Myotis rufoniger genome sequence and analyses: M. rufoniger's genomic feature and the decreasing effective population size of Myotis bats

Abstract

Myotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66× fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10× coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger's red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that the M. rufoniger also has bat-specific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat's reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since ~30k years ago. M. rufoniger's effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity.

Fig 1. Phylogenetic relationships and divergence times in bats and mammalian species.

The estimated divergence time (million years ago; MYA) is given at the nodes, with the 95% confidence intervals in parentheses. The calibration times of M. brandtii—H. sapiens (97.5 MYA), and M. brandtii—P. alecto (62.6 MYA) were derived from the TimeTree database. Colored branches and circles represent bat groups (blue: insect-eating microbat, red: fruits-eating mega bat). M. domestica, used as an outgroup species, was excluded in this figure.

Fig 2. Demographic history of Myotis bats.

T_surf, atmospheric surface air temperature (T indicates temperature, surf indicates surface); RSL, relative sea level; 10 m.s.l.e., 10 m sea level equivalent; g, generation time (years); μ, mutation rate per base pair per year.