Transposable Element Abundance and Variability in 28 Different Species in the Family Solanaceae

Mendieta, John P.

Undergraduate Honors Thesis

Transposable Element Abundance and Variability in 28 Different Species in the Family Solanaceae Public Deposited

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Citeable URL: https://scholar.colorado.edu/concern/undergraduate_honors_theses/mp48sd40x

Abstract

Transposable Elements (TEs) are small nucleic acid parasites that replicate and reinsert themselves into the genome of their host organism. These small genetic parasites have in recent times been seen as possible evolutionary drivers in the development and evolution of genomic adaptations as well as genomic architecture. While much is known about the possible effects of TEs on an individual organism, little is known about their dynamics on a family level scale. In order to investigate this relationship, TE types and abundances were analyzed for 28 species in the highly diverse plant family Solanaceae. Transposable Elements were identified and investigated by running the program RepeatExplorer on whole genome shotgun data sets from 28 different species in the Physaleae and Solanaea tribes in the Solanacea family. I identified the genomic proportion of repetitive elements in all species and found that on a family level, two TE types, LTR gypsy and unclassified repetitive content were the most abundant for all species. On a family level, class II TEs were found to be far less numerous in genomic proportion, but were far more variable on an individual level. These results indicated that while LTR gypsy and Unclassified TEs are more important for long-term genomic dynamics, Class II TEs act more significantly in the short term. Clades also appear to have a relationship on TE abundances with more closely related species having similar genomic percentage of TEs, but due to our lack of branch lengths in the phylogeny I was unable to calculate this metric. Finally, while these results are interesting, there is currently no all-encompassing biological explanation as to exactly why these family level genomic trends are being exhibited.

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