Zhang, Nicole – Short Interspersed Nuclear Element Bov- tA HEL17 Evolution in Artiodactyl Order (Dr. Brian Golding)

Transposons are known as “jumping genes”, a special class of DNA sequence that can replicate or relocate itself within the genome. It can cause nonsense mutations that affect an organism’s vitality and is tightly regulated in germ cells. Once it is inserted into a sequence, it is unlikely to get completely deleted and can accumulate mutations. Therefore, it provides a good marker for timing evolution events. Short interspersed nuclear elements (SINE) belong to Class I retro- transposons that lack replication machinery genes. The evolution of a group that share SINE elements can often be revealed by analyzing the difference between the elements present in the genome. Bov-tA is a SINE element that emerged after the Pecora speciation event in the Artiodactyl order. It is a tRNA derived SINE element and has two domains of consensus sequences. To unmask the evolution of Bov-tA SINE element within the Artiodactyl group, the Bov-tA subfamily element HEL17 and its flanking sequences in the 10 species whose whole genome sequence were available were found using NCBI blastn program with a e-value less than 1e-30. The longest sequence of HEL17 from each species are aligned to each other using MUSCLE then to generate a tree via Monte Carlo Markov Chain analysis (MCMC). By comparing the sequences, we found homology between the Bov-tA HEL17 phylogenetic tree and the consensus tree, and the abnormal location of the giraffe SINE element in the group suggests a translocation event that have likely contributed to the SINE element segmentation.