Patrick G.S. Grady from the University of Connecticut presented at London Calling 2023 a session entitled: “Unraveling chromosomal evolution in marsupials: comparative genomics and methylomics with telomere-to-telomere precision.” Grady spoke about the use of marsupials as a model. They have pentapedal locomotion, unique reproduction, and dynamic forms of cancer. Their genome scan be studied with long-read sequencing to compare marsupials.The genomic diversity complements the phenotypic diversity, said Grady, yet there are “wildly different evolutionary rates.” Grady spoke about the evolution of ultra-long read sequencing and now with two flow cells plus chromatin info marsupial genomes can be generated. With a Q score of 23 and an N50 of 161 kb, the team uses one LSK v14 PromethION flow cell and one 1 ULK v 114 run. Grady shared a table of assembly statistics with wallaby and other marsupials. Comparisons of genomes seem to indicate differences in the centromeres. A “stained glass plot” compared linear composition and epigenetics of genome features. Grady thinks there is a simple repeat that has caused these fusions. In some places this is a centromere and in some places it isn’t. With complete assemblies, the team is able to map more data to the Telomere-to-Telomere (T2T) assemblies and identify sequences and features. Comparative genomes at this resolution is possible thanks to the PromethION sequence datasets. I thought it was interesting to learn how Grady mapped sequences using FISH too. Grady assembled with Flye and Verkko assemblers using samples from males and females from each species.
