{"title":"Development of SSR markers in top-mouth culter (Erythroculter ilishaeformis) based on high-throughput sequencing","authors":"Huimin Xu, Bing Gong, Dandan Ju, Mingsong Xiao","doi":"10.1007/s12686-023-01336-0","DOIUrl":null,"url":null,"abstract":"<p>The top-mouth culter <i>Erythroculter ilishaeformis</i> is a kind of carnivorous fish that is currently a widely distributed fish in China, which is a commercially important freshwater fish in China. However, only few effective molecular markers on <i>E. ilishaeformis</i> are available. In this study, nine muscles and liver tissues of cDNA libraries of <i>E. ilishaeformis</i> were sequenced using Illumina HiSeq4000 paired-end sequencing technology. 86,574 sequences from 80,945,107 paired-end reads were generated. 55 novel simple sequence repeat (SSR) markers were developed based on high-throughput sequencing. After genetic diversity analysis, observed heterozygosity (<i>Ho</i>) was from 0.1613 to 0.4839. Expected heterozygosity (<i>He</i>) was from 0.1507 to 0.3728. Minor allele frequencies (<i>MAF</i>s) were from 0.3333 to 0.5000, and Hardy-Weinberg values were relatively balanced. These SSR markers developed from transcriptome sequencing will be as a useful tool to exploit populations genetic of <i>E. ilishaeformis</i>.</p>","PeriodicalId":10625,"journal":{"name":"Conservation Genetics Resources","volume":null,"pages":null},"PeriodicalIF":0.9000,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Conservation Genetics Resources","FirstCategoryId":"93","ListUrlMain":"https://doi.org/10.1007/s12686-023-01336-0","RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIODIVERSITY CONSERVATION","Score":null,"Total":0}
引用次数: 0
Abstract
The top-mouth culter Erythroculter ilishaeformis is a kind of carnivorous fish that is currently a widely distributed fish in China, which is a commercially important freshwater fish in China. However, only few effective molecular markers on E. ilishaeformis are available. In this study, nine muscles and liver tissues of cDNA libraries of E. ilishaeformis were sequenced using Illumina HiSeq4000 paired-end sequencing technology. 86,574 sequences from 80,945,107 paired-end reads were generated. 55 novel simple sequence repeat (SSR) markers were developed based on high-throughput sequencing. After genetic diversity analysis, observed heterozygosity (Ho) was from 0.1613 to 0.4839. Expected heterozygosity (He) was from 0.1507 to 0.3728. Minor allele frequencies (MAFs) were from 0.3333 to 0.5000, and Hardy-Weinberg values were relatively balanced. These SSR markers developed from transcriptome sequencing will be as a useful tool to exploit populations genetic of E. ilishaeformis.
期刊介绍：
Conservation Genetics Resources promotes the conservation of genetic diversity and advances the study of conservation genetics by providing rapid publication of technical papers and reviews on methodological innovations or improvements, computer programs, and genomic resources, as well as on the practical application of these resources towards the development of effective conservation policy and practice.
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