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

Abstract

Background Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO3), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species. Results Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2–3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome. Conclusions Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO3 resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

“…However, given that only 76.6% of PacBio CLR reads mapped to the final genome assembly (Table 1 ), it is likely that many repeat regions remain unresolved. The proportion of annotated genes in the Berghia genome was also quite high (77.8% with BLASTP hits), consistent with other published gastropod genomes [ 86 – 88 ].…”

A chromosome-level genome for the nudibranch gastropodBerghia stephanieaehelps parse clade-specific gene expression in novel and conserved phenotypes

“…However, given that only 76.6% of PacBio CLR reads mapped to the final genome assembly (Table 1), it is likely that many repeat regions remain unresolved. The proportion of annotated genes in the Berghia genome was also quite high (77.8% with BLASTP hits), consistent with other published gastropod genomes [55–57].…”

Genomics and conservation: Guidance from training to analyses and applications

“…Once annotated, comparisons of genome assemblies from different individuals, populations or species can capture the full range of genome variation, including SNPs, repetitive elements, copy‐number variants and structural variation (Dominguez Del Angel et al., 2018). For example, annotation of both repetitive elements and genic regions in a threatened and endemic land snail, Oreohelix idahoensis , revealed that expansions of long terminal repeats are responsible for differences in both genome size and gene composition, specifically expanding gene families related to stress and biomineralization compared to other Oreohelix species (Linscott et al., 2022). Structural variation that would go undetected in more fragmented assemblies can also provide critical information about the maintenance of polymorphisms within species.…”