Data from: "Identification of SNP markers for the endangered Ugandan red colobus (Procolobus rufomitratus tephrosceles) using RAD sequencing" in Genomic Resources Notes accepted 1 December 2014 to 31 January 2015

Despite dramatic growth in the field of primate genomics over the past decade, studies of primate population and conservation genomics in the wild have been hampered due to the difficulties inherent in studying non-model organisms and endangered species, such as lack of a reference genome and current challenges in de novo primate genome assembly. Here, we used Restriction-site Associated DNA (RAD) sequencing to develop a population-based SNP panel for the Ugandan red colobus (P. rufomitratus tephrosceles), which is a highly threatened monkey due to habitat loss. We analyzed blood samples from 24 individuals from Kibale National Park (Uganda) using single-end RAD sequencing. We obtained 70,773,857 reads, of which 58,814,906 passed the filtering steps. Using the program STACKS v. 1.11 we identified 113,376 loci, of which 50,558 were polymorphic and had a mean observed heterozygosity of 0.25. These data will be used to study the effects of habitat fragmentation on genomic diversity, dispersal, and disease transmission in this species. Our approach provides a good example of the potential of RAD sequencing in studies of wild primate populations.

尽管近十年来灵长类基因组学领域发展迅猛，但由于研究非模式生物（non-model organism）与濒危物种所固有的诸多难点——例如缺乏参考基因组（reference genome）以及当前灵长类de novo基因组组装面临的挑战——野生灵长类种群基因组学与保护基因组学研究仍受到诸多阻碍。本研究采用限制性酶切位点相关DNA（Restriction-site Associated DNA, RAD）测序技术，为因栖息地丧失而处于高度濒危状态的乌干达红疣猴（P. rufomitratus tephrosceles）开发了基于种群水平的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）分型标记集。我们采用单端RAD测序技术，对采自乌干达基巴莱国家公园的24只个体的血液样本进行了分析，共获得70,773,857条测序读段（reads），其中58,814,906条通过质量过滤步骤。本研究使用STACKS v.1.11软件共鉴定出113,376个基因位点（loci），其中50,558个为多态性位点，平均观测杂合度（observed heterozygosity）为0.25。上述数据将用于解析栖息地片段化对该物种基因组多样性、扩散模式及疾病传播的影响。本研究方法为RAD测序技术在野生灵长类种群研究中的应用潜力提供了良好范例。