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.

翘嘴红鲌是目前我国分布广泛的肉食性鱼类，是我国重要的商业淡水鱼。然而，对于翘嘴E. ilisaeformis有效的分子标记很少。本研究采用Illumina HiSeq4000双端测序技术对翘嘴鹬9个肌肉和肝脏组织的cDNA文库进行了测序。从 80,945,107 个双端读取中生成了 86,574 个序列。基于高通量测序开发了 55 个新型简单序列重复 (SSR) 标记。经过遗传多样性分析，观察到的杂合度（Ho）为0.1613至0.4839。预期杂合度 ( He ) 为 0.1507 至 0.3728。次要等位基因频率（MAF）为0.3333至0.5000，Hardy-Weinberg值相对平衡。这些通过转录组测序开发的 SSR 标记将成为开发鲫鱼种群遗传的有用工具。