<i>Myotis rufoniger</i> genome sequence and analyses: <i>M</i>. <i>rufoniger’s</i> genomic feature and the decreasing effective population size of <i>Myotis</i> bats

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.红毛鼠耳蝠（Myotis rufoniger）是鼠耳蝠属（Myotis）下的一种蝙蝠科燕蝠。本研究报道了红毛鼠耳蝠的全基因组序列及其相关分析。本研究共获得124 Gb的短读长DNA测序数据，预估基因组大小为1.88 Gb，测序深度达66倍。将所得测序序列比对至布氏鼠耳蝠（Myotis brandtii）参考基因组，比对率达96.50%，在10倍覆盖度下可覆盖95.71%的编码序列区域。经估算，鼠耳蝠属类群的分化时间约为1150万年前，红毛鼠耳蝠与其近缘物种大卫鼠耳蝠（Myotis davidii）的分化时间则约为1040万年前。相较于其他鼠耳蝠及哺乳动物基因组，本研究从929个基因中鉴定得到1239个可改变蛋白功能的红毛鼠耳蝠特异性氨基酸序列。对这929个基因开展功能富集分析后发现，黑色素相关的多巴色素互变异构酶（DCT）、溶质载体家族45成员2（SLC45A2）、酪氨酸酶相关蛋白1（TYRP1）以及眼皮肤白化病II型基因（OCA2）中存在氨基酸突变，该突变可能是红毛鼠耳蝠呈现红色毛发体色，以及鼠耳蝠属类群普遍存在毛色分化的潜在原因。与砷抗性相关的N6腺嘌呤甲基转移酶1（N6AMT1）基因在红毛鼠耳蝠中呈现出显著的功能改变。本研究进一步证实，红毛鼠耳蝠在促卵泡激素β亚基（FSHB）、生长激素受体（GHR）、胰岛素样生长因子1受体（IGF1R）、肿瘤蛋白p53（TP53）、小鼠双微体2（MDM2）、SLC45A2、RGS7结合蛋白（RGS7BP）、视紫红质（RHO）、视蛋白1短波敏感型（OPN1SW）以及环核苷酸门控通道β3亚基（CNGB3）等基因中存在蝙蝠特异性序列；上述基因此前已有研究证实与蝙蝠的繁殖、寿命、飞行能力、低视力以及回声定位功能相关。此外，种群历史动态分析结果显示，自约3万年前以来，鼠耳蝠支系的有效种群规模持续下降。红毛鼠耳蝠的有效种群规模在所有鼠耳蝠属物种中处于最低水平，这证实了其相对较低的遗传多样性。