After showing up a week late to the summer research party, I’ve had the opportunity to jump into the lab and bioinformatics work of the McFadden lab. It’s been a whirlwind learning all the lab techniques and the biology behind the work we’re doing, but I’m gaining a better understanding of the work done in this lab. I’ve also learned a ton about all the prior work done in and out of this lab that has attempted to resolve the phylogeny of Anthozoa.
I’ve spent most of my time doing library preparations on the sheared DNA of Sinularia, soft corals dubbed “leather corals.” This is the initial process to ultimately sequence and analyze the ultraconserved elements (UCEs) of their genomes. This week I am finishing up all the Sinularia samples we have, so I am also helping to finish the Actinaria (sea anemone) samples. In the next week or two, we will likely move forward and do targeted enrichment on the DNA libraries in order to prepare for sequencing. After sequencing, we will move forward with bioinformatics approaches, though the summer is likely to be over by the time this round of samples is finished.
However, there is other bioinformatics that I’ve been working on. I’ve just finished annotating the mitochondrial genomes of specimens in the hexacorallian order Zoantharia. This process involves taking assemblies done by Trinity, SPAdes, and/or Novoplasty and using MITOS 2 to annotate the genes. I’ve seen a couple differences so far in the presence of introns tRNAs, and genome length--between samples I’ve analyzed this summer and between our samples and the zoanthid mt genomes published in the literature. The mt genomes of Zoantharia have not been very thoroughly examined in the literature, so the work I am doing will help add to the scientific conversation, which is very exciting.
It’s been a lot of fun to work with the other students in the lab, and it’s a great experience to be able to work under people with as much knowledge as Prof. McFadden and Dr. Quattrini. I’m looking forward to analyzing some of our results more in depth and thinking about what they mean in the broader context of the phylogeny of anthozoans.
UCE Project Team
All things Anthozoa, Evolution and Ecology
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