PCR Amplification and DNA Sequence Analysis of the ß-Actin Gene from a Scyphozoan Jellyfish (Chrysaora quinquecirrha)

The scyphozoan jellyfish Chrysaora quinquecirrha (CQ) is becoming a major pest of Eastern bays and waterways due to changing environmental conditions, including the warming of inlet waters, man-made plastic bulkheads and reduced plant life which serve as havens for their predators. Their increasing numbers warrants investigations into population control of these animals. Therefore any information about them may help in understanding and eventually controlling jellyfish blooms. ß-actin is a ubiquitous cytoskeletal protein that has many essential functions. The protein and nucleotide sequences are highly conserved across all species, yet the number, size and sequences of the introns are highly variable. This makes ß-actin an interesting protein to study across many species in order to discover phylogenetic relationships. A partial (86%) nucleotide and amino acid sequence of the ß-actin gene from CQ genomic DNA has been identified and compared to a broad selection of species, including other cnidarians. It was found that this partial p-actin sequence from CQ is 98% identical to the box jellyfish Malo kingi, and 95% identical to the human form at the protein level. However, the nucleotide sequence is 84% identical for M. kingi while only 78% identical for human. The 2 introns in the CQ sequence are found at the same locations in Podocoryne carnea, a colonial Hydrozoan. A BLAST to the 60 amino acid ß-actin sequence from C. colorata shows 6 amino acid differences, a surprisingly high number in such a short segment. Further work to sequence the 5’ and 3’ ends, including UTRs, should bring to light further interesting aspects of ß-actin, since these regions are involved in mRNA and protein regulation

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu