A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies

Benjamin J Hanrahan; Kirat Alreja; Andre L M Reis; J King Chang; Duminda S B Dissanayake; Richard J Edwards; Terry Bertozzi; Jillian M Hammond; Denis O'Meally; Ira W Deveson; Arthur Georges; Paul Waters; Hardip R Patel

doi:10.1093/g3journal/jkaf046

A genome assembly and annotation for the Australian alpine skink Bassiana duperreyi using long-read technologies

G3 (Bethesda). 2025 Jun 4;15(6):jkaf046. doi: 10.1093/g3journal/jkaf046.

Authors

Benjamin J Hanrahan¹, Kirat Alreja², Andre L M Reis^{3

4

5}, J King Chang¹, Duminda S B Dissanayake⁶, Richard J Edwards^{1

7}, Terry Bertozzi^{8

9}, Jillian M Hammond^{3

4}, Denis O'Meally¹⁰, Ira W Deveson^{3

4

5}, Arthur Georges^{6

11}, Paul Waters¹, Hardip R Patel²

Affiliations

¹ School of Biotechnology and Biomolecular Science, Faculty of Science, University of New South Wales, Sydney, Sydney, NSW 2052, Australia.
² John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia.
³ Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia.
⁴ Centre for Population Genomics, Garvan Institute of Medical Research, Murdoch Children's Research Institute, Darlinghurst, NSW 2010, Australia.
⁵ Faculty of Medicine, University of New South Wales, Sydney, Sydney, NSW 2052, Australia.
⁶ Institute for Applied Ecology, University of Canberra, Bruce, ACT 2617, Australia.
⁷ Minderoo OceanOmics Centre at UWA, Oceans Institute, The University of Western Australia, Perth, WA 6009, Australia.
⁸ South Australian Museum, Adelaide, SA 5000, Australia.
⁹ School of Biological Sciences, The University of Adelaide, Adelaide, SA 5000, Australia.
¹⁰ Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA 91024, USA.
¹¹ Bioplatforms Australia (AusARG), Macquarie University, Sydney, NSW 2109, Australia.

Abstract

The eastern 3-lined skink (Bassiana duperreyi) inhabits the Australian high country in the southeast of the continent including Tasmania. It is a distinctive oviparous species because it undergoes sex reversal (from XX genotypic females to phenotypic males) at low incubation temperatures. We present a chromosome-scale genome assembly of a B. duperreyi XY male individual, constructed using PacBio HiFi and Oxford Nanopore Technologies long reads scaffolded using Illumina HiC data. The genome assembly length is 1.57 Gb with a scaffold N50 of 222 Mb, N90 of 26 Mb, 200 gaps, and 43.10% GC content. Most (95%) of the assembly is scaffolded into 6 macrochromosomes, 8 microchromosomes, and the X chromosome, corresponding to the karyotype. Fragmented Y chromosome scaffolds (n = 11 ≥ 1 Mb) were identified using Y-specific contigs generated by genome subtraction. We identified 2 novel alpha-satellite repeats of 187 and 199 bp in the putative centromeres that did not form higher-order repeats. The genome assembly exceeds the standard recommended by the Earth BioGenome Project: 0.02% false expansions, 99.63% k-mer completeness, 94.66% complete single-copy Benchmarking Universal Single-Copy Orthologs genes, and an average 98.42% of transcriptome data mappable to the genome assembly. The mitochondrial genome (17,506 bp) and the model rDNA repeat unit (15,154 bp) were assembled. The B. duperreyi genome assembly has high completeness for a skink and will provide a resource for research focused on sex determination and thermolabile sex reversal, as an oviparous foundation species for studies of the evolution of viviparity and for other comparative genomics studies of the Scincidae.

Keywords: Nanopore; PacBio; genome assembly; sex reversal; skink.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Australia
Female
Genome*
Genomics* / methods
Lizards* / genetics
Male
Molecular Sequence Annotation*

Associated data

figshare/10.25387/g3.27000865

Abstract

Publication types

MeSH terms

Associated data

Grants and funding