Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi, Japan.
Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
Genome Biol Evol. 2023 Nov 1;15(11). doi: 10.1093/gbe/evad208.
Semisulcospira habei is a freshwater snail species endemic to the Lake Biwa drainage and belongs to a species group radiated within the lake system. We report the chromosome-scale genome assembly of S. habei, including eight megascaffolds larger than 150 Mb. The genome assembly size is about 2.0 Gb with an N50 of 237 Mb. There are 41,547 protein-coding genes modeled by ab initio gene prediction based on the transcriptome data set, and the BUSCO completeness of the annotated genes was 92.2%. The repeat elements comprise approximately 76% of the genome assembly. The Hi-C contact map showed seven well-resolved scaffolds that correspond to the basic haploid chromosome number of S. habei inferred from the preceding karyotypic study, while it also exhibited one scaffold with a complicated mosaic pattern that is likely to represent the complex of multiple supernumerary chromosomes. The genome assembly reported here represents a high-quality genome resource in disentangling the genomic background of the adaptive radiation of Semisulcospira and also facilitates evolutionary studies in the superfamily Cerithioidea.
拟沼螺是一种分布于琵琶湖流域的淡水螺，属于在该湖系统内辐射形成的物种群。我们报告了拟沼螺的染色体规模基因组组装，其中包括 8 个大于 150Mb 的大片段。基因组组装大小约为 2.0Gb，N50 为 237Mb。基于转录组数据集进行的从头预测，共模拟出 41547 个蛋白质编码基因，注释基因的 BUSCO 完整性为 92.2%。重复元件约占基因组组装的 76%。Hi-C 接触图谱显示了 7 个分辨率良好的支架，这与先前的染色体组研究推断的拟沼螺基本单倍体染色体数一致，同时还显示了一个具有复杂镶嵌模式的支架，可能代表多个额外染色体的复合物。本报告的基因组组装代表了一个高质量的基因组资源，有助于解析拟沼螺辐射适应的基因组背景，也为 Cerithioidea 超科的进化研究提供了便利。
