河南农业科学 ›› 2020, Vol. 49 ›› Issue (11): 147-152.DOI: 10.15933/j.cnki.1004-3268.2020.11.019

• 畜牧·兽医 • 上一篇    下一篇

基于RNA-seq技术的奥利亚罗非鱼转录组SSR位点信息分析

周康奇1,潘贤辉1,黄姻1,覃俊奇1,徐俊龙2,杜雪松1,文露婷1陈忠1,潘志忠1,邓潜1,林勇1   

  1. 1.广西壮族自治区水产科学研究院/广西水产遗传育种与健康养殖重点实验室/广西水产良种南繁基地,广西 南宁 530021;2.广西钦州农业学校,广西 钦州 535000)
  • 收稿日期:2020-05-24 出版日期:2020-11-15 发布日期:2020-11-15
  • 通讯作者: 林勇(1969-),男,广西玉林人,研究员,本科,主要从事水产动物遗传育种研究。E-mail:linnn2005@126.com
  • 作者简介:周康奇(1990-),女,贵州都匀人,实习研究员,硕士,主要从事水产动物遗传繁育与资源增殖研究。E-mail:2472797247@qq.com。潘贤辉为同等贡献作者
  • 基金资助:
    广西创新驱动发展专项(AA17204080-5)

Analysis of SSR Site Information in Transcriptome of Oreochromis aurea Based on RNA-seq

ZHOU Kangqi1,PAN Xianhui1,HUANG Yin1,QIN Junqi1,XU Junlong2,DU Xuesong1,WEN Luting1,CHEN Zhong1,PAN Zhizhong1,DENG Qian1,LIN Yong1   

  1. (1.Guangxi Academy of Fishery Sciences/Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture/Guangxi Aquatic Breeding Base,Nanning 530021,China; 2. Guangxi Qinzhou Agricultural School,Qinzhou 535000,China)

  • Received:2020-05-24 Published:2020-11-15 Online:2020-11-15

摘要: 为了开发奥利亚罗非鱼有关耐盐性的分子标记,采用二代测序RNA-seq方法,挖掘奥利亚罗非鱼的微卫星标记。结果显示,拼接组装获得了71 009条Unigenes,并在所有序列中共发现了10 875个SSR位点,含有位点序列的数量为8 315条,占总序列的11.71%。奥利亚罗非鱼转录组中SSR位点类型较为丰富,共识别到5种不同核苷酸重复类型和126种不同重复基序。其中,二核苷酸串联重复单元类型的含量最多(5 779个),占总位点数的53.14%;而在二核苷酸重复类型中AC/GT基序类型出现频率最高(3 954个,占36.36%)。此外,SSR位点以6次重复次数为主(3 048个),占总位点数的27.77% ;SSR位点序列长度分布于12~254 bp,其中具有高度多态性位点3 480个(占比29.14%),中等多态性位点8 462个(占比70.86%)。

关键词: 奥利亚罗非鱼, 转录组, 多态性, SSR位点信息, RNA-seq

Abstract: In order to develop molecular markers related to salt tolerance in Oreochromis aurea,the nextgeneration sequencing RNA-seq method was used to mine microsatellite tags in O.aurea.The results showed that a total of 71 009 unigenes were obtained by splicing and assembly,and a total of 10 875 SSR loci were found in all sequences.The number of sequences contained SSR loci was 8 315,accounting for 11.71% of the total sequences.There were many types of SSR loci in the transcriptome of O.aurea,and 5 different nucleotide repeat types and 126 different repeat motifs were recognized.Among them,the content of the dinucleotide tandem repeat unit type was the most,with 5 779,accounting for 53.14% of the total number of sites.And among dinucleotide repeat types AC/GT the motif type had the highest frequency(3 954 times,36.36%).In addition,SSR loci were dominated by 6 repetitions(3 048),accounting for 27.77% of the total number of loci;SSR loci sequence length was 12—254 bp,of which 3 480 loci were highly polymorphic(29.14%),and 8 462 loci were moderate polymorphic(70.86%).

Key words: Oreochromis aurea, Transcriptome, Polymorphism, SSR site information, RNA-seq

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