It’s only been six weeks since I’ve started working in the McFadden lab, but I’ve been pipetting a lot and learning even more. As some of my other labmates have previously mentioned, one of the projects we are working on is to try resolve the phylogeny of Anthozoa. One of the ways we are doing this is through the analyzing the ultra-conserved elements (UCEs). This begins with library prep of DNA, which I have almost finished for the Alcyonium samples. Alcyonium is a genera of coral that are unique in the sense that they have no calcium carbonate skeleton. Despite the lack of a skeleton, species with Alcyonium are essential to marine habitats. However, the distinction between species is not well understood and so we hope that with the UCEs, we may be able to not only differentiate populations of Alcyonium but be able to delineate species within the genus as well. Hopefully we can soon obtain the reagents we need to finish target and enrichment and start analyzing UCEs because I am excited to see what new evolutionary insights we can learn.
On the bioinformatic side of things, I am also going through the process of annotating and cleaning up mitochondrial genomes of several octocorals. As Natasha and Brooks have mentioned, we have taken assemblies from several different programs and annotated them using MITOS 2. While MITOS 2 gives us a pretty good idea of the genes within the mitochondrial genome it isn’t perfect. We have to painstakingly fix contigs ourselves in order to get the proper gene length, codons, etc. However, we are working on a script to try and help automate the process and so I look forward to that. Once that’s done, we’ll be able to construct phylogenetic trees based off of mitochondrial genomes and compare it to other data. So far, majority of the mitochondrial genomes I have analyzed match the ancestral gene order presented in Brockman’s and McFadden’s 2012 paper on mitochondrial genomes with the exception of Protodendron repens, whose classification is within the family Alcyoniidae but mitochondrial genome better matches those within the family Xeniidae.
Overall, we’ve made a lot of progress in both in the wet and dry lab. Although our work isn’t done yet, I’m getting very excited for the potential discoveries we may encounter.
UCE Project Team
All things Anthozoa, Evolution and Ecology
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