title: Comparative optical genome analysis of two pangolin species: Manis pentadactyla and Manis javanica.
abstract: 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.
authors.affiliation: 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.
authors.forename: Huang
authors.initials: H
authors.lastname: Zhihai
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Jiang
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Xiao
authors.initials: X
authors.lastname: Shuiming
authors.affiliation: 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.
authors.forename: Liao
authors.initials: L
authors.lastname: Baosheng
authors.affiliation: Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China.
authors.forename: Gao
authors.initials: G
authors.lastname: Yuan
authors.affiliation: Ultravision-tech, Beijing 100089, China.
authors.forename: Zhai
authors.initials: Z
authors.lastname: Chaochao
authors.affiliation: 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.
authors.forename: Qiu
authors.initials: Q
authors.lastname: Xiaohui
authors.affiliation: 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.
authors.forename: Xu
authors.initials: X
authors.lastname: Wen
authors.affiliation: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Shilin
mesh_terms: D000818:Animals; D056727:Endangered Species; D016678:Genome; D006801:Humans; D008322:Mammals / Q000235:genetics*; D056972:Optical Restriction Mapping
keywords: Manidae; Optical mapping; Pangolin; Restriction maps