The genome sequence of Daubenton’s bat, Myotis daubentonii (Kuhl, 1817)

We present a genome assembly from an individual male Myotis daubentonii (Daubenton's bat; Chordata; Mammalia; Chiroptera; Vespertilionidae). The genome sequence is 2,127.8 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 17.34 kilobases in length.


Background
Daubenton's bats Myotis daubentonii (Kuhl, 1817) are small bats weighing 6-10 g and with a forearm length of 35-42 mm.Their dense, brownish dorsal fur contrasts with a whitish belly but their face (especially around eyes) is distinctively naked (Figure 1).They have relatively short ears and tragus.Their feet are long, making up more than 60% of their tibia length, which, together with their broad uropatagium, enables them to hunt aquatic insects over calm waters of rivers, canals, ponds, or lake shores.Daubenton's bats usually roost in hollow trees, where females form nursery colonies of typically 20 to 80 individuals.They are known to often change roost during the nursing season.Males also roost in trees or under bridges but occupy different, less productive habitats than those preferred by the females (Linton & Macdonald, 2019).During the autumnal mating season, they engage in a swarming behaviour, where males from several species aggregate near the entrance of underground roosts to attract females (Glover & Altringham, 2008;Parsons et al., 2003).These bats hibernate in natural or man-made undergrounds such as caves, tunnels, or mines.
The Daubenton's bat, a common and widespread European species is classified as Least Concern by the IUCN (Kruskop et al., 2021).Its new complete genome will be of high interest as M. daubentonii is associated with European lyssavirus 2 (Atterby et al., 2010), including in the Lake Geneva region (Megali et al., 2010), where the specimen used for genome sequencing originates.
Phylogenetic reconstructions place M. daubentonii within the Old World radiation of Myotis as a sister-species to the distinctive Bechstein's bat (Ruedi et al., 2013).However, reconstructions based on different regions of the genome (i.e.mitochondrial versus nuclear markers) provide conflicting phylogenetic perspectives (Foley et al., 2024;Morales et al., 2019).This new, complete genome associated with comparable Myotis genomes (e.g.Jebb et al., 2020), will thus provide new clues to better understand the evolution of this remarkable world-wide radiation.

Genome sequence report
The genome was sequenced from one male Myotis daubentonii collected from Cologny, Geneva, Switzerland (see Methods).A total of 40-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 48 missing joins or mis-joins and removed one haplotypic duplications, reducing the assembly length by 0.43% and the scaffold number by 25.15%, and increasing the scaffold N50 by 5.74%.
The final assembly has a total length of 2,127.8Mb in 121 sequence scaffolds with a scaffold N50 of 102.2 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 (98.8%) of the assembly sequence was assigned to 23 chromosomal-level scaffolds, representing 21 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).While 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.
The estimated Quality Value (QV) of the final assembly is 60.3 with k-mer completeness of 100.0%, and the assembly

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 SEQUEL II (HiFi) and Illumina NovaSeq 6000 (RNA-Seq) instruments.Hi-C data were also generated from muscle tissue of mMyoDau2 using the Arima2 kit and sequenced on the Illumina NovaSeq 6000 instrument.

Genome assembly, curation and evaluation
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 as described previously (Howe et al., 2021).Manual curation was performed using 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.
A Hi-C map for the final assembly was produced using bwa-mem2 (Vasimuddin et al., 2019)      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

Attila D Sándor
University of Veterinary Medicine, Budapest, Hungary This is a brief note providing details for the genome sequence of a Daubenton's bat from Central Europe.It presents the collection details, methodology and assessment of the genome, providing free access to the coded data, too.While the text is brief, it contains all the denominators one may need while accessing the data.The rationale is sound and the data will undoubtedly be a major gateway for further studies.
I have two minor details to highlight: Introduction lists a series of information on the species, including morphology and ecology.If those are not the author's own observations (highly unlikely, based on a single animal), a reference would be welcome.

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In addition, the issued weight range (6-10 g) covers less than 80 of the range I observed on the upper limit, I suggest to use 6-14 g.Reviewer Expertise: Zoologist, primarily working in vertebrate ecology, parasitology and biogeography, targeting the importance of genetic background in host-parasite-pathogen cycles, using bats and their parasites as model.
I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.

Figure 1 .
Figure 1.Photographs of Myotis daubentonii by Manuel Redi (not the specimen used for genome sequencing).

Figure 2 .
Figure 2. Genome assembly of Myotis daubentonii, mMyoDau2.1: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 2,127,824,474 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 (234,112,155 bp, shown in red).Orange and pale-orange arcs show the N50 and N90 scaffold lengths (102,234,773 and 57,790,901 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/CAUJLG01/dataset/CAUJLG01/snail.

Figure 3 .
Figure 3. Genome assembly of Myotis daubentonii, mMyoDau2.1: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/CAUJLG01/dataset/CAUJLG01/blob.

Figure 4 .
Figure 4. Genome assembly of Myotis daubentonii, mMyoDau2.1: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/CAUJLG01/dataset/CAUJLG01/cumulative.

Figure 5 .
Figure 5. Genome assembly of Myotis daubentonii, mMyoDau2.1:Hi-C contact map of the mMyoDau2.1 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=R61mZBFdSo22y-Q-aB7tVw.

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Is the rationale for creating the dataset(s) clearly described?YesAre the protocols appropriate and is the work technically sound?YesAre sufficient details of methods and materials provided to allow replication by others?YesAre the datasets clearly presented in a useable and accessible format?YesCompeting Interests: No competing interests were disclosed.

Table 3
contains a list of relevant software tool versions and sources.

the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests:
No competing interests were disclosed.

have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard.
This is an open access peer review report distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.