Cnidarian Mitogenomics
with emphases on Scyphozoa and Discomedusae
Jae-Seong Lee, Michael N Dawson, et al.


Project outline

Comparison of mitochondrial genomes offers one perspective (the whole mitochondrion is typically considered a single genetic 'locus') on the phylogeny of organisms. That perspective is seen with two eyes, one sees the pattern of genome structure, the other the pattern of sequence differences. Our mutual interests in these two aspects led to the initiation of this collaborative project. The goal is to document the changes in genome structure with evolution of Medusozoa and to reconstruct a robust mitochondrial-based hypothesis of phylogeny in Cnidaria, particularly Scyphozoa, with emphasis on Discomedusae (= Semaeostomeae + Rhizostomeae).



At this stage, we are gathering tissue samples for sequencing. Target species are listed in the table below. Those without brackets have been collected (and sequenced if bold), those in brackets are required (in some cases other taxa will be used instead), and "??" indicates that any species from that family is acceptable and is still needed. If you can contribute any of these specimens, please contact Mike Dawson (mdawson AT ucmerced DOT edu). The protocol for preservation of samples is a slight modification of the standard protocol for CnidToL, as follows.

After collecting the specimen(s) using your standard procedure, place it (each) in a large bucket of seawater filtered through 20-80 um plankton mesh. Keep the medusa there for 24-36 hours so that it clears its gut of prey, thus removing that potential source of contamination. Then, dissect out tissues rich in dermis (ideally gonad, or gastric tissue, or oral arms if they are not greatly thickened by mesoglea) until you have a quantity about half the size of your small finger. Preserve the tissue in excess 95% ethanol (i.e. about 10 times as much ethanol as tissue). Preserve the remainder of the medusa in 4-7% formalin-in-seawater such that the final concentration of formalin is 2-4%. Store the ethanol+tissue for 3-to-4 weeks in a refrigerator; invert the tube a few times to mix it every other day during the first week, then once or twice per week for the remaining few weeks. Finally, remove most of the liquid, pack the samples robustly (see shipping) and send the samples to the following address.
Dr. Michael N Dawson
School of Natural Sciences
University of California, Merced
P.O. Box 2039
Merced, CA 95344

We will sequence whole mtDNA and, separately from several specimens, COI and 16S using existing universal primers which we will compare with a broader sampling of taxa (see Global Phylogeography) as an error-checking mechanism to make sure there is no contamination of samples.


Why get involved?

Due to the highly technical nature of this project, the small number of samples needed (a few individuals of each of the taxa listed in the table ), and the lack of requirement for additional field data, it is unlikely that people who are not involved in the laboratory or phylogenetic analyses can justifiably be authors on publications arising from this project. (But if you have many months to spare to learn sequencing and phylogenetic analyses, it could be a different story.) So, why get involved? The major reason is that sequencing and comparison of this diversity of mitochondrial genomes will make available an off-the-shelf 'toolkit' of molecular markers for answering questions ranging from those about the highest (class) to the finest (population) levels of biological organization for any and all medusozoa. This will be a dramatic advance, allowing convincing statements about very recent events affecting population connectivity, invasive species, genetic diversity of populations, etc., to be made for the first time. Such knowledge is essential to making strong arguments about many other facets of ecology, such as adaption and selection. The easiest way to apply the new markers to the species in which you're interested is to have it's whole mitochondrion sequenced, because then you know exactly which tools to pull out of the toolbox. So, the question, really, is why not get involved? :-)

Source Genus species
> 20 in GenBank
?? (Halyclistus)
?? (Craterolophus)
?? (Aequorea)
?? (Aglantha)
?? (Periphylla periphylla)
?? (Linuche)
Chrysaora (Dactylometra) quinquecirrha**
Aurelia aurita*, Aurelia sp.1**
?? (Cassiopea)
?? (Cotylorhiza)
?? (Mastigias)

* Shao Z., S. Graf, O.Y. Chaga, & D.V. Lavrov (2006) Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): a linear DNA molecule encoding a putative DNA-dependent DNA polymerase. Gene 381: 92-101. [GenBank NC_008446]
** Jae-Seong Lee & colleagues (unpublished data)