文章摘要
基于全长转录组测序的金乌贼(Sepia esculenta)微卫星位点筛选与特征分析?
Microsatellite Screening and Characterization Analysis of Sepia esculenta Based on Full-length Transcriptome Sequencing
投稿时间:2019-06-26  修订日期:2019-09-27
DOI:
中文关键词: 金乌贼  转录组  SSR  重复基元  位点信息
英文关键词: Sepia esculenta  Transcriptome  SSR  Repeat motif  Loci information
基金项目:国家自然科学基金项目,中央级公益性科研院所基本科研业务费专项基金,山东省泰山学者专项基金
作者单位E-mail
张金勇 中国水产科学研究院 黄海水产研究所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潍坊学院现代设施渔业研究院山东省银鲑鱼健康养殖工程技术协同创新中心 njarghhs@126.com 
何暮春 中国海洋大学 海洋生命学院  
项子龙 中国水产科学研究院 黄海水产研究所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上海海洋大学 水产与生命学院  
柳淑芳 中国水产科学研究院 黄海水产研究所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南京农业大学 无锡渔业学院 liusf@ysfri.ac.cn 
庄志猛 中国水产科学研究院 黄海水产研究所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南京农业大学 无锡渔业学院  
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中文摘要:
      以金乌贼转录组测序获得的 177,951 条 Unigene 为对象,采用 Micro Satellite (MISA) 软件检测与分析其中的简单重复序列 (simple sequence repeat,SSR)位点信息。结果显示,在金乌贼转录组中共检测出 161,327 个 SSR 位点,分布在 64,933 条 Unigene 中,SSR 位点发生频率为 36.49%,出现频率为 90. 66%。其中,最主要的重复类型为单核苷酸、二核苷酸和三核苷酸分别占 SSR 总数的 46.00%、39.93%和 9.48%。 SSR 所包含的重复基元中, A/T是单核苷酸的优势重复基元,AT/AT 和 AC/GT是二核苷酸的优势重复基元类型。有66,004 个重复基元长度≥20bp,占 SSR 总数的 40. 91%,并且其中含有低级基元 (二、三核苷酸重复) SSR 位点数量占优。以上结果表明,金乌贼转录组中 SSR 位点出现频率较高且类型丰富、多态性潜能较高,研究结果为更好的开发金乌贼 SSR 分子标记和开展金乌贼种质资源保护利用、遗传多样性评价和未来分子标记辅助育种等提供了有力参考。
英文摘要:
      The golden cuttlefish, Sepia esculenta Hoyle, 1885, is an important fishery species endemic to the Northwest Pacific, inhabiting the coasts of China, south of Hokkaido in Japan, Southwest coasts of Korea and Philippines. As an economically important cephalopods species, wild-caught S. esculenta fishery has suffered a server decline due to over-fishing and ocean environmental damage. To better protect the resource of S. esculenta, we need to understand its population genetic structure. Microsatellites has become an important molecular marker for genetic diversity and marker-assisted breeding as its unique advantages, such as the abundant polymorphism, the rich information, the co-dominance and conservation. In this study, 177,951 Unigenes obtained by transcriptome sequencing of the golden cuttlefish were used to detect and analyze the simple sequence repeat (SSR) loci information using Micro Satellite (MISA) software. The results showed that 161,327 SSR loci were detected in the transcriptome of S. esculenta, which distributed in 64,933 Unigenes with a distribution frequency of SSR loci of 36.49%, and the frequency of occurrence was 90.66%. Among them, the main types of repeats were mononucleotide, dinucleotides and trinucleotides, which accounted for 46.00%, 39.93% and 9.48% of the total SSR, respectively. Among the repeat motifs contained in the SSR, A/T was the predominant repeat types of a mononucleotide, and AT/AT and AC/GT were the dominant repeat types of dinucleotides. There were 66,004 repeat motifs with a length of ≥20bp, accounting for 40.91% of the total number of SSRs, and the number of SSR loci in which low-level motifs (di- and tri- nucleotide repeats) are dominant. The above results indicated that the SSR loci in the transcriptome of golden cuttlefish had a high frequency and a rich variety and high polymorphic potential. The results provided a powerful reference for the better development of SSR molecular markers and the protection and utilization of S. esculenta germplasm resources, genetic diversity evaluation and future molecular marker-assisted breeding.
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