Data released on November 22, 2016
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 a single-strand DNA molecule for genome analysis at the mega-base 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, followed by labeling using fluorescent-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/100 kilobases) 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 NGS-based de novo assembly. Our data provide a resource for Manidae genome analysis and references for de novo assembly.