Discordant Classification of Transposable Elements in Segmental Duplications Raise Concerns About Subfamily Definitions

Patterson, Gilia, B.A., May 2016 Biology Discordant Classification of Transposable Elements in Segmental Duplications Raise Concerns About Subfamily Definitions Faculty Mentor: Travis Wheeler Most of the human genome comes from transposable elements (TEs), sequences of DNA that can move and insert copies of themselves throughout the genome. TE sequences both inform and complicate analyses of genomes, so it is important that TEs are annotated completely and accurately. Remnants of TEs are annotated and classified into subfamilies based on their DNA sequences. A subfamily represents all the copies generated in a burst of replication by a few closely related TEs. Wacholder et al. (2014) suggested that the current methods for representing subfamilies are not accurate and should be reevaluated. We expand on this discussion and show that many TE sequences that should belong to the same subfamily are classified into discordant subfamilies. When a segment of genome with a TE remnant is duplicated, the TE remnants in each copy are replicates and so should be assigned to the same subfamily. We identified the location and subfamily of all TEs in known segmental duplications and found that a large fraction are assigned to different subfamilies, suggesting that the current method of classifying TEs splits them too much.