Reference transcriptome and Alignments of candidate gene

Recently diverged taxa with contrasting phenotypes offer opportunities for unravelling the genetic basis of phenotypic variation in nature. Horseshoe bats are a speciose group that exhibit a derived form of high duty cycle echolocation in which the inner ear is finely tuned to echoes of the narrowband call frequency. Here, by focusing on three recently diverged subspecies of the intermediate horseshoe bat (Rhinolophus affinis) that display divergent echolocation call frequencies, we aim to identify candidate loci putatively involved in hearing frequency variation. We used de novo transcriptome sequencing of two mainland taxa (himalayanus and macrurus) and one island taxon (hainanus) to compare expression profiles of thousands of genes. By comparing taxa with divergent call frequencies (around 15 kHz difference), we identified 252 differentially expressed genes (DEGs), of which six have been shown to be involved in hearing or deafness in human/mouse. To obtain further validation of these...表型分化显著的近期分化类群，可为揭示自然界表型变异的遗传基础提供重要研究契机。菊头蝠（horseshoe bat）是一类物种多样性极高的类群，它们演化出特化的高占空比回声定位系统，其内耳可精准匹配窄带叫声频率的回声信号。本研究聚焦于3个近期分化的中菊头蝠（Rhinolophus affinis）亚种，这些亚种的回声定位叫声频率存在显著差异，旨在筛选出与听觉频率变异相关的候选基因位点。我们对两个大陆亚种（R. a. himalayanus与R. a. macrurus）及一个岛屿亚种（R. a. hainanus）开展从头转录组测序，以比较数千个基因的表达谱差异。通过对比叫声频率差异约15 kHz的类群，我们共鉴定出252个差异表达基因（differentially expressed genes, DEGs），其中6个基因已被证实与人类或小鼠的听觉功能及听觉障碍相关。为进一步验证上述结果……