Date of Award
Master of Science (MS)
College of Science and Mathematics
Thesis Sponsor/Dissertation Chair/Project Chair
John J. Gaynor
Paul A.X. Bologna
Scyphozoa--Atlantic Coast (U.S.), Jellyfishes, Transposons, Genomes
The Atlantic Bay Nettle, Chrysaora chesapeakei, is a Scyphozoan found commonly in the bays and brackish waters of estuaries of the eastern United States. Research has shown that there has been a significant increase in jellyfish populations over the past decade, likely the result of factors such as global climate change, eutrophication, overfishing, and the explosive growth of hardened surfaces for polyp attachment.
Transposable elements (TEs) are mobile genetic elements that are widespread and conserved throughout the biological world. Although TEs often comprise a large portion of eukaryotic genomes, their exact function is uncertain but they may provide a mechanism for genetic diversity and recombination. Although previous research has suggested the presence of Tc1 and Mariner DNA transposons within Hydra (Class Hydrozoa), the presence of TEs in other Cnidarians has not previously been examined. Based on RNA-seq and direct DNA sequence analysis of gDNA, I have discovered the presence of a member of the Tc1-Mariner superfamily, POGO, within C. chesapeakei. This is the first definitive evidence of TEs in a member of the Class Scyphozoa.
Two putative consensus sequences, TR1 and TR2, were generated averaging 1,028 bp using two different DNA templates. Analysis of the putative translation products of TR1 and TR2 (BLASTx) indicates modest conservation (38% homology) for the length of each fragment, however, analysis of regions confined to conserved domains were upwards of 60% homologous. Furthermore, two variable regions, VR1 and VR2, were identified within our consensus sequences. VR2, in particular, showed a higher degree of variability with indels, SNPs, and five heterozygosities found within the sequences directly flanking the region perhaps suggesting varying copies within genomes of this element. The fact that these TEs were first identified from RNA-Seq libraries of Chrysaora chesapeakei verifies that this element is transcriptionally active in this jellyfish.
Bioinformatic analysis shows that the overwhelming majority of BLASTx matches corresponded to POGO transposable elements with KRAB domains (Krüppelassociated boxes). POGK is one of many genes to be derived from transposable elements and previously believed to be confined to humans and other mammals. Our data suggests that we have partially cloned a homolog of this gene from Chrysaora chesapeakei. Completion of the intact TE will likely require additional amplification of gDNA using inverse PCR.
Medina, Jonathan C., "Evidence of POGO Transposable Elements in the Atlantic Bay Nettle (Chrysaora chesapeakei) Genome" (2018). Theses, Dissertations and Culminating Projects. 143.