Abstract: Objective　To study the characteristics of microsatellites in the transcriptome of Sigmodon hispidus, develop microsatellite molecular markers,and promote the open sharing of these animal resources.Methods　RNA-seq sequencing technology was used to perform transcriptome sequenceing and bioinformatics analysis on five tissues (heart, liver, spleen, lungs, and kidney) of Sigmodon hispidus. MISA software was used to search microsatellite loci. In addition, PCR validation was performed on 30 randomly selected predicted microsatellite sequences. Results　Based on transcriptome sequencing, 216 139 unigenes were obtained for Sigmodon hispidus. A total of 114 469 microsatellite loci were searched, which were distributed in sequences of 69 631 unigenes. Among all microsatellite loci,there were 6 types of repeats,mainly single nucleotide (53.32%) and dinucleotide (34.52%). The frequency of A/T and AC/GT repeat motifs was relatively high, accounting for 49.47% and 24.26% of the total number of microsatellites, respectively. The sequence length distribution of microsatellites ranged from 10 to 617 bp, with 83 761 microsatellites ranging from 10 to 20 bp, accounting for 73.17% of the total number of microsatellites. 30 microsatellite sequences were randomly selected for PCR validation, and 25 of them were successfully verified.Conclusion　This study obtained rich microsatellite information from Sigmodon hispidus through transcriptome sequencing analysis, laying the foundation for further research on microsatellite molecular markers, genetic quality evaluation, and development and utilization of germplasm resources in Sigmodon hispidus.

Key words: Sigmodon hispidus, RNA-seq sequencing, microsatellite

摘要： 目的　全面研究刚毛棉鼠转录组中微卫星特征,开发微卫星分子标记,促进该实验动物资源的开放共享。 方法　采用RNA-seq测序技术对刚毛棉鼠的5种组织(心脏、肝、脾、肺和肾)进行转录组测序,使用MISA软件进 行微卫星位点的检索。随机挑选30条预测的微卫星序列进行PCR验证。结果　基于刚毛棉鼠转录组测序获得的 216 139条unigenes,搜索到114 469个微卫星位点,这些微卫星位点分布于69 631个unigenes序列中。所有的微卫 星共用6种重复形式,核苷酸重复类型以单核苷酸和二核苷酸为主,分别占微卫星总数的53.32%和34.52%。A/T 和AC/GT重复单元出现频率较高,分别占刚毛棉鼠微卫星总数的49.47%和24.26%。微卫星的序列长度分布为 10~617 bp,其中10~20 bp的微卫星数量为83 761条,占微卫星总数的73.17%。随机选取30个微卫星序列设计 引物进行PCR验证,结果25个扩增成功。结论　本研究通过转录组测序分析获得了刚毛棉鼠丰富的微卫星信息, 为进一步研究刚毛棉鼠的微卫星分子标记、遗传质量评价和种质资源的开发利用奠定了基础。

关键词: 刚毛棉鼠, 转录组测序, 微卫星