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

Date Published: July 5, 2017

Publisher: Public Library of Science

Author(s): Youngjune Bhak, Yeonsu Jeon, Sungwon Jeon, Oksung Chung, Sungwoong Jho, JeHoon Jun, Hak-Min Kim, Yongsoo Cho, Changhan Yoon, Seungwoo Lee, Jung-Hoon Kang, Jong-Deock Lim, Junghwa An, Yun Sung Cho, Doug-Young Ryu, Jong Bhak, Chongle Pan.

http://doi.org/10.1371/journal.pone.0180418

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.

Partial Text

M. rufoniger is a species of vesper bat in the family Vespertilionidae [1]. It can be distinguished from other bats by its rusty orange fur (S1 Picture) and is therefore called ‘golden bat’ or ‘red bat’ in South Korea (Republic of Korea). Recently, its scientific name has been re-assigned to M. rufoniger from Myotis formosus tsuensis based on a molecular phylogeny and morphological study of bats [2]. Although its population is not assessed systematically, it is apparently a rare species that has only been collected in a handful of localities [2]. In South Korea, M. rufoniger is protected and designated as a natural monument. Being one of the most well-known and iconic protected wild animals in South Korea, even an M. rufoniger exhibition center is also in operation (golden bat exhibition center in Hampyeong County, South Korea).

The function-altering variants containing genes of the M. rufoniger were concentrated in reproduction associated pathways. Prolonged sperm storage is a common behavior in Vespertilionidae (including genus Myotis, Pipistrellus, Nyctalus, Eptesicus, Vesoertilio, Chalinolobus, and Plecotus) and Rhinolophidae family species [16–18], and thus it is probably not M. rufoniger specific as reproduction related genes are always under strong natural selection. Therefore, such hits can be regarded as general or even a kind of artefact. Therefore, further detailed functional verification is necessary to understand the roles of each uAAC in functional categories such as reproduction.

 

Source:

http://doi.org/10.1371/journal.pone.0180418

 

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