Exploring the TE landscape of elephant and CR1 accumulation, evolution and effects of selection in the class Chondrichthyes

Transposable elements (TEs) are mobile DNA sequences that have been widely identified in bacteria, plants, and animals. They generally represent large fractions of the genome, but this varies depending on the species. TE insertions are generally either neutral or deleterious. In some cause, TEs have been associated with genomic variation, alteration of gene expression and regulatory sequences. With the birth of next-generation sequencing, TEs have been investigated more toughly, allowing us to further understand the part TEs play in the evolution of vertebrate genomes. Here, we investigate the TE landscape of a cartilaginous fish, the elephant shark, ensuring the accurate annotation of this genome using a combination of sequence-homology and manual curation. We discovered that much of the genome (29%) was composed of non-LTR retrotransposons such as SINE and LINES. Interestingly the LINE CR1 showed peaks of accumulation in the distant past. We estimated that these insertions occurred ~ 400 million years ago (mya). Further investigation was performed to better understand CR1 evolution, accumulation patterns, and the effects selection has had in the ORF region of the CR1 in the three genomes. We utilized three representative genomes from the class Chondrichthyes (elephant shark, little skate and whale shark). They showed different patterns of CR1 accumulation in each genome. The whale shark genome consists of ~16% of its genome as CR1, while the little skate and elephant shark showed that 9% and 4% of their genomes were CR1s, respectively. Taken together, the results of our analysis highlights the similarities in evolutionary patterns between CR1s in Chondrichthyes and other vertebrate genomes that have been investigated such as avian and crocodilian genomes.

Author dc:creator

• Blanco-Berdugo, Laura Alejandra

Contributors dc:contributor

• Ray, David A
• Densmore, Lou
• Phillips, Caleb

Handle dc:identifier.uri

https://hdl.handle.net/2346/104557

OAI identifier oai:identifier

oai:tdl-ir.tdl.org:2346/104557