Genomic Environments and Their Influence on Transposable Element Communities

Background: Despite decades of research the factors that cause differences in transposable element (TE) distribution and abundance within and between genomes are still unclear. Transposon Ecology is a new field of TE research that promises to aid our understanding of this often-large part of the genome by treating TEs as species within their genomic environment, allowing the use of methods from ecology on genomic TE data. Community ecology methods are particularly well suited for application to TEs as they commonly ask questions about how diversity and abundance of a community of species is determined by the local environment of that community. Results: Using a redundancy analysis, we found that ~ 50% of the TEs within a diverse set of genomes are distributed in a predictable pattern along the chromosome, and the specific TE superfamilies that show these patterns are relate to the phylogeny of the host taxa. In a more focused analysis, we found that ~60% of the variation in the TE community within the human genome is explained by its location along the chromosome, and of that variation two thirds (~40% total) was explained by the 3D location of that TE community within the genome (i.e. what other strands of DNA physically close in the nucleus). Of the variation explained by 3D location half (20% total) was explained by the type of regulatory environment (sub compartment) that TE community was located in. Using an analysis to find indicator species, we found that some TEs could be used as predictors of the environment (sub compartment type) in which they were found; however, this relationship did not hold across different chromosomes. Conclusions: These analyses demonstrated that TEs are non-randomly distributed across many diverse genomes and were able to identify the specific TE superfamilies that were non-randomly distributed in each genome. Furthermore, going beyond the one-dimensional representation of the genome as a linear sequence was important to understand TE patterns within the genome. Additionally, we extended the utility of traditional community ecology methods in analyzing patterns of TE diversity.