鲸类味觉的丢失及鲸类适应性进化的比较基因组学分析

发布时间：2018-07-07 14:13

  本文选题：鲸类 + 味觉基因　； 参考：《南京师范大学》2016年博士论文

【摘要】：人类可以感知5种基本的味觉,即酸、甜、苦、咸和鲜,这5种味觉在哺乳动物的生理和生态适应过程中发挥重要作用。在陆生哺乳动物中,这些味觉受体基因的分子遗传学研究已经较为广泛,然而在海洋哺乳动物中相应的研究却较为稀缺。本研究在代表性的鲸类物种中调查了5种味觉感知相关的受体基因。通过对这些味觉受体基因的序列比对,我们在编码酸、甜、鲜和苦味的受体基因上检测到了移码和／或提前终止密码子突变,通过把第一位提前终止密码子标注到假基因的蛋白二级结构上,我们发现这些突变均导致了蛋白二级结构的缩短,从而导致其丧失了原有的功能。进一步的选择压力分析表明编码酸、甜和鲜味的受体基因上的选择压力并未完全放松,提示它们的假基因化可能是近期事件,而苦味受体所受到的选择压力几乎完全放松,表明它们的假基因化可能发生的较早。编码咸味受体的3个基因在鲸类中仍然是完整的,我们推测这可能和咸味受体在肾脏、肺、皮肤等处的钠离子吸收功能相关,至于鲸类是否保留有咸味感知能力仍有待于进一步研究。为了进一步了解鲸类对全水生环境的适应,我们利用已发表的鲸类基因组(白淍豚和小须鲸)并重测了3个瓶鼻海豚进行了种间和种内的比较基因组学分析。基于白淍豚、小须鲸、牛、狗、人和小鼠的单拷贝直系同源基因,我们利用PAML正选择分析揭示了在鲸类起源及其随后的分化过程中,它们的先天性免疫系统出现了普遍的适应性进化。正选择分析还进一步揭示了和脂肪酸转运、活化以及三酰甘油合成相关的基因在白淍豚和小须鲸中均是受到正选择的,这和它们拥有厚厚的鲸脂也是一致的。此外,涉及到渗透调节、骨密度调控和低氧耐受的基因在鲸类中也是受到正选择的,这和它们需要应对截然不同的渗透压、快速游泳和潜水等行为是息息相关的。为了进一步挖掘鲸类对咸淡水的适应,我们利用海洋鲸类(小须鲸和瓶鼻海豚)和淡水鲸类(白淍豚)的重测序数据筛选单核苷酸多态性位点,并用PROVEAN软件评估这些氨基酸替换对蛋白功能的影响。PROVEAN分析进一步揭示了咸水和淡水鲸类中拥有种间核苷酸差异的基因涉及到嗅觉和视觉系统、DNA损伤修复和色素沉着等。基于MSMC的种群动态分析也表明白淍豚的功能性灭绝可能是栖息地的破坏和极端的人类活动造成的,这与之前的白淍豚基因组分析结果也是一致的。
[Abstract]:Humans can perceive five basic taste senses, namely, sour, sweet, bitter, salty and fresh, which play an important role in the physiological and ecological adaptation of mammals. In terrestrial mammals, the molecular genetics of these taste receptor genes has been widely studied, but the corresponding research in marine mammals is relatively scarce. This study investigated five receptor genes associated with taste perception in a typical cetacean species. By sequencing these taste receptor genes, we detected frameshift and / or early termination codon mutations in receptor genes that encode acid, sweet, fresh and bitter. By tagging the first early termination codon to the protein secondary structure of the pseudogenic gene, we found that these mutations all led to the shortening of the protein secondary structure, which resulted in the loss of its original function. Further selection stress analysis showed that the selection pressure on the genes encoding acid, sweet and delicious receptors was not completely relaxed, suggesting that their pseudogenization might be a recent event, while the selection pressure on bitter receptors was almost completely relaxed. This suggests that their pseudogenization may have occurred earlier. The three genes that encode salty receptors are still intact in whales, and we speculate that this may be related to sodium absorption in the kidneys, lungs, skin, etc. Whether cetaceans retain saltwater perception remains to be further studied. In order to further understand the adaptation of cetaceans to the whole aquatic environment, we used the published cetacean genomes (white porpoises and minke whales) to re-measure the comparative genomics analysis of three flask dolphins in both species and species. Based on the single-copy lineal homologous genes of white porpoises, minke whales, cattle, dogs, humans and mice, we used PAML positive selection analysis to reveal the origin and subsequent differentiation of cetaceans. Their innate immune system has developed a general adaptive evolution. The positive selection analysis further revealed that genes associated with fatty acid transport, activation and triglyceride synthesis were both positively selected in both white porpoises and minke whales, which were consistent with their possession of thick blubber whales. In addition, genes involved in osmotic regulation, bone mineral density regulation and hypoxia tolerance are also being selected in whales, which is closely related to their response to radically different osmotic pressures, rapid swimming and diving. To further explore the adaptation of whales to brackish water, we used resequencing data from marine whales (minke whales and flask dolphins) and freshwater whales (white porpoises) to screen single nucleotide polymorphisms. The effect of these amino acid substitutions on protein function was evaluated by PROVEAN software. The results further revealed that genes with interspecific nucleotide differences in brackish water and freshwater whales were involved in DNA damage repair and pigmentation of olfactory and visual systems. The population dynamics analysis based on MSMC also showed that the functional extinction may be caused by habitat destruction and extreme human activities, which is consistent with the previous results of genome analysis.
【学位授予单位】：南京师范大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q953
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本文编号：2105215