Zhihai Huang, Jiang Xu, Shuiming Xiao, Baosheng Liao, Yuan Gao, Chaochao Zhai, Xiaohui Qiu, Wen Xu, Shilin Chen
Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, and China Academy of Chinese Medical Sciences Guangdong Branch, China Academy of Chinese Medical Sciences, Guangzhou 510006, China.
Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
Gigascience. 2016 Dec 1;5(1):1-5. doi: 10.1093/gigascience/giw001.
The pangolin is a Pholidota mammal with large keratin scales protecting its skin. Two pangolin species ( Manis pentadactyla and Manis javanica ) have been recorded as critically endangered on the International Union for Conservation of Nature Red List of Threatened Species. Optical mapping constructs high-resolution restriction maps from single DNA molecules for genome analysis at the megabase scale and to assist genome assembly. Here, we constructed restriction maps of M. pentadactyla and M. javanica using optical mapping to assist with genome assembly and analysis of these species.
Genomic DNA was nicked with Nt.BspQI and then labeled using fluorescently labeled bases that were detected by the Irys optical mapping system. In total, 3,313,734 DNA molecules (517.847 Gb) for M. pentadactyla and 3,439,885 DNA molecules (504.743 Gb) for M. javanica were obtained, which corresponded to approximately 178X and 177X genome coverage, respectively. Qualified molecules (≥150 kb with a label density of >6 sites per 100 kb) were analyzed using the de novo assembly program embedded in the IrysView pipeline. We obtained two maps that were 2.91 Gb and 2.85 Gb in size with N50s of 1.88 Mb and 1.97 Mb, respectively.
Optical mapping reveals large-scale structural information that is especially important for non-model genomes that lack a good reference. The approach has the potential to guide de novo assembly of genomes sequenced using next-generation sequencing. Our data provide a resource for Manidae genome analysis and references for de novo assembly. This note also provides new insights into Manidae evolutionary analysis at the genome structure level.
穿山甲是一种有鳞目哺乳动物，其体表覆盖着大型角质鳞片以保护皮肤。两种穿山甲物种（中华穿山甲和爪哇穿山甲）在国际自然保护联盟濒危物种红色名录中被列为极度濒危物种。光学图谱技术可从单个DNA分子构建高分辨率限制酶图谱，用于兆碱基规模的基因组分析及辅助基因组组装。在此，我们利用光学图谱技术构建了中华穿山甲和爪哇穿山甲的限制酶图谱，以辅助这两个物种的基因组组装和分析。
基因组DNA用Nt.BspQI酶切产生切口，然后用荧光标记的碱基进行标记，通过Irys光学图谱系统进行检测。总共获得了3313734个中华穿山甲的DNA分子（517.847 Gb）和3439885个爪哇穿山甲的DNA分子（504.743 Gb），分别对应约178倍和177倍的基因组覆盖度。使用IrysView流程中嵌入的从头组装程序对合格分子（≥150 kb，标记密度 > 每100 kb 6个位点）进行分析。我们获得了两个图谱分别为2.91 Gb和2.85 Gb，N50分别为1.88 Mb和1.97 Mb。
光学图谱揭示了大规模的结构信息,这对于缺乏良好参考基因组的非模式生物基因组尤为重要。该方法有潜力指导使用下一代测序技术测序的基因组的从头组装。我们的数据为穿山甲科基因组分析提供了资源，也为从头组装提供参考。本研究还在基因组结构层面为穿山甲科进化分析提供了新见解。
