De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes

Genome assemblies. (A) Methodological workflow for the generation of turtle genome assemblies. (B) Repetitive DNA abundance in the turtle genomes assembled here for Staurotypus triporcatus (STR) and Apalone spinifera (ASP), plus those of Trachemys scripta elegans (TSC) (Simison et al. 2020) as corrected by Lee et al. (2020), and Gopherus evgoodei (GVE) (Rhie et al. 2021) that serve as reference for comparison. (C) Circos plots (of sequences >3 kbp) depicting genomic chromosomal syntenies and comparative genomic characteristics (Log₁₀ of normalized Transcripts Per Million—TPM—gene expression, GC, and gene content) between ASP and STR. (D) GC content, gene density, and average gene length as a function of chromosome length in four turtle species and chicken, Gallus gallus (Warren et al. 2023).