A chromosomal-level genome assembly for the giant African snail Achatina fulica

Abstract

Background Achatina fulica, the giant African snail, is the largest terrestrial mollusk species. Owing to its voracious appetite, wide environmental adaptability, high growth rate, and reproductive capacity, it has become an invasive species across the world, mainly in Southeast Asia, Japan, the western Pacific islands, and China. This pest can damage agricultural crops and is an intermediate host of many parasites that can threaten human health. However, genomic information of A. fulica remains limited, hindering genetic and genomic studies for invasion control and management of the species.FindingsUsing a k-mer–based method, we estimated the A. fulica genome size to be 2.12 Gb, with a high repeat content up to 71%. Roughly 101.6 Gb genomic long-read data of A. fulica were generated from the Pacific Biosciences sequencing platform and assembled to produce a first A. fulica genome of 1.85 Gb with a contig N50 length of 726 kb. Using contact information from the Hi-C sequencing data, we successfully anchored 99.32% contig sequences into 31 chromosomes, leading to the final contig and scaffold N50 length of 721 kb and 59.6 Mb, respectively. The continuity, completeness, and accuracy were evaluated by genome comparison with other mollusk genomes, BUSCO assessment, and genomic read mapping. A total of 23,726 protein-coding genes were predicted from the assembled genome, among which 96.34% of the genes were functionally annotated. The phylogenetic analysis using whole-genome protein-coding genes revealed that A. fulica separated from a common ancestor with Biomphalaria glabrata ∼182 million years ago.ConclusionTo our knowledge, the A. fulica genome is the first terrestrial mollusk genome published to date. The chromosome sequence of A. fulica will provide the research community with a valuable resource for population genetics and environmental adaptation studies for the species, as well as investigations of the chromosome-level of evolution within mollusks.

Thede novogenome of the “Spanish” slugArion vulgarisMoquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

“…Finally, single nucleotide polymorphisms (SNPs) calling was implemented in Genome Analysis Toolkit (GATK) v 4.1.6.0 using default parameters [42], and a number of filtering steps were performed to reduce the false positives, including: 1) remove SNPs with more than two alleles; 2) remove SNPs with quality score less than 30; 3) remove SNPs at or within 5bp from any InDels; 4) remove sites with extremely low (less than one-third average depth) or extremely high (more than three-fold average depth) coverage. We observed an average genome-wide heterozygosity rate of 1.55 per hundred base pair in A. vulgaris, which is about three times of the published most closely related species, Achatina fulica (Stylommatophora, heterozygosity rate: 0.47 per hundred base pair) [23], however, throughout all reported gastropod genomes (heterozygosity rate from 0.08 to 3.66 per hundred base pair) [5], its heterozygosity is at an intermediate level.…”

“…We conducted a comprehensive comparison of the proportion of the different type of TEs and their divergence rate among A. vulgaris and other published Heterobranchia species (Ac. fulica [23], Ac. immaculata [22], Biomphalaria glabrata [47], Radix auricularia [48], Aplysia californica, and Elysia chlorotica [49]).…”

“…For homology-based prediction, protein sequences of six mollusk species (Ac. fulica [23], B. glabrata [47], Ap. californica, E. chlorotica [49], P. canaliculata [53], Haliotis rufescens [54]) were downloaded from NCBI and aligned against the assembled genome with MMseqs v 11.e1a1c [55].…”

“…In recent years, genome research has shown its advantages and potential in revealing evolutionary and adaptive mechanisms. However, so far only two land snail genomes were published [22,23]. Compared to land snails, land slugs have 'sacrificed' the protective function of a calcareous shell for less weight and energy costs, less dependence on calcium uptake, better mobility, fast body movements and ability to occupy very small spaces [5].…”

Giant African snail genomes provide insights into molluscan whole-genome duplication and aquatic-terrestrial transition

“…The genomes of aquatic mollusks such as California sea hare 31 , Pacific oyster 32 , pearl oyster 33, 34 , owl limpet 35 , California two-spot octopus 36 , golden mussel 37 , Biomphalaria glabrata 38 , and golden apple snail 39 have been sequenced, whereas few terrestrial species in Mollusca have well-documented genomic information. Recently, the genomic data of the invasive land snail A. fulica were released, but without in-depth studies of related biological issues 40 . To address the genetic and evolutionary characteristics of terrestrial mollusks, we report the genome of another giant African snail with a larger body size and greater invasiveness (Fig.…”