Abstract
We present a genome assembly from an individual male Vespertilio murinus (the particolored bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 1,925.6 megabases in span. Most of the assembly is scaffolded into 20 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.96 kilobases in length.
Keywords: Vespertilio murinus, particolored bat, genome sequence, chromosomal, Chiroptera
Species taxonomy
Eukaryota; Opisthokonta; Metazoa; Eumetazoa; Bilateria; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Dipnotetrapodomorpha; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Boreoeutheria; Laurasiatheria; Chiroptera; Yangochiroptera; Vespertilionidae; Vespertilio; Vespertilio murinus Linnaeus, 1758 (NCBI:txid59485).
Background
The Parti-coloured bat ( Vespertilio murinus) is a medium-sized bat, characterised by its long fur on the back that is unmistakably bicoloured: a dark brown base and silvery white tips ( Figure 1). Until the 20th century, the species has been confounded in literature with the Greater mouse-eared bat ( Myotis myotis, Borkhausen 1797) that originally was named Vespertilio murinus by Borkhausen, the reason for which some authors used the name ‘ Vespertilio discolor’ for the Parti-coloured bat ( Rydell & Baagøe, 1994).
Figure 1. A male Vespertilio murinus resting on the outside of a large building at the seafront in Blankenberge, Belgium, 13 Sept. 2023.
Along the North Sea coast, this behaviour has been observed frequently in this species - as it is in Pipistrellus nathusii - during migration. (Image © Bob Vandendriessche).
The species is listed by the IUCN Red list as “Least Concern” globally with a stable population trend ( Coroiu, 2016), although it is not considered common in large parts of its range. It has a wide distribution in the northern Palaearctic, from France and Britain in the west, through central, northern and eastern Europe and Siberia to the Pacific coast. The southern limit of its range passes through the Balkans, central Asia and China ( Coroiu, 2016). In parts of its range, it is known to migrate seasonally over long distances up to over 800 kilometres ( Masing, 1989) and single movements as far as 1787 kilometres are known ( Markovets et al., 2004), and so are offshore detections ( Brabant et al., 2020).
With a litter size of two, or rarely three, offspring that is typical for migratory species, the females have two pairs of functional teats, which is a unique feature of this species and distinguishes it from all other European bat species ( Safi, 2006). Overall, there is very little sexual dimorphism. The maximum life span has been reported to be 12 years, based on one ringed individual ( Červený & Bürger, 1989).
In summer, the species is known to roost mainly in buildings, exceptionally in trees. Remarkably, winter roosts are not known, apart from anecdotal findings of individuals ( Safi, 2006). Females prefer to forage over large open waters, while males also hunt along rivers, over large agricultural or urban areas. Its preference for open areas makes the species particularly vulnerable for wind turbines.
The genome of the particolored bat, Vespertilio murinus, was sequenced as part of the Darwin Tree of Life Project (DToL) project, the Bat1K Project and the Vertebrate Genomes Project (VGP). Here we present a chromosomally complete genome sequence for Vespertilio murinus, based on one male specimen from Ostend, Belgium.
Genome sequence report
The genome was sequenced from a male Vespertilio murinus collected from Ostend, Belgium. A total of 44-fold coverage in Pacific Biosciences single-molecule HiFi long reads was generated. Primary assembly contigs were scaffolded with chromosome conformation Hi-C data. Manual assembly curation corrected 49 missing joins or mis-joins and removed 4 haplotypic duplications, reducing the scaffold number by 11.88%.
The final assembly has a total length of 1,925.6 Mb in 177 sequence scaffolds with a scaffold N50 of 186.3 Mb ( Table 1). The snail plot in Figure 2 provides a summary of the assembly statistics, while the distribution of assembly scaffolds on GC proportion and coverage is shown in Figure 3. The cumulative assembly plot in Figure 4 shows curves for subsets of scaffolds assigned to different phyla. Most (97.66%) of the assembly sequence was assigned to 20 chromosomal-level scaffolds, representing 18 autosomes and the X and Y sex chromosomes. Chromosome-scale scaffolds confirmed by the Hi-C data are named in order of size ( Figure 5; Table 2). not fully phased, the assembly deposited is of one haplotype. Contigs corresponding to the second haplotype have also been deposited. The mitochondrial genome was also assembled and can be found as a contig within the multifasta file of the genome submission.
Figure 2. Genome assembly of Vespertilio murinus, mVesMur1.1: metrics.
The BlobToolKit snail plot shows N50 metrics and BUSCO gene completeness. The main plot is divided into 1,000 size-ordered bins around the circumference with each bin representing 0.1% of the 1,925,577,803 bp assembly. The distribution of scaffold lengths is shown in dark grey with the plot radius scaled to the longest scaffold present in the assembly (219,009,580 bp, shown in red). Orange and pale-orange arcs show the N50 and N90 scaffold lengths (186,292,382 and 49,547,305 bp), respectively. The pale grey spiral shows the cumulative scaffold count on a log scale with white scale lines showing successive orders of magnitude. The blue and pale-blue area around the outside of the plot shows the distribution of GC, AT and N percentages in the same bins as the inner plot. A summary of complete, fragmented, duplicated and missing BUSCO genes in the laurasiatheria_odb10 set is shown in the top right. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Vespertilio_murinus/dataset/GCA_963924515.1/snail.
Figure 3. Genome assembly of Vespertilio murinus, mVesMur1.1: BlobToolKit GC-coverage plot.
Sequences are coloured by phylum. Circles are sized in proportion to sequence length. Histograms show the distribution of sequence length sum along each axis. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Vespertilio_murinus/dataset/GCA_963924515.1/blob.
Figure 4. Genome assembly of Vespertilio murinus mVesMur1.1: BlobToolKit cumulative sequence plot.
The grey line shows cumulative length for all sequences. Coloured lines show cumulative lengths of sequences assigned to each phylum using the buscogenes taxrule. An interactive version of this figure is available at https://blobtoolkit.genomehubs.org/view/Vespertilio_murinus/dataset/GCA_963924515.1/cumulative.
Figure 5. Genome assembly of Vespertilio murinus mVesMur1.1: Hi-C contact map of the mVesMur1.1 assembly, visualised using HiGlass.
Chromosomes are shown in order of size from left to right and top to bottom. An interactive version of this figure may be viewed at https://genome-note-higlass.tol.sanger.ac.uk/l/?d=MQFBPCWcQBGnl_BQz6w8Fw.
Table 1. Genome data for Vespertilio murinus, mVesMur1.1.
| Project accession data | ||
|---|---|---|
| Assembly identifier | mVesMur1.1 | |
| Species | Vespertilio murinus | |
| Specimen | mVesMur1 | |
| NCBI taxonomy ID | 59485 | |
| BioProject | PRJEB71534 | |
| BioSample ID | Genome sequencing: SAMEA112247429
Hi-C scaffolding: SAMEA112247429 |
|
| Isolate information | mVesMur1 | |
| Assembly metrics * | Benchmark | |
| Consensus quality (QV) | 61.8 | ≥ 50 |
| k-mer completeness | 100.0% | ≥ 95% |
| BUSCO ** | C:95.1%[S:93.5%,D:1.6%],
F:0.7%,M:4.2%,n:12,234 |
C ≥ 95% |
| Percentage of assembly
mapped to chromosomes |
97.66% | ≥ 95% |
| Sex chromosomes | XY | localised homologous pairs |
| Organelles | Mitochondrial genome: 16.96 kb | complete single alleles |
| Raw data accessions | ||
| PacificBiosciences Revio | ERR12408784, ERR12408785 | |
| Hi-C Illumina | ERR12512729 | |
| PolyA RNA-Seq Illumina | ERR12512730 | |
| Genome assembly | ||
| Assembly accession | GCA_963924515.1 | |
| Accession of alternate haplotype | GCA_963924695.1 | |
| Span (Mb) | 1,925.6 | |
| Number of contigs | 1,158 | |
| Contig N50 length (Mb) | 3.3 | |
| Number of scaffolds | 177 | |
| Scaffold N50 length (Mb) | 186.3 | |
| Longest scaffold (Mb) | 219.01 | |
* Assembly metric benchmarks are adapted from column VGP-2020 of “Table 1: Proposed standards and metrics for defining genome assembly quality” from Rhie et al. (2021).
** BUSCO scores based on the laurasiatheria_odb10 BUSCO set using version 5.4.3. C = complete [S = single copy, D = duplicated], F = fragmented, M = missing, n = number of orthologues in comparison. A full set of BUSCO scores is available at https://blobtoolkit.genomehubs.org/view/Vespertilio_murinus/dataset/GCA_963924515.1/busco.
Table 2. Chromosomal pseudomolecules in the genome assembly of Vespertilio murinus, mVesMur1.
| INSDC accession | Name | Length (Mb) | GC% |
|---|---|---|---|
| OZ004704.1 | 1 | 219.01 | 41.5 |
| OZ004705.1 | 2 | 202.11 | 42.0 |
| OZ004706.1 | 3 | 201.28 | 42.5 |
| OZ004707.1 | 4 | 196.85 | 41.5 |
| OZ004708.1 | 5 | 186.29 | 44.5 |
| OZ004709.1 | 6 | 172.14 | 44.0 |
| OZ004711.1 | 7 | 86.93 | 42.0 |
| OZ004712.1 | 8 | 74.91 | 42.5 |
| OZ004713.1 | 9 | 70.16 | 44.5 |
| OZ004714.1 | 10 | 56.84 | 45.5 |
| OZ004715.1 | 11 | 55.96 | 45.5 |
| OZ004716.1 | 12 | 51.82 | 49.0 |
| OZ004717.1 | 13 | 50.86 | 43.5 |
| OZ004718.1 | 14 | 49.55 | 49.5 |
| OZ004719.1 | 15 | 40.76 | 48.5 |
| OZ004720.1 | 16 | 27.46 | 51.5 |
| OZ004721.1 | 17 | 14.38 | 49.0 |
| OZ004722.1 | 18 | 10.12 | 53.5 |
| OZ004710.1 | X | 106.65 | 41.0 |
| OZ004723.1 | Y | 6.49 | 47.5 |
| OZ004724.1 | MT | 0.02 | 37.0 |
The estimated Quality Value (QV) of the final assembly is 61.8 with k-mer completeness of 100.0%, and the assembly has a BUSCO v5.4.3 completeness of 95.1% (single = 93.5%, duplicated = %), using the laurasiatheria_odb10 reference set ( n = 12,234).
Metadata for specimens, barcode results, spectra estimates, sequencing runs, contaminants and pre-curation assembly statistics are given at https://links.tol.sanger.ac.uk/species/59485.
Methods
Sample acquisition and nucleic acid extraction
The specimen collected for this research, an adult male Vespertilio murinus (specimen ID SAN00002659, ToLID mVesMur1), was suffering upper arm (humerus) fracture, with a nearby wind turbine as a plausible cause. The animal was collected on 2022-09-08 by the Ostend Wildlife Rehab centre, who contacted the author (Bob Vandendriessche) for advice. It was transferred to the faculty of veterinary medicine (Ghent University) in Merelbeke, where it was euthanised following the AVMA Guidelines for the Euthanasia of Animals. After an inhalation anaesthetic overdose with isoflurane, sodium pentobarbital (0.11mg/g body weight) was administered intraperitoneally. Samples taken from the animal were preserved in RNA later at –70°C.
The workflow for high molecular weight (HMW) DNA extraction at the Wellcome Sanger Institute (WSI) Tree of Life Core Laboratory includes a sequence of core procedures: sample preparation; sample homogenisation, DNA extraction, fragmentation, and clean-up. In sample preparation, the mVesMur1 sample was weighed and dissected on dry ice ( Jay et al., 2023). For sample homogenisation, tissue was cryogenically disrupted using the Covaris cryoPREP ® Automated Dry Pulverizer ( Narváez-Gómez et al., 2023).
HMW DNA was extracted using the Automated MagAttract v2 protocol ( Oatley et al., 2023a). DNA was sheared into an average fragment size of 12–20 kb in a Megaruptor 3 system with speed setting 31 ( Bates et al., 2023). Sheared DNA was purified by solid-phase reversible immobilisation ( Oatley et al., 2023b): in brief, the method employs a 1.8X ratio of AMPure PB beads to sample to eliminate shorter fragments and concentrate the DNA. The concentration of the sheared and purified DNA was assessed using a Nanodrop spectrophotometer, Qubit Fluorometer and Qubit dsDNA High Sensitivity Assay kit. Fragment size distribution was evaluated by running the sample on the FemtoPulse system.
RNA was extracted from tissue of mVesMur1 in the Tree of Life Laboratory at the WSI using the RNA Extraction: Automated MagMax™ mirVana protocol ( do Amaral et al., 2023). The RNA concentration was assessed using a Nanodrop spectrophotometer and a Qubit Fluorometer using the Qubit RNA Broad-Range Assay kit. Analysis of the integrity of the RNA was done using the Agilent RNA 6000 Pico Kit and Eukaryotic Total RNA assay.
Protocols developed by the WSI Tree of Life laboratory are publicly available on protocols.io ( Denton et al., 2023).
Sequencing
Pacific Biosciences HiFi circular consensus DNA sequencing libraries were constructed according to the manufacturers’ instructions. Poly(A) RNA-Seq libraries were constructed using the NEB Ultra II RNA Library Prep kit. DNA and RNA sequencing was performed by the Scientific Operations core at the WSI on Pacific Biosciences Revio (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments. Hi-C data were also generated from muscle tissue of mVesMur1 using the Arima v2 kit. The Hi-C sequencing was performed using paired-end sequencing with a read length of 150 bp on the Illumina NovaSeq 6000 instrument.
Genome assembly and curation
Assembly was carried out with Hifiasm ( Cheng et al., 2021) and haplotypic duplication was identified and removed with purge_dups ( Guan et al., 2020). The assembly was then scaffolded with Hi-C data ( Rao et al., 2014) using YaHS ( Zhou et al., 2023). The assembly was checked for contamination and corrected using the TreeVal pipeline ( Pointon et al., 2023). Manual curation was performed using JBrowse2 ( Diesh et al., 2023), HiGlass ( Kerpedjiev et al., 2018) and PretextView ( Harry, 2022). The mitochondrial genome was assembled using MitoHiFi ( Uliano-Silva et al., 2023), which runs MitoFinder ( Allio et al., 2020) or MITOS ( Bernt et al., 2013) and uses these annotations to select the final mitochondrial contig and to ensure the general quality of the sequence.
Evaluation of final assembly
The final assembly was post-processed and evaluated with the three Nextflow ( Di Tommaso et al., 2017) DSL2 pipelines “sanger-tol/readmapping” ( Surana et al., 2023a), “sanger-tol/genomenote” ( Surana et al., 2023b), and “sanger-tol/blobtoolkit” ( Muffato et al., 2024). The pipeline sanger-tol/readmapping aligns the Hi-C reads with bwa-mem2 ( Vasimuddin et al., 2019) and combines the alignment files with SAMtools ( Danecek et al., 2021). The sanger-tol/genomenote pipeline transforms the Hi-C alignments into a contact map with BEDTools ( Quinlan & Hall, 2010) and the Cooler tool suite ( Abdennur & Mirny, 2020), which is then visualised with HiGlass ( Kerpedjiev et al., 2018). It also provides statistics about the assembly with the NCBI datasets ( Sayers et al., 2024) report, computes k-mer completeness and QV consensus quality values with FastK and MerquryFK, and a completeness assessment with BUSCO ( Manni et al., 2021).
The sanger-tol/blobtoolkit pipeline is a Nextflow port of the previous Snakemake Blobtoolkit pipeline ( Challis et al., 2020). It aligns the PacBio reads with SAMtools and minimap2 ( Li, 2018) and generates coverage tracks for regions of fixed size. In parallel, it queries the GoaT database ( Challis et al., 2023) to identify all matching BUSCO lineages to run BUSCO ( Manni et al., 2021). For the three domain-level BUSCO lineage, the pipeline aligns the BUSCO genes to the Uniprot Reference Proteomes database ( Bateman et al., 2023) with DIAMOND ( Buchfink et al., 2021) blastp. The genome is also split into chunks according to the density of the BUSCO genes from the closest taxonomically lineage, and each chunk is aligned to the Uniprot Reference Proteomes database with DIAMOND blastx. Genome sequences that have no hit are then chunked with seqtk and aligned to the NT database with blastn ( Altschul et al., 1990). All those outputs are combined with the blobtools suite into a blobdir for visualisation.
All three pipelines were developed using the nf-core tooling ( Ewels et al., 2020), use MultiQC ( Ewels et al., 2016), and make extensive use of the Conda package manager, the Bioconda initiative ( Grüning et al., 2018), the Biocontainers infrastructure ( da Veiga Leprevost et al., 2017), and the Docker ( Merkel, 2014) and Singularity ( Kurtzer et al., 2017) containerisation solutions.
Table 3 contains a list of relevant software tool versions and sources.
Table 3. Software tools: versions and sources.
Wellcome Sanger Institute – Legal and Governance
The materials that have contributed to this genome note have been supplied by a Darwin Tree of Life Partner. The submission of materials by a Darwin Tree of Life Partner is subject to the ‘Darwin Tree of Life Project Sampling Code of Practice’, which can be found in full on the Darwin Tree of Life website here. By agreeing with and signing up to the Sampling Code of Practice, the Darwin Tree of Life Partner agrees they will meet the legal and ethical requirements and standards set out within this document in respect of all samples acquired for, and supplied to, the Darwin Tree of Life Project.
Further, the Wellcome Sanger Institute employs a process whereby due diligence is carried out proportionate to the nature of the materials themselves, and the circumstances under which they have been/are to be collected and provided for use. The purpose of this is to address and mitigate any potential legal and/or ethical implications of receipt and use of the materials as part of the research project, and to ensure that in doing so we align with best practice wherever possible. The overarching areas of consideration are:
• Ethical review of provenance and sourcing of the material
• Legality of collection, transfer and use (national and international)
Each transfer of samples is further undertaken according to a Research Collaboration Agreement or Material Transfer Agreement entered into by the Darwin Tree of Life Partner, Genome Research Limited (operating as the Wellcome Sanger Institute), and in some circumstances other Darwin Tree of Life collaborators.
Acknowledgements
Dr An Martel (UGhent) provided information on the euthanasia and the dissection of the specimen.
Funding Statement
This work was supported by Wellcome through core funding to the Wellcome Sanger Institute [206194, <a href=https://doi.org/10.35802/206194>https://doi.org/10.35802/206194</a>] and the Darwin Tree of Life Discretionary Award [218328, <a href=https://doi.org/10.35802/218328>https://doi.org/10.35802/218328 </a>]. SCV was supported by a UKRI Future Leaders Fellowship (MR/T021985/1) and an ERC Consolidator Grant (101001702; BATSPEAK). ECT is supported by Irish Research Council Laureate Award IRCLA/2017/58 and Science Foundation Ireland Future Frontiers 19/FFP/6790.
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
[version 1; peer review: 3 approved]
Data availability
European Nucleotide Archive: Vespertilio murinus (particolored bat). Accession number PRJEB71534; https://identifiers.org/ena.embl/PRJEB71534 ( Wellcome Sanger Institute, 2024). The genome sequence is released openly for reuse. The Vespertilio murinus genome sequencing genome sequencing initiative is part of the Darwin Tree of Life (DToL) project, the Bat1K Project and the Vertebrate Genomes Project (VGP). All raw sequence data and the assembly have been deposited in INSDC databases. The genome will be annotated using available RNA-Seq data and presented through the Ensembl pipeline at the European Bioinformatics Institute. Raw data and assembly accession identifiers are reported in Table 1.
Author information
Members of the Darwin Tree of Life Barcoding collective are listed here: https://doi.org/10.5281/zenodo.4893703.
Members of the Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team are listed here: https://doi.org/10.5281/zenodo.10066175.
Members of Wellcome Sanger Institute Scientific Operations: Sequencing Operations are listed here: https://doi.org/10.5281/zenodo.10043364.
Members of the Wellcome Sanger Institute Tree of Life Core Informatics team are listed here: https://doi.org/10.5281/zenodo.10066637.
Members of the Tree of Life Core Informatics collective are listed here: https://doi.org/10.5281/zenodo.5013541.
Members of the Darwin Tree of Life Consortium are listed here: https://doi.org/10.5281/zenodo.4783558.
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