Genomics

RepeatOBserver is an R package that can be run on any chromosome scale reference genome assembly (e.g. fasta file). RepeatOBserver returns many plots describing the tandem repeats and clusters of transposons found across each chromosome. Based on the repeat patterns, RepeatOBserver also returns a predicted centromere location for each chromosome based on the repeat diversity across that chromosome.

Github: https://github.com/celphin/RepeatOBserverV1

You can learn more about the interpretations of the plots in our manuscript here: https://www.biorxiv.org/content/10.1101/2023.12.30.573697v1

I was recently invited to lead an alpine/Arctic plants committee for the Canadian Biogenomes Project. This project has funding to build complete reference genomes for 40 Arctic and alpine species. In June 2024, I gathered an International committee to begin to discuss the best species to sequence. As an essential part of this project, I want to consult with Inuit communities across the Canadian Arctic to determine the best species to sequence as well as who will own and control the sequence data collected in the Arctic.

To determine if the environmentally induced differentially methylated regions can be inherited, we grew the offspring of the 102 sequenced plants in controlled growth chamber conditions and sequenced their DNA methylation.

Ongoing studies at International Tundra Experiment (ITEX) sites throughout the Arctic have maintained experimental warming studies for up to 27 years in a variety of tundra plant communities. Using whole-genome bisulfite sequencing on Dryas octopetala (Mountain Avens) plants from the warmed and control plots across the ITEX sites, I am determining the methylation patterns that are consistently associated with artificial warming. See this webpage about this project: https://cassandraelphinsto.wixsite.com/genomebc

At Alexandra Fiord and Sverdrup Pass on Ellesmere Island, ancient Arctic White Heather (Cassiope tetragona) has been well preserved under the glacial ice. Samples were also collected across its range: the Canadian Arctic, the Rocky Mountains, British Columbia’s Coastal Mountains, Greenland, Svalbard, Northern Europe, and Russia. I am investigating the genomes of both the ancient and present-day Arctic White Heather populations using genotyping by sequencing (GBS). The genomics of these plants can help us better understand how populations change and move across space after major climatic changes. Photos: https://photos.app.goo.gl/810ER60WCZtJn2nD3

We generated RNAseq data for 64 wild individuals to help us clarify the effect of the DNA methylation on transcription. These wild plants were sampled from Norway, Sweden, Alaska and Nunavut in 2021 with 8 samples from the warming plots and 8 from control plots at each site.