The Genome Sequence of the Ruddy Darter, (Müller, 1764)

Overview

Journal Wellcome Open Res

Specialty Biomedical Engineering

Date 2025 Mar 3

PMID 40027405

Authors

Liam M Crowley

Denise C Wawman

Affiliations

Soon will be listed here.

Abstract

We present a genome assembly from a male specimen of (Ruddy Darter; Arthropoda; Insecta; Odonata; Libellulidae). The haplotype-resolved assembly contains two haplotypes with total lengths of 1,500.53 megabases and 1,304.05 megabases. Most of haplotype 1 is scaffolded into 13 chromosomal pseudomolecules, including the X sex chromosome, while haplotype 2 is scaffolded into 12 autosomes.

References

Formenti G, Abueg L, Brajuka A, Brajuka N, Gallardo-Alba C, Giani A . Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs. Bioinformatics. 2022; 38(17):4214-4216. PMC: 9438950. DOI: 10.1093/bioinformatics/btac460. View

. UniProt: the Universal Protein Knowledgebase in 2023. Nucleic Acids Res. 2022; 51(D1):D523-D531. PMC: 9825514. DOI: 10.1093/nar/gkac1052. 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

Danecek P, Bonfield J, Liddle J, Marshall J, Ohan V, Pollard M . Twelve years of SAMtools and BCFtools. Gigascience. 2021; 10(2). PMC: 7931819. DOI: 10.1093/gigascience/giab008. 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

Challis R, Kumar S, Sotero-Caio C, Brown M, Blaxter M . Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life. Wellcome Open Res. 2023; 8:24. PMC: 9971660. DOI: 10.12688/wellcomeopenres.18658.1. View

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

Quinlan A, Hall I . BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010; 26(6):841-2. PMC: 2832824. DOI: 10.1093/bioinformatics/btq033. View

10.

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

11.

Wakeling J, Ellington C . Dragonfly flight. I. Gliding flight and steady-state aerodynamic forces. J Exp Biol. 1997; 200(Pt 3):543-556. DOI: 10.1242/jeb.200.3.543. View

12.

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

13.

Crowley L, Allen H, Barnes I, Boyes D, Broad G, Fletcher C . A sampling strategy for genome sequencing the British terrestrial arthropod fauna. Wellcome Open Res. 2023; 8:123. PMC: 10318377. DOI: 10.12688/wellcomeopenres.18925.1. View

14.

Ewels P, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A . The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020; 38(3):276-278. DOI: 10.1038/s41587-020-0439-x. View

15.

Veiga Leprevost F, Gruning B, Alves Aflitos S, Rost H, Uszkoreit J, Barsnes H . BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017; 33(16):2580-2582. PMC: 5870671. DOI: 10.1093/bioinformatics/btx192. View

16.

Wakeling J, Ellington C . Dragonfly flight. III. Lift and power requirements. J Exp Biol. 1997; 200(Pt 3):583-600. DOI: 10.1242/jeb.200.3.583. View

17.

Kurtzer G, Sochat V, Bauer M . Singularity: Scientific containers for mobility of compute. PLoS One. 2017; 12(5):e0177459. PMC: 5426675. DOI: 10.1371/journal.pone.0177459. View

18.

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

19.

. Sequence locally, think globally: The Darwin Tree of Life Project. Proc Natl Acad Sci U S A. 2022; 119(4). PMC: 8797607. DOI: 10.1073/pnas.2115642118. View

20.

Twyford A, Beasley J, Barnes I, Allen H, Azzopardi F, Bell D . A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project. Wellcome Open Res. 2024; 9:339. PMC: 11462125. DOI: 10.12688/wellcomeopenres.21143.1. View