ArticleGigaScience2016
Comparative optical genome analysis of two pangolin species: Manis pentadactyla and Manis javanica.
Article in GigaScience, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 43 citations in OpenAlex.
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- Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern.Molecular ecology · 2021Article
- Genomic consequences of population decline in critically endangered pangolins and their demographic histories.National science review · 2020Article
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- Characterization of the Complete Chloroplast Genome ofBioMed research international · 2019Article
- Modelling BioNano optical data and simulation study of genome map assembly.Bioinformatics (Oxford, England) · 2018Article
- Complete Chloroplast Genome Sequence and Phylogenetic Analysis ofMolecules (Basel, Switzerland) · 2018Article
- Genome-Wide Characterization and Expression Analyses ofInternational journal of molecular sciences · 2018Article
- Investigation on Species Authenticity for Herbal Products ofMolecules (Basel, Switzerland) · 2018Article
- Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii.Molecules (Basel, Switzerland) · 2018Article
- Panax ginseng genome examination for ginsenoside biosynthesis.GigaScience · 2017Article
- Complete Chloroplast Genome Sequence and Phylogenetic Analysis of the Medicinal Plant Artemisia annua.Molecules (Basel, Switzerland) · 2017Article
- Comprehensive Characterization for Ginsenosides Biosynthesis in Ginseng Root by Integration Analysis of Chemical and Transcriptome.Molecules (Basel, Switzerland) · 2017Article
- Transcriptomic analysis identifies genes and pathways related to myrmecophagy in the Malayan pangolin (PeerJ · 2017Article
- Comparative optical genome analysis of two pangolin species: Manis pentadactyla and Manis javanica.GigaScience · 2016Article
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Authors and funding
9 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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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