The Genome Sequence of the Surf Clam, (Linnaeus, 1758)

Overview

Journal Wellcome Open Res

Specialty Biomedical Engineering

Date 2024 May 20

PMID 38764973

Authors

Anna Holmes

Affiliations

Soon will be listed here.

Abstract

We present a genome assembly from an individual (the surf clam; Mollusca; Bivalvia; Venerida; Mactridae). The genome sequence is 932.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,833 protein coding genes.

Citing Articles

Chromosome-level genome assembly of the clam, Xishi tongue Coelomactra antiquata.

Shen Y, Wang Y, Kong L Sci Data. 2025; 12(1):422.

PMID: 40069159 PMC: 11897284. DOI: 10.1038/s41597-025-04734-1.

References

Chow W, Brugger K, Caccamo M, Sealy I, Torrance J, Howe K . gEVAL - a web-based browser for evaluating genome assemblies. Bioinformatics. 2016; 32(16):2508-10. PMC: 4978925. DOI: 10.1093/bioinformatics/btw159. View

Rao S, Huntley M, Durand N, Stamenova E, Bochkov I, Robinson J . A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159(7):1665-80. PMC: 5635824. DOI: 10.1016/j.cell.2014.11.021. View

Uliano-Silva M, R N Ferreira J, Krasheninnikova K, Formenti G, Abueg L, Torrance J . MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics. 2023; 24(1):288. PMC: 10354987. DOI: 10.1186/s12859-023-05385-y. View

Rhie A, Walenz B, Koren S, Phillippy A . Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 2020; 21(1):245. PMC: 7488777. DOI: 10.1186/s13059-020-02134-9. View

Manni M, Berkeley M, Seppey M, Simao F, Zdobnov E . BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes. Mol Biol Evol. 2021; 38(10):4647-4654. PMC: 8476166. DOI: 10.1093/molbev/msab199. View

Simao F, Waterhouse R, Ioannidis P, Kriventseva E, Zdobnov E . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-2. DOI: 10.1093/bioinformatics/btv351. View

Howe K, Chow W, Collins J, Pelan S, Pointon D, Sims Y . Significantly improving the quality of genome assemblies through curation. Gigascience. 2021; 10(1). PMC: 7794651. DOI: 10.1093/gigascience/giaa153. View

Allio R, Schomaker-Bastos A, Romiguier J, Prosdocimi F, Nabholz B, Delsuc F . MitoFinder: Efficient automated large-scale extraction of mitogenomic data in target enrichment phylogenomics. Mol Ecol Resour. 2020; 20(4):892-905. PMC: 7497042. DOI: 10.1111/1755-0998.13160. View

Zhou C, McCarthy S, Durbin R . YaHS: yet another Hi-C scaffolding tool. Bioinformatics. 2022; 39(1). PMC: 9848053. DOI: 10.1093/bioinformatics/btac808. View

10.

Di Tommaso P, Chatzou M, Floden E, Prieto Barja P, Palumbo E, Notredame C . Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017; 35(4):316-319. DOI: 10.1038/nbt.3820. View

11.

Guan D, McCarthy S, Wood J, Howe K, Wang Y, Durbin R . Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics. 2020; 36(9):2896-2898. PMC: 7203741. DOI: 10.1093/bioinformatics/btaa025. View

12.

Abdennur N, Mirny L . Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2019; 36(1):311-316. PMC: 8205516. DOI: 10.1093/bioinformatics/btz540. View

13.

Kerpedjiev P, Abdennur N, Lekschas F, McCallum C, Dinkla K, Strobelt H . HiGlass: web-based visual exploration and analysis of genome interaction maps. Genome Biol. 2018; 19(1):125. PMC: 6109259. DOI: 10.1186/s13059-018-1486-1. View

14.

Rhie A, McCarthy S, Fedrigo O, Damas J, Formenti G, Koren S . Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021; 592(7856):737-746. PMC: 8081667. DOI: 10.1038/s41586-021-03451-0. View

15.

. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2018; 47(D1):D506-D515. PMC: 6323992. DOI: 10.1093/nar/gky1049. View

16.

Challis R, Richards E, Rajan J, Cochrane G, Blaxter M . BlobToolKit - Interactive Quality Assessment of Genome Assemblies. G3 (Bethesda). 2020; 10(4):1361-1374. PMC: 7144090. DOI: 10.1534/g3.119.400908. View

17.

Cheng H, Concepcion G, Feng X, Zhang H, Li H . Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods. 2021; 18(2):170-175. PMC: 7961889. DOI: 10.1038/s41592-020-01056-5. View

18.

Aken B, Ayling S, Barrell D, Clarke L, Curwen V, Fairley S . The Ensembl gene annotation system. Database (Oxford). 2016; 2016. PMC: 4919035. DOI: 10.1093/database/baw093. View