Xu Yuan, Liu Hanyu, Jiang Xinshuai, Zhang Xinning, Liu Jiayu, Tian Yaguang, Bai Xiujuan, Cui Shiquan, Di Shengwei
College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Road, Xiangfang District, Harbin 150030, China.
Animals (Basel). 2024 Oct 14;14(20):2968. doi: 10.3390/ani14202968.
is one of the important aquaculture species in Northeast China. The fallopian tubes of female are used to prepare oviductus ranae (an important traditional Chinese medicine). Therefore, females have higher economical value than males. An increasing female population can increase the benefits from culture. However, the genome of amphibians is complex, making it difficult to investigate their sex determination mechanism. In this study, we analyzed the genome of male using next-generation sequencing technology. A total of 200,046,452,400 bp of clean data were obtained, and the K-mer analysis indicated that the depth was 50×. The genome size of was approximately 3585.05 M, with a heterozygosity rate, repeat sequence ratio, and genome GC content of 1.15%, 68.96%, and approximately 43.0%, respectively. In total, 270,785 contigs and 498 scaffolds were generated. The size of the contigs and scaffolds was 3,748,543,415 and 3,765,862,278 bp, respectively, with the N50 length of 31,988 and 336,385,783. The longest contig and scaffold were of the size 137,967,485 and 1,808,367,828 bp, respectively. The number of contigs and scaffolds > 10K nt was 99,620 and 451, respectively. Through annotation, 40,913 genes were obtained, including 156,609 CDS (i.e., 3.83 CDS per gene). Sequence alignment was performed with the assembled scaffolding genome in this study. Two and one fragment had high homology with two male-specific DNA molecular markers of discovered previously (namely, MSM-222 and MSM-261, respectively). In addition, the gene of was obtained with a length of 18,893 bp by comparison and splicing. The forward primers amplifying MSM-222 and MSM-261 were located at 322-343 and 14,501-14,526 bp of , respectively. However, sequence alignment revealed that MSM-222 and MSM-261 were not located on , and only some homologous parts were observed. This indicated that in addition to , other important genes may play a crucial role in the sex determination mechanism of . Our study provided a foundation for the subsequent high-quality genome construction and provided important genomic resources for future studies on .
是中国东北地区重要的水产养殖物种之一。雌性的输卵管用于制备哈士蟆油（一种重要的传统中药）。因此，雌性比雄性具有更高的经济价值。增加雌性种群数量可以提高养殖效益。然而，两栖动物的基因组复杂，难以研究其性别决定机制。在本研究中，我们使用下一代测序技术分析了雄性的基因组。共获得200,046,452,400 bp的 clean数据，K-mer分析表明深度为50×。的基因组大小约为3585.05 M，杂合率、重复序列比例和基因组GC含量分别为1.15%、68.96%和约43.0%。总共产生了270,785个重叠群和498个支架。重叠群和支架的大小分别为3,748,543,415和3,765,862,278 bp，N50长度分别为31,988和336,385,783。最长的重叠群和支架大小分别为137,967,485和1,808,367,828 bp。长度大于10K nt的重叠群和支架数量分别为99,620和451。通过注释，获得了40,913个基因，包括156,609个CDS（即每个基因3.83个CDS）。在本研究中，对组装的支架基因组进行了序列比对。有两个片段和一个片段分别与先前发现的的两个雄性特异性DNA分子标记（即MSM - 222和MSM - 261）具有高度同源性。此外，通过比对和拼接获得了长度为18,893 bp的的基因。扩增MSM - 222和MSM - 261的正向引物分别位于的322 - 343和14,501 - 14,526 bp处。然而，序列比对显示MSM - 222和MSM - 261并不位于上，仅观察到一些同源部分。这表明除了外，其他重要基因可能在的性别决定机制中起关键作用。我们的研究为后续高质量基因组构建奠定了基础，并为未来关于的研究提供了重要的基因组资源。
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