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A chromosomal-level genome assembly for the giant African snail Achatina fulica.
Gigascience 2019; 8(10)G

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.

Authors+Show Affiliations

National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Science, Fudan University, Shanghai 200438, China.Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China. State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Science, Fudan University, Shanghai 200438, China.National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention; Key Laboratory of Parasite and Vector Biology, Ministry of Health; WHO Collaborating Centre for Tropical Diseases; Chinese Centre for Tropical Diseases Research, Shanghai 200025, P. R. China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31634388

Citation

Guo, Yunhai, et al. "A Chromosomal-level Genome Assembly for the Giant African Snail Achatina Fulica." GigaScience, vol. 8, no. 10, 2019.
Guo Y, Zhang Y, Liu Q, et al. A chromosomal-level genome assembly for the giant African snail Achatina fulica. Gigascience. 2019;8(10).
Guo, Y., Zhang, Y., Liu, Q., Huang, Y., Mao, G., Yue, Z., ... Xiao, N. (2019). A chromosomal-level genome assembly for the giant African snail Achatina fulica. GigaScience, 8(10), doi:10.1093/gigascience/giz124.
Guo Y, et al. A Chromosomal-level Genome Assembly for the Giant African Snail Achatina Fulica. Gigascience. 2019 Oct 1;8(10) PubMed PMID: 31634388.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A chromosomal-level genome assembly for the giant African snail Achatina fulica. AU - Guo,Yunhai, AU - Zhang,Yi, AU - Liu,Qin, AU - Huang,Yun, AU - Mao,Guangyao, AU - Yue,Zhiyuan, AU - Abe,Eniola M, AU - Li,Jian, AU - Wu,Zhongdao, AU - Li,Shizhu, AU - Zhou,Xiaonong, AU - Hu,Wei, AU - Xiao,Ning, PY - 2019/01/08/received PY - 2019/05/09/revised PY - 2019/09/27/accepted PY - 2019/10/22/entrez PY - 2019/10/22/pubmed PY - 2019/10/22/medline KW - Achatina fulica KW - Hi-C KW - Pacific Biosciences KW - chromosome assembly KW - giant African snail JF - GigaScience JO - Gigascience VL - 8 IS - 10 N2 - 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. SN - 2047-217X UR - https://www.unboundmedicine.com/medline/citation/31634388/A_chromosomal-level_genome_assembly_for_the_giant_African_snail_Achatina_fulica L2 - https://academic.oup.com/gigascience/article-lookup/doi/10.1093/gigascience/giz124 DB - PRIME DP - Unbound Medicine ER -