Razorback sucker

Methylation is an epigenetic mark that adds a layer of information to the genomic DNA and is best known for its effect that it has on repression of transcription resulting from methylation at CpG sites. Other effect of methylation can vary from leading to new opportunities for gene control by TE-based regulatory sites to helping genomes with the massive amount of new, unstable genetic information that is produced from a whole genome duplication (WGD). Many organisms, from plants to fish, have gone through recent WGD. Unfortunately, the vast majority of the current knowledge about WGDs were studied in plants, due to the fact the WGDs occur less frequently in vertebrates, leaving a knowledge gap on how vertebrates manage this genome shock.

In the interest of shrinking this knowledge gap within the scientific community we propose using the Catostomus family, a family that underwent a recent WGD at a minimum of 65 million years ago, to understand and assess the evolutionally pathway within a taxonomical family after a WGD. In collaboration with Thomas Dowling, we have created draft or chromosome-level genomes of Xyrauchen texanus (razorback sucker) and Myxocyprinus asiaticus (Chinese banded sucker) using a new advance DNA sequencing technology (e.g., Oxford Nanopore) is the ability to generate long (>100 kilobase) sequences from individual DNA molecules while simultaneously generating real time methylation readings.

The razorback sucker and the Chinese banded sucker are endangered with both species being completely reliant on hatcheries. With the information gain through our work the hatchery would be able to better help their conservation efforts. We aim to gain a deeper understating of not only the evolutionary pathways, but the role methylation play after a WGD event. Comprehend how vertebrates can go through a WGD, which is a rare occurrence will help us answering the question of which features from a WGD are shared or unique to vertebrates when compared to polyploid plants. This novel pipeline of analyzing this untapped and vast data will reshape the way the scientific community perceive and uses methylation.