Chromosome-Scale Genome Assembly of the Freshwater Snail Semisulcospira habei from the Lake Biwa Drainage System

Abstract

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.

Supplementary material 1 from: Sawada N, Fuke Y, Miura O, Toyohara H, Nakano T (2024) Redescription of Semisulcospira reticulata (Mollusca, Semisulcospiridae) with description of a new species from Lake Biwa, Japan. Evolutionary Systematics 8(1): 127-144. https://doi.org/10.3897/evolsyst.8.124491

“…Low-quality bases (Q < 30) and the adapter sequences were removed with fastp v0.20.1 (Chen et al 2018) and the read length was trimmed to 109 bp to match the shorter Read 1. Quality-controlled reads were mapped to the whole genome sequence assembly of S. habei (GenBank accession number: BTPG01000001-BTPG01000578) (Miura et al 2023) using Strobealign v0.13.0 (Sahlin 2022) with the default settings. SNP detection was performed using the ref_map.pl pipeline of Stacks.…”