Li Jun, Guo Ce, Xie Meiling, Wang Kai, Wang Xianghe, Zou Bishan, Hou Fanghui, Ran Chongyang, Bi Shiman, Xu Yanchun, Hua Yan
Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China.
College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China.
BMC Genomics. 2024 Dec 4;25(1):1176. doi: 10.1186/s12864-024-11063-x.
Pangolin is one of the most endangered mammals with many peculiar characteristics, yet the understanding of its sensory systems is still superficial. Studying the genomic basis of adaptation and evolution of pangolin's sensory system is expected to provide further potential assistance for their conservation in the future.
In this study, we performed a comprehensive comparative genomic analysis to explore the signature of sensory adaptation and evolution in pangolins. By comparing with the aardvark, Cape golden mole, and short-beaked echidna, 124 and 152 expanded gene families were detected in the genome of the Chinese and Malayan pangolins, respectively. The enrichment analyses showed olfactory-related genomic convergence among five concerned mammals. We found 769 and 733 intact OR genes, and 704 and 475 OR pseudogenes in the Chinese and Malayan pangolin species, respectively. Compared to other mammals, far more intact members of OR6 and OR14 were identified in pangolins, particularly for four genes with large copy numbers (OR6C2, OR14A2, OR14C36, and OR14L1). On the genome-wide scale, 1,523, 1,887, 1,110, and 2,732 genes were detected under positive selection (PSGs), intensified selection (ISGs), rapid evolution (REGs), and relaxed selection (RSGs) in pangolins. GO terms associated with visual perception were enriched in PSGs, ISGs, and REGs. Those related to rhythm and sound perception were enriched in both ISGs and REGs, ear development and morphogenesis were enriched in ISGs, and mechanical stimulus and temperature adaptation were enriched in RSGs. The convergence of two vision-related PSGs (OPN4 and ATXN7), with more than one parallel substituted site, was detected among five concerned mammals. Additionally, the absence of intact genes of PKD1L3, PKD2L1, and TAS1R2 and just six single-copy TAS2Rs (TAS2R1, TAS2R4, TAS2R7, TAS2R38, TAS2R40, and TAS2R46) were found in pangolins. Interestingly, we found two large insertions in TAS1R3, distributed in the N-terminal ectodomain, just in pangolins.
We found new features related to the adaptation and evolution of pangolin-specific sensory characteristics across the genome. These are expected to provide valuable and useful genome-wide genetic information for the future breeding and conservation of pangolins.
穿山甲是最濒危的哺乳动物之一，具有许多独特特征，但对其感觉系统的了解仍很肤浅。研究穿山甲感觉系统适应与进化的基因组基础有望为未来其保护提供进一步的潜在帮助。
在本研究中，我们进行了全面的比较基因组分析，以探索穿山甲感觉适应与进化的特征。通过与土豚、开普金鼹和短吻针鼹比较，在中国穿山甲和马来穿山甲基因组中分别检测到124个和152个扩张基因家族。富集分析显示了五种相关哺乳动物之间嗅觉相关的基因组趋同。我们在中国穿山甲和马来穿山甲物种中分别发现了769个和733个完整的嗅觉受体（OR）基因，以及704个和475个OR假基因。与其他哺乳动物相比，穿山甲中鉴定出的OR6和OR14完整成员要多得多，特别是对于四个具有大量拷贝数的基因（OR6C2、OR14A2、OR14C36和OR14L1）。在全基因组范围内，在穿山甲中检测到1523个、1887个、1110个和2732个处于正选择（PSG）、强化选择（ISG）、快速进化（REG）和放松选择（RSG）的基因。与视觉感知相关的基因本体（GO）术语在PSG、ISG和REG中富集。与节律和声音感知相关的术语在ISG和REG中均有富集，耳朵发育和形态发生在ISG中富集，机械刺激和温度适应在RSG中富集。在五种相关哺乳动物中检测到两个与视觉相关的PSG（OPN4和ATXN7）的趋同，具有多个平行替代位点。此外，在穿山甲中发现不存在完整的多囊蛋白1样3（PKD1L3）、多囊蛋白2样1（PKD2L1）和味觉受体1型成员2（TAS1R2）基因，仅有六个单拷贝的味觉受体2型（TAS2R）基因（TAS2R1、TAS2R4、TAS2R7、TAS2R38、TAS2R40和TAS2R46）。有趣的是，我们仅在穿山甲的味觉受体1型成员3（TAS1R3）中发现了两个大的插入片段，分布在N端胞外结构域。
我们在全基因组中发现了与穿山甲特异性感觉特征适应与进化相关的新特征。这些有望为未来穿山甲的繁育和保护提供有价值且有用的全基因组遗传信息。
