A genome assembly of the Yuma myotis bat, Myotis yumanensis - PubMed (original) (raw)

. 2024 Feb 3;115(1):139-148.

doi: 10.1093/jhered/esad053.

Devaughn Fraser 2, Merly Escalona 3, Colin W Fairbairn 4, Samuel Sacco 4, Ruta Sahasrabudhe 5, Oanh Nguyen 5, William Seligmann 4, Peter H Sudmant 6, Erin Toffelmier 1, Juan Manuel Vazquez 6, Robert Wayne 1, H Bradley Shaffer 1 7, Michael R Buchalski 8

Affiliations

A genome assembly of the Yuma myotis bat, Myotis yumanensis

Joseph N Curti et al. J Hered. 2024.

Abstract

The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of 12 bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these 12 species have genome resources available, which limits the ability of resource managers to use genomic techniques to track the responses of bat populations to white-nose syndrome generally. Here we present the first de novo genome assembly for Yuma myotis, generated as a part of the California Conservation Genomics Project. The M. yumanensis genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. This high-quality genome is one of the most complete bat assemblies available, with a contig N50 of 28.03 Mb, scaffold N50 of 99.14 Mb, and BUSCO completeness score of 93.7%. The Yuma myotis genome provides a high-quality resource that will aid in comparative genomic and evolutionary studies, as well as inform conservation management related to white-nose syndrome.

Keywords: Myotis yumanensis; CCGP; California Conservation Genomics Project; chiroptera; long-read assembly; reference genome.

© The American Genetic Association. 2023.

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Figures

Fig. 1.

Fig. 1.

(A) Profile view and (B) front-on view of Yuma myotis bats (Myotis yumanensis). (C) M. yumanensis day roost in a longitudinal joint of a bridge in Riverside County, California, USA.

Fig. 2.

Fig. 2.

Visual overview of genome assembly metrics. (A) K-mer spectra output generated from PacBio HiFi data without adapters using GenomeScope2.0. The bimodal pattern observed corresponds to a diploid genome. K-mers covered at lower coverage and lower frequency correspond to differences between haplotypes, whereas the higher coverage and higher frequency k-mers correspond to the similarities between haplotypes. (B) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 2 for the M. yumanensis primary assembly (mMyoYum1.0.hap1). The plot circle represents the full size of the assembly. From the inside-out, the central plot covers length-related metrics. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly. The dark versus light blue area around it shows mean, maximum, and minimum GC versus AT content at 0.1% intervals (Challis et al. 2020). (C-D) The Omni-C contact map for the primary (C) and alternate (D) genome assemblies generated with PretextSnapshot. Omni-C contact maps translate proximity of genomic regions in 3D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between two such regions. Scaffolds are separated by black lines, and higher density corresponds to higher levels of fragmentation (See online version for color figure).

Fig. 3.

Fig. 3.

NGx plot comparing contiguity of available de novo reference genomes for bats in the genus Myotis. The plot depicts the fraction of the genome (x-axis) that is covered by scaffolds of a given size in Mb (y-axis). The vertical dashed line depicts the N50 value, or half of the genome. The thick pink line is the genome of M. yumanensis presented in this paper.

References

    1. Abdennur N, Mirny LA.. Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics. 2020:36:311–316. 10.1093/bioinformatics/btz540. -DOI -PMC -PubMed
    1. Allen H. Monograph of North American bats. Smithsonian Misc Collect. 1864:7:184.
    1. 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. 2020:20:892–905. 10.1111/1755-0998.13160. -DOI -PMC -PubMed
    1. Brandies P, Peel E, Hogg CJ, Belov K.. The value of reference genomes in the conservation of threatened species. Genes. 2019:10:846. 10.3390/genes10110846. -DOI -PMC -PubMed
    1. Braun JK, Yang B, Gonzalez-Perez SB, Mares MA.. Myotis yumanensis (Chiroptera: Vespertilionidae). Mamm Species. 2015:47:1–14. 10.1093/mspecies/sev001. -DOI

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