Chromosome-Level Genome Assembly of the Asian Tramp Snail Bradybaena similaris (Stylommatophora: Camaenidae)

Abstract

While terrestrial land snails have long been used for evolutionary research, a lack of high-quality genomic resources has impeded recent progress. Bradybaena snails in particular have numerous intriguing traits that make them a good model for studying evolution, including shell pattern polymorphism and convergent evolution. They are also introduced and invasive across the world. In this study, we present a chromosome-level genome assembly of the Asian tramp snail Bradybaena similaris, utilizing 88-fold Illumina short-read sequences, 125-fold Nanopore long-read sequences, 63-fold PacBio HiFi sequences, and 47-fold Hi-C sequences. The assembled genome of 2.18 Gb is anchored to 28 chromosomes and exhibits high completeness (single copy, 91.7%; duplicates, 7.1%) and contiguity (N50 of 75.6 Mb). Additionally, we also obtained a high-quality transcriptome for annotation. This resource represents the first chromosome-level assembly for snails in the superfamily Helicoidea, which includes more than 5,000 species of terrestrial snails, and will facilitate genomic study in Bradybaena and, more broadly, in the superfamily Helicoidea.

Keywords: Bradybaenidae; Heterobranchia; Mollusca; Stylommatophora; chromosome-scale assembly; land snail.

Fig. 1.

Overview of the results. a) Photograph of B. similaris. b) GenomeScope k-mer profile plot for B. similaris, displaying observed k-mer frequency (bar plot), full model fitted by GenomeScope (black line). len, estimated genome size; uniq, the proportion of non-repetitive sequences; aa, homozygosity rate; ab, heterozygosity rate; kcov, mean k-mer coverage for heterozygous bases; err, error rates of the reads; dup, average rate of read duplications; k, k-mer size; p, ploidy. c) Hi-C contact map for B. similaris with chromosomal scaffolds (blue boxes). Darker red indicates higher contact density. d) Comparison of OMArk statistics for Panpulmonata snails. All data were sourced from OMArk web server. The shown species and accession numbers (in parentheses) are the following: Biomphalaria glabrata (BglaB1, UP001165740, and GCF_947242115.1), Biomphalaria pfeifferi (GCA_030265305.1), B. similaris (this study), Bulinus truncatus (GCA_021962125.1), C. unifasciata (UP000678393 and GCA_905116865.2), Elysia chlorotica (UP000271974 and GCA_003991915.1), Elysia crispate (GCA_033675545.1), Elysia marginata (GCA_019649035.1), Lymnaea stagnalis (GCA_964033795.1), Physella acuta (GCF_028476545.1), and Plakobranchus ocellatus (GCA_019648995.1).