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

Yunhai Guo,Yun Huang,Zhongdao Wu,Zhiyuan Yue,Ning Xiao,Eniola M Abe,Shizhu Li,Wei Hu,Yi Zhang,Xiaonong Zhou,Guangyao Mao,Jian Li,Qin Liu

doi:10.1093/gigascience/giz124

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.

Highlights

The giant African snail, Achatina fulica (NCBI:txid6530), is a Gastropod species (Fig. 1)
Protein sequences of closely related species including Aplysia californica, B. glabrata, Crassostrea gigas, Lottia gigantea, and Patinopecten yessoensis were downloaded from the Ensembl database and aligned to the A. fulica genome with TBLASTN2.6.0 (TBLASTN, RRID:SCR 011822)
We identified 25,448 gene families for A. fulica and the related species; among them 675 single-copy ortholog families were detected

Summary

Introduction

The giant African snail, Achatina fulica (NCBI:txid6530), is a Gastropod species (Fig. 1). We compared the sequence number and contig N50 length of A. fulica with publicly available mollusk genomes and found that our assembly has a high quality on contig and scaffold N50 among mollusk genomes (Table 3). The resulting de novo data, combined with the known repeat library from Repbase [55], were used to identify TEs in the A. fulica genome by means of RepeatMasker0 (RepeatMasker, RRID:SCR 012954) [56] software. Protein sequences of closely related species including Aplysia californica, B. glabrata, Crassostrea gigas, Lottia gigantea, and Patinopecten yessoensis were downloaded from the Ensembl database and aligned to the A. fulica genome with TBLASTN2.6.0 (TBLASTN, RRID:SCR 011822). Using single-copy orthologs, we could probe the phylogenetic relationships for A. fulica and other mollusks To this end, protein sequences of single-copy genes were aligned using CLUSTALX2.0 (Clustal X, RRID:SCR 017055) [66]. We found that A. fulica was most closely related to B. glabrata, and the 2 species diverged from their common ancestor ∼243 million years ago (MYA) (Fig. 4)

Conclusion

Findings

Ethics Statement