Skip to main content
Dryad logo

C porosus genotype data

Citation

Fukuda, Yusuke; Banks, Sam (2022), C porosus genotype data, Dryad, Dataset, https://doi.org/10.5061/dryad.bcc2fqz94

Abstract

We collected 714 tissue samples of non-captive saltwater crocodiles Crocodylus porosus from Australia and its neighbouring countries and got them genotyped by Diversity Arrays Technology (Canberra, Australia) between 2016 and 2019. The folder contains two files named 'Report_DCroc19-4196_4_moreOrders_SNP_mapping_2.csv' and 'IDpop_sample_data_.csv'. The former contains the single-nucleotide polymorphism (SNP) data and latter has attributes (population ID, GPS coordinates, species, country) of each sample.

Methods

DNA extraction and genotyping were conducted at Diversity Arrays Technology (Canberra, Australia) using the DArTseq approach (Kilian et al., 2012). DArTseq uses genome complexity reduction and NGS approaches conceptually similar to RADseq, in this case based around a SphI enzyme digestion of genomic DNA and Illumina HiSeq 2500 sequencing. We ran 30% of samples twice as technical replicates to assess the repeatability of single-nucleotide polymorphism (SNP) calls. These are pre-filtering data for analyses.

Reference

Kilian, A., Wenzl, P., Huttner, E., Carling, J., Xia, L., Blois, H., … Uszynski, G. (2012). Diversity Arrays Technology: a generic genome profiling technology on open platforms. In Methods in Molecular Biology. Data Production and Analysis in Population Genomics (pp. 67–89). doi: 10.1007/978-1-61779-870-2_5

Funding

Australian National University

Northern Territory Government

National Geographic Society, Award: 51-16

Holsworth Wildlife Research Endowment, Award: HWRE2016R2027NEW

IUCN-SSC Crocodile Specialist Group Student Research Assistance Scheme, Award: 15/5

ACT Herpetological Association