UC Berkeley

Viewed through the lens of comparative genomics, how have chromosomes and karyotypes evolved, particularly under extreme scenarios of rapid or torpid evolution? To examine this question, I produced and analyzed new high-quality, chromosome-scale genome assemblies, representing cases of extreme chromosome evolution. The interplay between convergent and divergent genomic architectures can further our understanding into the maintenance of chromosome structure and organization as well as the underlying biological mechanisms.

Despite their recent divergence, muntjac deer show striking karyotype differences. In Chapter 2, I produced new chromosome-scale genome assemblies for the Chinese and Indian muntjacs, Muntiacus reevesi (2n=46) and Muntiacus muntjak (2n=6/7), and analyzed their evolution and architecture. I identified six fusion events shared by both species relative to the cervid ancestor and, therefore, present in the muntjac common ancestor, six fusion events unique to the M. reevesi lineage, and 26 fusion events unique to the M. muntjak lineage. One of these M. muntjak fusions reversed an earlier fission in the cervid lineage. Although comparative Hi-C analysis uncovered differences in long-range genome contacts and A/B compartment structures, I discovered widespread conservation of local chromatin contacts between the muntjacs, even near the fusion sites. Analysis of the muntjac genomes revealed new insights into this unique case of rapid karyotype evolution and the resulting biological variation.

In contrast to muntjacs, frogs are a more phylogenetically ancient order, with two prominent species, Xenopus laevis and Xenopus tropicalis, being utilized as vertebrate cell and developmental model systems. In Chapter 3, I reported new chromosome-scale genome assemblies for three distantly related frogs: the common coquí (Eleutherodactylus coqui), the túngara frog (Engystomops pustulosus), and the Zaire dwarf clawed frog (Hymenochirus boettgeri). Through comparative sequence analysis of these and other frog genomes, I identified long-range and even chromosome-scale synteny, denoting the stability and pervasiveness of this type of genomic conservation across the frog phylogeny. These chromosome-scale comparisons also revealed the 13 ancestral chromosomes, with limited Robertsonian translocations and end-to-end fusions explaining the observed chromosome variations. These assemblies, encompassing over a billion years of evolutionary divergence, unmasked insights into torpid karyotype evolution in frogs.