Analysis of Indel Mutations in A. thaliana

Mutations are a primary source of genetic variation. Up until recently point mutations were the main focus of many genetic studies because of a lack of technology to read long-read sequences. One of the main organisms that is oftentimes used as the test subject for mutation studies is Arabidopsis thaliana, because of the establishment of mutation accumulation lines in this plant species. In this study we will be focusing on the insertion and deletion mutations (indel) in the chloroplasts and mitochondria of Arabidopsis thaliana. Studying the mutations in the organelles of this plant will allow us to identify structural mutations in Arabidopsis thaliana. In order to identify structural mutations in Arabidopsis thaliana we utilized the Nanopore MinION sequencer for our data collection. We used six samples of Arabidopsis thaliana DNA from both the chloroplasts and mitochondria, barcoded them, then sequenced them through the MinION for approximately 24 hours. We will then be comparing the sequence data we collected to a reference chloroplast and mitochondrial genomes to observe insertions and deletions that occurred in Arabidopsis thaliana. We aim to quantify the number of insertion and deletion mutations that occurred in the individual and estimate the indel mutation rate.