De novogenome assembly of the land snailCandidula unifasciata(Mollusca: Gastropoda)

Abstract

Among all molluscs, land snails are a scientifically and economically interesting group comprising edible species, alien species and agricultural pests. Yet, despite their high diversity, the number of genome drafts publicly available is still scarce. Here, we present the draft genome assembly of the land snail Candidula unifasciata, a widely distributed species along central Europe, belonging to the Geomitridae family, a highly diversified taxon in the Western-Palearctic region. We performed whole genome sequencing, assembly and annotation of an adult specimen based on PacBio and Oxford Nanopore long read sequences as well as Illumina data. A genome draft of about 1.29 Gb was generated with a N50 length of 246 kb. More than 60% of the assembled genome was identified as repetitive elements. 22,464 protein-coding genes were identified in the genome, of which 62.27% were functionally annotated. This is the first assembled and annotated genome for a geometrid snail and will serve as reference for further evolutionary, genomic and population genetic studies of this important and interesting group.

De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis)

“…The estimated heterozygosity of the O. idahoensis genome using genomescope was lower than other published land snail genomes (e.g. C. nemoralis: 1.42%; C. fasciata: 1.09%) [22][23], which likely re ects the isolation and small population size of this threatened species [24]. The genome was fairly complete in regards to coding regions as 86.6% of metazoan Benchmarking Universal Single-Copy Orthologs (BUSCO) genes were single-copy or duplicated in the assembly (single copy: 77.3%, duplicated: 9.1%, fragmented: 6.6%) [25].…”

“…Mean gene size was 34,594 bp which is roughly three times larger than previous land snail genome assemblies (e.g. C. nemoralis mean gene size: 9,629 bp; C. fasciata median gene size: 11,931 bp) [22][23], re ecting the in uence of repetitive elements on intron size (Table 2). A total of 92.1% of all genes had a hit to either the NCBI non-redundant nucleotide database, InterProscan [27], or UniProt (Supplementary Table 2).…”

“…In terms of contiguity and BUSCO scores, the O. idahoensis genome assembly compares favorably to many other large molluscan genomes (Table 1). The nal annotation set produced by integrating transcript, protein and ab-initio evidence contained 27,692 predicted protein-coding genes which is within the range of other known gastropod genome assemblies [23,26]. Mean gene size was 34,594 bp which is roughly three times larger than previous land snail genome assemblies (e.g.…”

“…Convergence was assessed visually using Tracer v.1.7.1 and effective sample size was con rmed to be greater than 200 for all parameters. We chose to omit the C. nemoralis genome assembly in our phylogenetic analysis due to the large number of genes in the C. nemoralis genome which may be a result of incomplete repeat masking [22][23]. The inclusion of nonmasked repetitive elements can affect downstream gene family expansion by altering estimates of ancestral gene family size between species [40].…”

Deep structure, long‐distance migration and admixture in the colour polymorphic land snail Cepaea nemoralis

“…Colours are in accordance with the clusters defined by Gaussian finite mixture modelling available draft genome (Saenko et al, 2021) and the ddRAD method, supplemented with a wide geographic survey of mtDNA data, with a primary aim to begin to understand the post-glacial history of the species, but also to provide context for future studies on the evolutionary origins of the supergene, and the roles that selection and drift have in determining the local colour polymorphism. Of course, these methods are now standard in many animal groups, but the study is relatively novel for snails, partly because molluscs in general lag behind (Davison & Neiman, 2021), with, for example, only a few other land snail species having a genome assembly (Chueca et al, 2021b;Guo et al, 2019;Liu et al, 2021). The reality is that although phylogeographic and genomic studies are relatively common in other invertebrates, there are remarkably few similar studies in snails or even the wider group of molluscs.…”