| The topic of genome architecture is of great interest to evolutionary biologists. Small to large chromosome rearrangements have been reorganizing the genome information, including genes and heterochromatic regions such as centromeres and telomeres. Transposable elements (TEs) are an essential component of the genomes of all life forms studied until now, not only because of their abundance but also because of their influence on reshaping the genome architecture. Multiple studies have provided evidence that TEs are located in particular regions of the genome (e.g. GC-rich regions for Alus, or AT-rich regions for L1s). Here, using abundant genomic data and statistical methods as diverse as pair-wise non-parametric tests, multiple linear regression, multiple negative binomial regression, multiple logistic regression, interval testing procedure (ITP), and functional logistic regression (FLR), we addressed two questions about TE biology: 1. How do Alus', DNA transposons', and endogenous retroviruses' (ERVs') neighboring regions reflect integration site preferences and fixation processes for these TEs? What genomic features are associated with their presence genome-wide? 2. Can we capture integration site preferences alone using data from young, polymorphic or ex vivo integrations?;The results from the TE analyses contributed to our understanding of fixation and integration site preferences genome-wide providing abundant information from diverse genomic features. This information is of great importance to direct studies of insertional mutagenesis and gene therapy. Additionally, we provided a set of statistical tools to analyze complex genomic datasets.;Moreover, we explored the genes on the Y chromosome of gorilla. We performed this by first, generating Y-specific transcripts from testis RNAseq data; second, by evaluating their structure in the Y chromosome assembly; third, by using these transcripts to scaffold the Y chromosome assembly. Finally, we predicted novel genes from the assembly that could have been transposed from other chromosomes. This project allowed us to create a workflow to assemble Y transcripts from testis samples; this protocol will be applied in future studies. In addition, we proved the usefulness of transcriptome data to scaffold genomes. |
