Conference Paper
Fish(ing) in the Hi(gh)-C(sea)
Biswas, T., Paulson, A., Hall, K, and Rohner, N.
Record Number:
5619
Year:
2022
Journal:
AIM 2022
Pages:
26
Abstract:
Cave dwelling morphs of Astyanax mexicanus have shown exceptional adaptation to survive in the dark, food scarce caves. Compared to their surface counterpart, multiple independently evolved cavefish morphs show repertoire of parallelly evolved evolutionary
innovations. Some of these parallelly evolved features are conspicuous, like the loss of eye and pigmentation, while some are equally intriguing but more subtle, like the metabolic adaptations to food scarcity. However, our understanding of mechanisms
underlying such parallel evolution, both in cave fish and in general, is not entirely clear. With the benefit of having multiple independently evolved Astyanax morphs in lab, we wanted to explore the genetic features guiding parallel evolution. Previous studies have shown that mutational hotspots, DNA fragility and genome instability at these fragile sites
contribute to parallel evolution of specific traits. Interestingly, these contributors have a strong association to a more global feature of the genome, i.e., the 3D architecture of the genome. In this study, we explore the 3D genome architecture in cave and surface morphs to understand the cave-specific 3D features which might be driving parallel evolution in cavefish. Focusing on metabolic adaptation as a model, we compare surface and cavefish livers. We use HiC – a high-throughput sequencing technique to map genome-wide chromatin contacts, to capture 3D genome organization of the liver cells. Initially using surface and Pachón, we found significant differences in 3D organization of the genome, including differential organization of topologically associating domains
(TADs), DNA-looping and chromosomal inversions at multiple locations. Further, we are extending the study to Tinaja to identifying conserved cave-specific features. Assimilating our HiC data with available QTL and transcriptomic datasets, we plan to explore the role of 3D genome organization in parallel evolution of metabolic innovations in cavefish.
Times Cited:
1
Relevent Species: