生物多样性正处于第六次的灭绝危机中，如何减缓并最终扭转这一趋势是人类目前面临的重大挑战之一。保护基因组学通过对受胁生物的基因组特征进行研究，对受胁生物的遗传多样性进行准确评估，揭示受胁生物的演化历史与致危的遗传机制，为制定和实施受胁生物保护策略提供重要的理论指导。 角雉属（Tragopan）是分布于喜马拉雅山脉至我国东南山地的森林雉类，包括黑头角雉（T. melanocephalus）、红胸角雉（T. satyra）、灰腹角雉（T. blythii）、红腹角雉（T. temminckii）和黄腹角雉（T. caboti）五个物种，呈现替代分布，大多为受胁物种。其中黄腹角雉仅分布于我国东南部的亚热带山地，为我国特有种，国家I级野生保护动物，被列入IUCN红色名录易危物种和CITES附录I。 本研究对黄腹角锥的基因组进行de novo测序，并结合转录组测序数据和脊椎动物的蛋白质数据库对其进行了注释。利用SOAPdenovo组装得到的黄腹角雉de novo基因组为1.13G，contig N50为422.64k，scaffold N50 为7.52M，组装质量较高。转录组测序共获得191,124条转录本序列。结合基因组、转录组和脊椎动物蛋白质数据，整合从头预测、基于转录组数据预测和基于同源蛋白质数据预测三种方法进行了基因组注释，共预测基因17,580个基因，其中92%与已知基因具有同源性。 对黄腹角雉、红腹角雉、灰腹角雉、红胸角雉和黑头角雉共19只个体进行了基因组重测序。获得单核苷酸多态性位点（SNPs）23,947,967个。红胸角雉的遗传多样性最高（π = 0. 6179%），其次是红腹角雉（π = 0.5968%）与灰腹角雉（π = 0.5525%），黄腹角雉的遗传多样性最低，仅为0.4562%。红腹角雉的杂合度最高（0.3159%），其次是红胸角雉（0.2180%）和黄腹角雉（0.1916%），灰腹角雉（0.1052%）的杂合度最低。基于贝叶斯法重建的系统发育树表明，分布于横断山以东的黄腹角雉和红腹角雉形成一个单系群，而主要分布于喜马拉雅山地的灰腹角雉、红胸角雉和黑头角雉形成另外一个单系群，表明祖先类群在喜马拉雅山与横断山之间发生了首次分化，随后再递次分化为五个物种。遗传结构的聚类分析和主成分分析结果均与系统发育树相互验证，表明角雉属间存在稳定的遗传分化。利用基因组扫描计算黄腹角雉和红腹角雉在基因组水平上的遗传分化，结果表明种间具有稳定的遗传差异（Fst = 0.30），仅在少数几个scaffold上存在高分化位点。 基于PSMC方法的种群历史动态分析结果表明，角雉属的物种分化自500万年前开始，可能与喜马拉雅山和青藏高原在中新世的快速隆升有关。黄腹角雉与分化后有效种群数量长期维持在较为稳定的水平，而红腹角雉的有效种群数量持续增长了4-5倍，但在最大末次冰期（LGM，10万年前至2万年前）两种角雉的种群数量均经历了显著的下降。灰腹角雉和红胸角雉的种群动态较为相似，在希夏邦马冰期（约117万年前至80万年前）其种群数量都经历了一次下降，随后种群开始增长，于10万年前开始，在LGM经历了显著的下降。气候变化与物种演化历史中形成的适应能力可能塑造了角雉属物种各异的种群历史动态。更新世多次冰期，特别是末次盛冰期的气候变化可能导致角雉属物种遗传多样性的下降，使其更容易受到来自人类活动的压力，形成了当前高度受胁的状况。

We are now in the midst of the sixth mass extinction, in which biodiversity loss at a rapid rate than ever. How to slow down and eventually reverse this trend is one of the major challenges we are facing. By charactering genomic signature, conservation genomics provides an excellent tool to accurately evaluate genetic diversity, and reveals the evolution history and genetic mechanism of threatened species, which provides theoretical framework for sustainability strategy formulation and implementation of endangered species. The genus Tragopan, including T. melanocephalus, T. satyra, T. blythii, T. temminckii and T. caboti, is alternatively distributed from Himalayas to the southeast of China. Most of species in the genus Tragopan are being threatened. T. caboti, which is endemic to China and only distributed in subtropical mountainous area of southeast China, is categorized as Vulnerable in IUCN list and listed in the First-Grade State Protection Animal and CITES appendix I. In this study, we de novo sequenced a male T. caboti as a reference genome which was annotated with the combination of genomic data, transcriptomic data and protein database of vertebrate animals. We used SOAPdevono to assemble the genome whose size is 1.13G, contig N50 is 422.64k and scaffold N50 is 7.52M, demonstrating high quality of genome assembly. We obtained 191,124 transcriptome sequences. Combining genome and transcriptome of T. caboti and protein database of vertebrate animals, we integrated results of ab initio gene prediction, transcriptome-driven and protein-driven gene prediction to annotate the reference genome. A total of 17,580 genes were predicted, and 92% of them could be identified by homologous genes. We resequened 19 individuals from species of T. caboti, T. temminckii, T. blythii, T. satyra and T. melanocephalus. A set of 23,947,967 single nucleotide polymorphisms (SNPs) were obtained after SNP calling and filtering. The genetic diversity of T. temminckii (π = 0. 6179%) was the highest, followed by T. satyra (π = 0.5968%) and T. blythii (π = 0.5525%), and of which T. caboti was the lowest, only 0.4562%. The heterozygosity of T. temminckii was the highest (0.3159%), followed by T. satyra (0.2180%) and T. caboti (0.1916%), while T. blythii (0.1052%) was the lowest. Based on the Bayesian method, we reconstructed the phylogenetic tree of Tragopan, respectively. The results showed that the species of T. caboti and T. temminckii, mainly inhibiting in the east of Hengduan mountain, are a monophyly, while T. temminckii, T. satyra and T. melanocephalus which are distributed in the Himalaya region are another monophyly. That indicates the ancestor of Tragopan first differentiated two groups between the Himalayas and Hengduan mountains and divided into five species subsequently. Genetic structure inferred by clustering analysis and principle component analysis is consistent with the result of the phylogenomic tree, suggesting significant genetic differentiation among Tragopan species. We calculated the level of genomic differentiation by genome scanning, demonstrating highly genomic differentiation (Fst = 0.30) between species with several scaffolds highly differentiated. Results of PSMC showed that the species differentiation of Tragopan began 5 Mya, which probably be related to the uplift of Himalayas and Tibetan plateau in the Miocene. The effective population size (Ne) of T. caboti remained stable after species differentiation, while the Ne of T. temminckii increased by four to five times in 2 million years. Both of them have experienced significant declines during the Last Glacial Maximum (LGM, 10kya – 2kya). And T. satyra and T. blythii shared similar demographic histories, of which population declined during the period of Shishapangma ice age (about 1.17Mya – 0.8Mya) and then began to grow. From 0.1Mya, their population experienced a significant decline in LGM. Climate change and different adaptation abilities among species may have played joint important role in shaping the heterogeneous demographic histories of Tragopan. Ice ages during Pleistocene, especially the LGM, may have reduced genetic diversity of Tragopan, making them more vulnerable to the disturbance of human activities, and becoming severely threatened.