London Calling 2023: Unraveling chromosomal evolution in marsupials: comparative genomics and methylomics with telomere-to-telomere precision

Advances in Oxford Nanopore duplex sequencing have pushed the capabilities of genome assembly to new heights and allowed us to address decades-long questions about chromosomal evolution. Marsupials such as the Tammar wallaby have long served as models for chromosomal study, reproductive biology, and drug discovery. The latest sequencing technology has allowed us to rapidly expand to wide-scale comparative genomics of marsupials at large. Here, we present comparisons of telomere-to-telomere genomes and epigenomes across multiple marsupial orders (including Diprotodontia and Dasyuromorphia). These genomes were assembled with Q20+ PromethION long reads and ultra-long reads, resulting in extremely accurate and contiguous assemblies including the elusive centromeres, telomeres, and miniscule Y chromosomes. These analyses reveal a multitude of interesting patterns throughout the marsupial genome, such as marsupial-specific centromere and repetitive element structures. We address the significant differences between sex chromosomes, potential mechanisms of karyotypic instability, and what we have learned from the epigenome.