London Calling 2023: From genome assembly to epigenome characterisation: a nanopore journey in the footsteps of an endangered tortoise

Pyxis arachnoides is a critically endangered tortoise that lives in a narrow coastal ecoregion of Madagascar. Investigating the genetic structure of its population and identifying the sex of individuals in a fast and non-invasive way is of pivotal importance to monitoring the conservation status of the species. Furthermore, like most Testudines, this species undergoes temperature-dependent sex determination, representing an interesting subject to dissect the molecular and evolutionary aspects of this developmental process. In this study, we obtained a high-quality, chromosome-level P. arachnoides reference genome by combining Q30+ shotgun sequencing and Pore-C scaffolding. Then, we characterised its sex-related methylome dimorphisms and highlighted biologically relevant, differentially methylated CpG islands. This project demonstrates the feasibility of an end-to-end approach relying solely on Oxford Nanopore long-read sequencing for both de novo genome assembly and functional exploration of a novel species.