Supporting data for "Comparative optical genome analysis of two Pangolin species Manis pentadactyla and Manis javanica"

Dataset type: Genomic, Genome-Mapping
Data released on November 22, 2016

Zhihai H; Jiang X; Shuiming X; Baosheng L; Yuan G; Chaochao Z; Xiaohui Q; Wen X; Shilin C (2016): Supporting data for "Comparative optical genome analysis of two Pangolin species Manis pentadactyla and Manis javanica" GigaScience Database. http://dx.doi.org/10.5524/100248

DOI10.5524/100248

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.

Additional details

Read the peer-reviewed publication(s):

Zhihai, H., Jiang, X., Shuiming, X., Baosheng, L., Yuan, G., Chaochao, Z., … Shilin, C. (2016). Comparative optical genome analysis of two pangolin species: Manis pentadactyla and Manis javanica. GigaScience, 5(1). doi:10.1093/gigascience/giw001





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
DN9974 Malayan pangolinManis javanica Description:The Sunda pangolin (Manis javanica), a...
Tissue:blood
Amount or size of sample collected:3
...
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ZH143292 Chinese pangolinManis pentadactyla Description:The Chinese pangolin (Manis pentadacty...
Tissue:blood
Amount or size of sample collected:3
...
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Displaying 1-2 of 2 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
DNOptical mapUNKNOWN16.22 MB2016-11-01
DNotherUNKNOWN891.63 MB2016-11-01
ZHOptical mapUNKNOWN13.48 MB2016-11-01
ZHotherUNKNOWN944.76 MB2016-11-01
ReadmeTEXT2.14 KB2016-11-01
Displaying 1-5 of 5 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China 81403053
National Natural Science Foundation of China 81503469

Protocols.io:

Date Action
November 22, 2016 Dataset publish
December 7, 2016 External Link updated :
December 7, 2016 External Link updated :
January 6, 2017 Manuscript Link added : 10.1093/gigascience/giw001
January 18, 2017 External Link removed :
January 18, 2017 External Link removed :