鳓鱼全基因组survey分析及微卫星位点分布  

Whole-genome analysis and microsatellite distribution of Ilisha elongata

作　　者：高鲁修 陈诗逸 冯桃波 刘炳舰 柳意樊 沈豪迪 黄文化 梁旭东 GAO Luxiu;CHEN Shiyi;FENG Taobo;LIU Bingjian;LIU Yifan;SHEN Haodi;HUANG Wenhua;LIANG Xudong(National Engineering Research Center for Marine Aquaculture,Zhejiang Ocean University,Zhoushan 316022,China;Marine Science and Technology College,Zhejiang Ocean University,Zhoushan 316022,China)

机构地区：[1]浙江海洋大学国家海洋设施养殖工程技术研究中心,浙江舟山316022 [2]浙江海洋大学海洋科学与技术学院,浙江舟山316022

出　　处：《水产科技情报》2024年第5期283-289,共7页Fisheries Science & Technology Information

基　　金：国家自然科学基金项目(41806156);国家级大学生创新创业训练计划项目(202110340031);浙江省自然科学基金项目(LY22D060001&LY20C190008);舟山市科技项目(2020C21016)。

摘　　要：为研究鳓鱼(Ilisha elongata)的遗传演化概况,对鳓鱼基因组进行了高通量测序并开展了survey分析和基因组范围内的遗传标记开发。K-mer分析结果显示,鳓鱼基因组大小约为692.8 Mb,杂合率为0.18%,重复序列比例为39.6%。基因组初步组装Scaffold N50为27694 bp,Contig N50为6306 bp。利用MISA软件对鳓鱼基因组的微卫星标记(simple sequence repeat,SSR)进行检索和分析,总共检测到786123个SSR位点,相对丰度为1204个/Mb。在所有类型中,重复最多的是二碱基,占SSR总量的75.94%,其SSR重复频率主要集中在6~28次;其次为单碱基和四碱基,分别占SSR总量的15.31%和4.25%。对二碱基类型而言,AC型具有最多的重复数量,为131732个,单碱基重复数量最多的则是A型,有48775个。研究结果表明,鳓鱼基因组经组装后可得到高质量的全基因组序列,经过筛选的SSR位点可为后续的遗传分子标记开发提供有力支持,研究结果可为鳓鱼种质资源管理和保护、生物进化和群体遗传等研究工作提供基础资料。To study the genetic evolutionary profile of Ilisha elongata,high-throughput sequencing was performed on the I.elongata genome,and survey analysis and genome-wide genetic marker development were conducted.Results showed that the genome size of I.elongata,as determined by K-mer analysis,was approximately 692.8 Mb,with a heterozygosity rate of 0.18%and the repeated sequence rate of 39.6%.The preliminary genome assembly results showed that the Scaffold N50 was 27694 bp and the Contig N50 was 6306 bp.The simple sequence repeats(SSRs)of I.elongata genome were searched and analyzed using MISA software,and a total of 786123 SSR loci were detected,with a relative abundance of 1204 per Mb.Among all types,dinucleotides were the most abundant repeats,which accounting for 75.94%of the total SSRs and the SSR repeat frequencies mainly concentrated between 6 and 28 times.This was followed by mononucleotide and tetranucleotide repeats,accounting for 15.31%and 4.25%of the total SSRs,respectively.For dinucleotide repeats,type AC had the highest number of repeats at 131732,while type A had the highest number of mononucleotide repeats at 48775.The results showed that the genome of I.elongata could be assembled to obtain high-quality whole genome sequences,and the SSR loci could provide strong support for the subsequent genetic molecular marker development,as well as basic information for research work on germplasm resource management and conservation,biological evolution and population genetics of I.elongata.

关 键 词：鳓鱼 全基因组survey 微卫星标记 高通量测序 生物遗传 

分 类 号：S917.4[农业科学—水产科学]