In the McFadden Lab, we have been studying coral phylogenetics, hoping to examine how past events have affected the evolutionary relationships between corals and their relatives, so we can better understand the effects of climate change. Over the past 5 weeks, we have started building phylogenetic trees from a) mitochondrial DNA b) Ultraconserved Elements (UCEs) and c) nuclear rDNA for different coral samples. The nuclear rDNA and mitochondrial DNA from which those trees are being developed are byproducts of the UCE assembly data. With some UCE test run data from 16 octocorals, I have extracted primarily complete mitochondrial genomes. These genomes were annotated using MITOS. When the annotated results were not complete, and genes were missing or fragmented, I returned to the original genomes to find and extract the genes. These genes were then aligned using MAFFT and concatenated. Phylogenies are going to be created from these alignments using RAxML. For the UCEs, I have prepped another 72 samples for sequencing using Kapa HyperPrep kits. We will keep you updated! Alicia Pentico (Harvey Mudd ’19)
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UCE Project TeamAll things Anthozoa, Evolution and Ecology Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation
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