Manis pentadactyla
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA298142 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2591032_1.fastq.gz | Fastqsanger.gz | |||
| SRR2591032_2.fastq.gz | Fastqsanger.gz |
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Project description:Manis pentadactyla Genome sequencing and assembly
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Project description:Background: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. Findings: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. Conclusions: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.
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Project description:Chinese Pangolins (Manis pentadactyla) are Critically Endangered and one of the most illegally traded mammals globally. We generated first COI sequences from five individuals of this species from Nepal. BLASTn search of our 600 bp sequences at GenBank showed pair-wise identity between 99.17% and 100% to M. pentadactyla. There were three haplotypes and a total of five variable sites among five M. pentadactyla sequences. Neighbor-joining tree revealed that all M. pentadactyla from Nepal clustered into same group further splitting into two sub-groups albeit with low bootstrap value, suggesting potential multiple geographic origins. The K2P distance was 0.3% within group and 0.7% between four sequences from Bhaktapur and Kavrepalanchok districts (Mape2, Mape3, Mape5 and Mape6) and museum sample (Mape10). This study has generated reference samples for M. pentadactyla from Nepal and will be helpful in understanding dynamics of illegal trade of this species and in successful identification of M. pentadactyla from Nepal even in the absence of intact specimens.
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