Whole-genome sequencing of six green sea turtles (Chelonia mydas) from Malaysia for reproducible small-variant discovery and caller benchmarking
Whole-genome sequencing of six adult female green sea turtles (Chelonia mydas) sampled in Terengganu, Malaysia: two wild-nesting healthy individuals from Chagar Hutang Turtle Sanctuary, Pulau Redang, and four captive individuals from the Turtle Conservation and Information Centre, Rantau Abang - two healthy and two presenting active skin lesions. Blood-derived DNA was sequenced as 150 bp paired-end reads on an Illumina NovaSeq X Plus to a mean depth of 39-58x per individual, all six libraries in a single batch on one flow cell. These data support the development of ReproVar-NM, a reproducible workflow for small-variant discovery, fair multi-caller comparison and simulation-calibrated benchmarking in small-cohort, non-model vertebrate genomes. Reads were aligned to the chromosome-level reference assembly rCheMyd1.pri.v2 (GCF_015237465.2) and variants called independently with GATK HaplotypeCaller and DeepVariant, producing a curated whole-genome SNP and indel catalogue for Malaysian C. mydas. Sampling was conducted under Universiti Malaysia Terengganu Research Ethics Committee approval UMT/JKEPHMK/2023/89 and Terengganu State Department of Fisheries reference DOF.TR.TCIC.2689(23).
Whole-genome sequencing of six adult female green sea turtles (Chelonia mydas) sampled in Terengganu, Malaysia: two wild-nesting healthy individuals from Chagar Hutang Turtle Sanctuary, Pulau Redang, and four captive individuals from the Turtle Conservation and Information Centre, Rantau Abang - two healthy and two presenting active skin lesions. Blood-derived DNA was sequenced as 150 bp paired-end reads on an Illumina NovaSeq X Plus to a mean depth of 39-58x per individual, all six libraries in a single batch on one flow cell. These data support the development of ReproVar-NM, a reproducible workflow for small-variant discovery, fair multi-caller comparison and simulation-calibrated benchmarking in small-cohort, non-model vertebrate genomes. Reads were aligned to the chromosome-level reference assembly rCheMyd1.pri.v2 (GCF_015237465.2) and variants called independently with GATK HaplotypeCaller and DeepVariant, producing a curated whole-genome SNP and indel catalogue for Malaysian C. mydas. Sampling was conducted under Universiti Malaysia Terengganu Research Ethics Committee approval UMT/JKEPHMK/2023/89 and Terengganu State Department of Fisheries reference DOF.TR.TCIC.2689(23).