基于焦河蓝蛤全长转录组的SSR位点筛选及特征分析  

SSR screening and characterization analysis based on full-length transcriptome sequencing of Potamocorbula ustulate

作　　者：吴明钰 姜波 何京 何琳[1] 林志华 WU Mingyu;JIANG Bo;HE Jing;HE Lin;LIN Zhihua(Zhejiang Key Laboratory of Aquatic Germplasm Resources,College of Biological&Environmental Sciences,Zhejiang Wanli University,Ningbo Zhejiang 315100,China;Ninghai Marine Biological Seed Industry Research Institute,Zhejiang Wanli University,Ninghai Zhejiang 315604,China)

机构地区：[1]浙江万里学院生物与环境学院,浙江省水产种质资源高效利用技术研究重点实验室,浙江宁波315100 [2]浙江万里学院宁海海洋生物种业研究院,浙江宁海315604

出　　处：《海洋渔业》2024年第3期316-324,共9页Marine Fisheries

基　　金：浙江省重点研发计划(2022C02027);浙江省“三农九方”农业科技协作计划项目(2022SNJF063);宁波市公益性科技计划项目(2022S164)。

摘　　要：为了全面了解焦河蓝蛤(Potamocorbula ustulata)转录组中SSR的分布特点,充分开发SSR分子标记用于实践,使用Illumina RNA-Seq技术和SMRT技术对焦河蓝蛤进行全长转录组测序,利用MISA软件筛选并分析SSR位点的分布规律及组成特征。结果显示:基于焦河蓝蛤全长转录组测序共获得38964条Unigenes,其中有4746个SSR位点,分布于3962条Unigenes,平均每11.33 kb出现一个SSR位点。SSR的主要重复类型为单核苷酸、二核苷酸和三核苷酸,分别占总数的47.64%、13.7%、23.56%,其中A/T为单核苷酸的优势重复类型,AT/TA为二核苷酸的优势重复类型,表明焦河蓝蛤转录组SSR位点分布对A/T具有偏好性。SSR位点以重复5~10次为主(2951个),占总数的62.18%,长度大部分集中在12~20 bp,占总数的42.58%。长度大于20 bp的占11.53%,且以含有低级重复基元(二、三核苷酸重复)的SSR位点为主。研究表明,焦河蓝蛤转录组中SSR位点类型丰富、多态性较高。研究结果为进一步开展焦河蓝蛤SSR分子标记研究、遗传多样性评价、种质资源利用等奠定了基础。The paper is to comprehensively understand the distribution characteristics of SSR in the transcriptome of Potamocorbula ustulata,and to fully develop SSR molecular markers for practical use.P.ustulata,a kind of small type shellfish,is widely distributed in China’s estuary areas.P.ustulata has a delicious taste and is rich in nutrients,so it is an excellent natural food for shrimp and crab,resulting in a significant reduction in resources.To better protect the resource of P.ustulata,it is necessary to understand its population genetic structure.P.ustulata with a shell length of(20.18±1.21)mm and a weight of(1.16±0.24)g were collected.In genetics,microsatellites have become important molecular markers for genetic diversity and marker-assisted breeding,because of their unique advantages,such as abundant polymorphism,codominance and conservation.Transcriptome sequencing technology can simplify and enhance the development of SSR markers.SMRT sequencing can generate longer reads based on second-generation sequencing,and it can be used to explore new genes and discover new SSR loci.In this study,Illumina RNA-Seq technology and SMRT sequencing technology were used for full-length transcriptome sequencing of P.ustulata.MISA software was used to screen SSR loci and analyze their compositional characteristics,providing important basic data for subsequent genetic research and marker-assisted breeding of P.ustulata.Based on transcriptome sequencing,38964 Unigenes were obtained for P.ustulata.MISA software was used to analyze the distribution of simple sequence repeat(SSR)in its transcriptome,resulting in the detection of 4746 SSR loci distributed among 3962 Unigenes,and there were 144 types of SSR repeat motifs.The frequency of occurrence was 12.18%,with an occurence frequency of 10.17%,and on average,one SSR site appeared every 11.33 kb.In addition,593 Unigenes contained two or more SSR loci,and 473 Unigenes contained compound SSR loci.The SSR repeat nucleotide types in the transcriptome of P.ustulata were analyzed,and

关 键 词：焦河蓝蛤 全长转录组 SSR 

分 类 号：S917.4[农业科学—水产科学]