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

• Published in: Gigascience Vol. 8; no. 10
• Main Authors: Guo, Yunhai, Zhang, Yi, Liu, Qin, Huang, Yun, Mao, Guangyao, Yue, Zhiyuan, Abe, Eniola M, Li, Jian, Wu, Zhongdao, Li, Shizhu, Zhou, Xiaonong, Hu, Wei, Xiao, Ning
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01.10.2019
• Subjects: Achatina fulica; Adaptability; Animals; Chromosomes; Gene Library; Gene mapping; Genes; Genome; Genomes; Genomics; Genomics - methods; Growth rate; Introduced Species; Invasive species; Mollusks; Nucleotide sequence; Peptide mapping; Phylogeny; Population genetics; Proteins; Sequence Analysis, RNA; Snails - genetics; Technical Note; chromosome assembly; Hi-C; giant African snail; Pacific Biosciences; Achatina fulica
• ISSN: 2047-217X; 2047-217X
• 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. Findings Using 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. Conclusion To 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.