3 to 6, with an average of 4.69 alleles per locus, and the heterozygosity and expected heterozygosity were 0.467 鈮，
本文编号：2500742
[Abstract]:Purple clam, a kind of marine bivalve shellfish, is distributed in the surrounding areas of China, Japan and South Korea. Because of its high nutrition and economic value, it has become an important economic seafood. In recent years, due to overfishing and environmental deterioration, the natural resources of clam have been declining. In order to protect the wild population, it is necessary to develop and use molecular markers to carry out genetic analysis of the wild population of clam. In this study, we sequenced the Gill of clam by Illumina Hiseq 2500 sequencing platform in order to obtain the data of transcriptional group and develop molecular markers, which laid a foundation for genetic diversity analysis and molecular marker assisted breeding of this species. In the sequencing report, 100480000 original reading segments were obtained, and 68080636 clean reading segments were obtained after removing low quality sequences, rRNA and connector sequences. Using these reading segments to assemble, a total of 5115494 overlapping groups, 120479 transcripts and 66388 unigenes. were obtained. Compared with the NCBI database, a total of 26781 unigenes have been commented on. Using bioinformatics software, 414 microsatellite sequences were screened from 66388 unigene sequences in the transcriptional group database, including two base repeats, three base repeats and 58 four base repeats, accounting for 32.6%, 52.4% and 14% of the total microsatellite sequences, respectively. Thirty-five microsatellite sequences were randomly selected to design primers, and 26 primers were used to amplify the target products. The microsatellite polymorphism was detected by 30 individuals of the clam, 13 of which proved to have polymorphism sites. The further results showed that the alleles varied from 3 to 6, with an average of 4.69 alleles per locus, and the heterozygosity and expected heterozygosity were 0.467 鈮，
本文编号：2500742
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