川金丝猴全基因组测序解析其植食性机制与进化史Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history研究对象：川金丝猴期刊：Nature Genetics 影响因子：29.352合作单位：中国科学院动物研究所发表时间：2014年11月摘 要Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the genome of a male golden snub-nosed monkey (Rhinopithecus roxellana ) and resequencing at 30× coverage of three related species (Rhinopithecus bieti , Rhinopithecus brelichi andRhinopithecus strykeri ). Comparative analyses showed that Asian colobines have an enhanced ability to derive energy from fatty acids and to degrade xenobiotics. We found evidence for functional evolution in the colobine RNASE1 gene, encoding a key secretory RNase that digests the high concentrations of bacterial RNA derived from symbiotic microflora. Demographic reconstructions indicated that the profile of ancient effective population sizes for R. roxellana more closely resembles that of giant panda rather than its congeners. These findings offer new insights into the dietary adaptations and evolutionary history of colobine primates.关键词金丝猴；重测序；植食性；进化研究背景金丝猴（Rhinopithecu spp.)隶属于灵长目（Primates）、疣猴亚科（Colobinae）、仰鼻猴属（Rhinopithecus ），目前共有5个种，即川、滇、黔、缅甸和越南金丝猴。
通过对金丝猴基因组以及肠道基因组进行全面系统的研究，解析了金丝猴的植食性分子遗传机制，为了解疣猴亚科的系统进化、功能适应性奠定了遗传基础，同时开展了仰鼻猴属的进化历史和遗传多态性分析。
物4、进化分析对与植食性紧密相关的基因RNASE1进行研究，结果支持“一次复制假说”，同时结果也支持“平行进化假说”。
进化分析发现北部物种（川金丝猴和黔金丝猴）与喜马拉雅物种（滇金丝猴和缅甸金丝猴）约在160万年以前发生了分化；北部物种形成时间约在62万年前，喜马拉雅物种形成时间约在15万年前。
5、群体遗传学分析结合重测序对来自云南的滇金丝猴、贵州的黔金丝猴和云南怒江的缅甸金丝猴进行群体遗传分析，黔、滇和缅甸金丝猴的群体趋势则与川金丝猴分歧较大，其中黔金丝猴在末次盛冰期的时候有一个小的上升（图2）。
研究结果1、金丝猴基因图谱采用全基因组de novo 测序获得金丝猴基因组大小为3.05 Gb，组装结果contig N50: 25.5 Kb，scaffold N50: 1.55 Mb。
其中蛋白编码基因为21,813个，转座元件比例为44.17%。
2、基因家族分析金丝猴基因组与其他已发表的灵长类动物进行了比对分析，结果发现它们共有基因家族10,244个；与旧世界猴及人猿物种比较分析，金丝猴基因家族未出现明显的基因家族扩张或收缩。
3、金丝猴植食性适应的分子机制解析比较基因组学分析发现金丝猴外源物质降解基因和唾液分泌蛋白编码基因发生显著扩张；与牛的趋同进化分析鉴定出33个快速进化嗅觉基因，其中69.7%的基因可能与水果、植物等气味相关；此外分析发现金丝猴的肠道微生物群落与牛的相似，其群落与前肠发酵相关（图1）。
图1 金丝猴植食性机制的分析图2 金丝猴有效群体大小分析参考文献Zhou X, Wang B, Pan Q, et al . Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history [J]. Nature genetics, 2014, 46(12): 1303-1310.巴克夏猪的起源和驯化机制Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin研究对象：巴克夏猪期刊：Scitenfic Reports 影响因子：5.578合作单位：四川农业大学发表时间：2014年4月摘 要Domesticated organisms have experienced strong selective pressures directed at genes or genomic regions controlling traits of biological, agricultural or medical importance. The genome of native and domesticated pigs provide a unique opportunity for tracing the history of domestication and identifying signatures of artificial selection. Here we used whole-genome sequencing to explore the genetic relationships among the European native pig Berkshire and breeds that are distributed worldwide, and to identify genomic footprints left by selection during the domestication of Berkshire. Numerous nonsynonymous SNPs-containing genes fall into olfactory-related categories, which are part of a rapidly evolving superfamily in the mammalian genome. Phylogenetic analyses revealed a deep phylogenetic split between European and Asian pigs rather than between domestic and wild pigs. Admixture analysis exhibited higher portion of Chinese genetic material for the Berkshire pigs, which is consistent with the historical record regarding its origin. Selective sweep analyses revealed strong signatures of selection affecting genomic regions that harbor genes underlying economic traits such as disease resistance, pork yield, fertility, tameness and body length. These discoveries confirmed the history of origin of Berkshire pig by genome-wide analysis and illustrate how domestication has shaped the patterns of genetic variation.关键词巴克夏猪；驯化机制；全基因组测序研究背景巴克夏猪是典型的欧洲地方驯化品种，早在18世纪早期就开始经历高强度人工选择，使其能够快速积累肌肉组织和人们期望的猪肉品质，如多汁、风味、嫩度、粉红色调和加深纹理。
为了综合探讨猪的丰富表型的遗传基础，本文研究了巴克夏猪（3个个体）和世界各地的猪（38头）之间的遗传关系，探索巴克夏猪在人工选择下的遗传变异规律。
and domestication动物研究结果1、通过进行变异检测发现大量非同义SNP变异基因与嗅觉功能相关，该类基因是哺乳动物基因组中一个迅速发展的基因家族的一部分。
2、系统发育分析结果表明欧亚的地理隔离造成的遗传结构差异超过了野生和驯化的差异（图1）。
图1 系统发育分析图2 种群基因交流分析图3 巴克夏猪中受强选择的基因区域4、选择性清除分析结果证实，巴克夏猪对于潜在的经济性状相关基因具有强选择信号，如抗病、猪肉产量、生育、温顺和体长等。
在受选择性信号最强的区域发现NR6A1基因，而该基因是与脊背的伸长和椎骨数量增加非常相关的候选基因（图3）。
参考文献Li M, Tian S, Yeung C K L, et al. Whole-genome sequencing of Berkshire (European native pig)provides insights into its origin and domestication [J]. Scientific reports, 2014, 4: 4678.3、种群基因交流分析（D-statistics）结果显示巴克夏猪中具有更高比例的中国猪的遗传物质，这与该猪的历史起源记录一致（图2）。