The Genome Sequence of the Soprano Pipistrelle, (Leach, 1825)

Overview

Journal Wellcome Open Res

Specialty Biomedical Engineering

Date 2024 May 20

PMID 38764969

Authors

Manuel Ruedi

Sonja C Vernes

Emma C Teeling

Meike Mai

Affiliations

Soon will be listed here.

Abstract

We present a genome assembly from an individual male (the Soprano Pipistrelle; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 1,895.1 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.18 kilobases in length.

Citing Articles

The genome sequence of the Brown Long-eared bat, (Linnaeus 1758).

Millar A, Vernes S, Teeling E, Mai M Wellcome Open Res. 2024; 9:246.

PMID: 39045151 PMC: 11263909. DOI: 10.12688/wellcomeopenres.21501.1.

A haplotype-resolved reference genome of a long-distance migratory bat, Pipistrellus nathusii (Keyserling & Blasius, 1839).

Driller M, Brown T, Currie S, Hiller M, Winkler S, Pippel M DNA Res. 2024; 31(4).

PMID: 38847751 PMC: 11215541. DOI: 10.1093/dnares/dsae018.

The genome sequence of the Soprano Pipistrelle, (Leach, 1825).

Ruedi M, Vernes S, Teeling E, Mai M Wellcome Open Res. 2024; 8:360.

PMID: 38764969 PMC: 11101169. DOI: 10.12688/wellcomeopenres.19895.1.

References

Teeling E, Springer M, Madsen O, Bates P, OBrien S, Murphy W . A molecular phylogeny for bats illuminates biogeography and the fossil record. Science. 2005; 307(5709):580-4. DOI: 10.1126/science.1105113. View

Hulva P, Horacek I, Strelkov P, Benda P . Molecular architecture of Pipistrellus pipistrellus/Pipistrellus pygmaeus complex (Chiroptera: Vespertilionidae): further cryptic species and Mediterranean origin of the divergence. Mol Phylogenet Evol. 2004; 32(3):1023-35. DOI: 10.1016/j.ympev.2004.04.007. 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

Bernt M, Donath A, Juhling F, Externbrink F, Florentz C, Fritzsch G . MITOS: improved de novo metazoan mitochondrial genome annotation. Mol Phylogenet Evol. 2012; 69(2):313-9. DOI: 10.1016/j.ympev.2012.08.023. 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

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

10.

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

11.

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

12.

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

13.

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

14.

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

15.

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

16.

Teeling E, Vernes S, Davalos L, Ray D, Gilbert M, Myers E . Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species. Annu Rev Anim Biosci. 2017; 6:23-46. DOI: 10.1146/annurev-animal-022516-022811. View

17.

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

18.

Ruedi M, Vernes S, Teeling E, Mai M . The genome sequence of the Soprano Pipistrelle, (Leach, 1825). Wellcome Open Res. 2024; 8:360. PMC: 11101169. DOI: 10.12688/wellcomeopenres.19895.1. View

19.

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

20.

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