Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes
Gene expression vs. sequence divergence: comparative transcriptome sequencing among natural Rhinolophus ferrumequinum populations with different acoustic phenotypes
复制标题
基因表达与序列差异：具有不同声学表型的天然马菊菊群体的转录组测序比较
DOI：
10.1186/s12983-019-0336-7
复制
发表时间：
2019-09-13
影响因子：
2.8
通讯作者：
Feng, Jiang
中科院分区：
文献类型：
--
作者：
Zhao, Hanbo;Wang, Hui;Feng, Jiang
背景
虽然感觉驱动假说可以解释某些蝙蝠物种回声定位频率的地理差异，但这种现象背后的分子机制仍然不清楚。大菊头蝠（Rhinolophus ferrumequinum）在中国东北、中东部和西南三个谱系的回声定位叫声的静息频率（RF）具有显著的地理差异。由于它们的耳蜗有一个对窄频率范围高度敏感的听凹，我们报道了从三个遗传谱系中收集的耳蜗转录组。ferrumequinum是研究回声定位信号地理变异的理想生物，并试图通过分析基因表达和序列变异来了解这种蝙蝠现象背后的机制。
结果
共鉴定出8190个差异表达基因（DEG）。我们从所有DEG中确定了与RF或前臂长度（FL）显著相关的五个模块。在RF相关模块的DEG显着丰富的神经活动，学习和声音反应的基因类别。FL相关模块中的DEG在与肌肉和肌动蛋白功能相关的通路中显著富集。使用21，945个单核苷酸多态性，我们确定了18个与听力相关的候选unigenes，其中5个在三个人群中差异表达。此外，调控内耳中多种细胞过程（如细胞增殖和分化）的基因ERBB4是最大的模块。从3个R. ferrumequinum谱系和其他三个翼手目物种。
结论
在分子水平上的基因表达和序列差异的变化可能提供的证据，可以帮助阐明地理变异的遗传基础上的回声定位信号的大马蹄蝙蝠。
Background
Although the sensory drive hypothesis can explain the geographic variation in echolocation frequencies of some bat species, the molecular mechanisms underlying this phenomenon are still unclear. The three lineages of greater horseshoe bat (Rhinolophus ferrumequinum) in China (northeast, central-east, and southwest) have significant geographic variation in resting frequencies (RF) of echolocation calls. Because their cochleae have an acoustic fovea that is highly sensitive to a narrow range of frequencies, we reported the transcriptomes of cochleae collected from three genetic lineages of R. ferrumequinum, which is an ideal organism for studying geographic variation in echolocation signals, and tried to understand the mechanisms behind this bat phenomenon by analyzing gene expression and sequence variation.
Results
A total of 8190 differentially expressed genes (DEGs) were identified. We identified five modules from all DEGs that were significantly related to RF or forearm length (FL). DEGs in the RF-related modules were significantly enriched in the gene categories involved in neural activity, learning, and response to sound. DEGs in the FL-related modules were significantly enriched in the pathways related to muscle and actin functions. Using 21,945 single nucleotide polymorphisms, we identified 18 candidate unigenes associated with hearing, five of which were differentially expressed among the three populations. Additionally, the gene ERBB4, which regulates diverse cellular processes in the inner ear such as cell proliferation and differentiation, was in the largest module. We also found 49 unigenes that were under positive selection from 4105 one-to-one orthologous gene pairs between the three R. ferrumequinum lineages and three other Chiroptera species.
Conclusions
The variability of gene expression and sequence divergence at the molecular level might provide evidence that can help elucidate the genetic basis of geographic variation in echolocation signals of greater horseshoe bats.