The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
Cell Res. 2013 Sep;23(9):1091-105. doi: 10.1038/cr.2013.104. Epub 2013 Aug 6.
Crocodilians are diving reptiles that can hold their breath under water for long periods of time and are crepuscular animals with excellent sensory abilities. They comprise a sister lineage of birds and have no sex chromosome. Here we report the genome sequence of the endangered Chinese alligator (Alligator sinensis) and describe its unique features. The next-generation sequencing generated 314 Gb of raw sequence, yielding a genome size of 2.3 Gb. A total of 22 200 genes were predicted in Alligator sinensis using a de novo, homology- and RNA-based combined model. The genetic basis of long-diving behavior includes duplication of the bicarbonate-binding hemoglobin gene, co-functioning of routine phosphate-binding and special bicarbonate-binding oxygen transport, and positively selected energy metabolism, ammonium bicarbonate excretion and cardiac muscle contraction. Further, we elucidated the robust Alligator sinensis sensory system, including a significantly expanded olfactory receptor repertoire, rapidly evolving nerve-related cellular components and visual perception, and positive selection of the night vision-related opsin and sound detection-associated otopetrin. We also discovered a well-developed immune system with a considerable number of lineage-specific antigen-presentation genes for adaptive immunity as well as expansion of the tripartite motif-containing C-type lectin and butyrophilin genes for innate immunity and expression of antibacterial peptides. Multifluorescence in situ hybridization showed that alligator chromosome 3, which encodes DMRT1, exhibits significant synteny with chicken chromosome Z. Finally, population history analysis indicated population admixture 0.60-1.05 million years ago, when the Qinghai-Tibetan Plateau was uplifted.
鳄鱼是潜水爬行动物，可以在水下长时间屏住呼吸，是具有出色感官能力的黄昏动物。它们与鸟类构成姊妹进化枝，没有性染色体。在这里，我们报告了濒危的中国扬子鳄（Alligator sinensis）的基因组序列，并描述了其独特的特征。下一代测序产生了 314 Gb 的原始序列，产生了 2.3 Gb 的基因组大小。使用从头开始的、基于同源性和 RNA 的组合模型，共预测了 22200 个基因。长潜水行为的遗传基础包括碳酸氢盐结合血红蛋白基因的重复，常规磷酸盐结合和特殊碳酸氢盐结合氧运输的共同功能，以及积极选择的能量代谢、碳酸氢铵排泄和心肌收缩。此外，我们阐明了扬子鳄强大的感觉系统，包括显著扩展的嗅觉受体库、快速进化的神经相关细胞成分和视觉感知，以及与夜视相关的视蛋白和声音检测相关的耳石的正选择。我们还发现了一个发达的免疫系统，具有大量用于适应性免疫的特异性抗原呈递基因，以及用于先天免疫的含三部分基序的 C 型凝集素和丁酰磷蛋白基因的扩张，以及抗菌肽的表达。多荧光原位杂交显示，编码 DMRT1 的扬子鳄染色体 3与鸡染色体 Z 具有显著的同线性。最后，种群历史分析表明，当青藏高原隆起时，种群混合发生在 0.60-1.05 百万年前。
