Question: Is There Any Useful Information To Be Gathered Analyzing The Genomes Of Different Populations Of Cicadas?
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gravatar for Scott
8.9 years ago by
Scott70
Scott70 wrote:

This is more of a general question as I am new to this site. I teach at a community college and am trying to determine some projects that 1st year and 2nd year biology students could do. Ideally, the project would be able to be continuous as 1. the turnover rate for the students would be pretty quick and 2. this couldn't be research done at universities.

One thought I had involved the periodical cicadas. These cicadas have life cycles where they are underground for either 13 or 17 years. As a result, there are different populations of cicadas that are genetically isolated from each other. One population will come out in 2011, another one in 2013 etc. etc. When the populations emerge varies from state to state.

Would there be any value to sequencing these different populations? What type of analysis would I do for each one? There are a lot of details to be figured out and I would have to write a grant to get some equipment. I would also partner with a local university to see if I could use some of their equipment. Before I start trying to figure out the smaller details though, I just wanted some feedback to see if this would be worthwhile and what are some other details I may not have thought of.

The only other idea I had was sequencing some fungi as this area has not gotten a lot of attention. Any ideas or comments are welcome. Thank you!

project education • 2.4k views
ADD COMMENTlink modified 8.9 years ago by Jarretinha3.3k • written 8.9 years ago by Scott70
2

If you want to do something around the chronobiology of the cicadas, maybe mail Bora Zivkovic (Coturnix@gmail.com) for ideas and/or advice. He's an expert in this matter (see his blog http://scienceblogs.com/clock)

ADD REPLYlink written 8.9 years ago by Jeroen Van Goey2.2k

you could make some very good research on it, because there are few models of complex eukaryotes like this, in which you can compare individuals coming from different generations. I remember having read an old article on The scientist on a study like this, on a fungus... when I will be back at home today I will look for it and then I can answer you here.

ADD REPLYlink written 8.9 years ago by Giovanni M Dall'Olio26k

Any help would be greatly appreciated - thanks!

ADD REPLYlink written 8.9 years ago by Scott70

life cycles of cicadas happen to be prime numbers :-) cf. WP

ADD REPLYlink written 8.9 years ago by Pierre Lindenbaum117k

One good thing about cicadas is that people can relate to them ... Thus anything you may find has a better chance to be talked about in the news and other circles. As Pierre said those are prime numbers, and prime numbers are quite uncommon in nature. Finding out how that time is kept has many implications. Definitely team up with someone who has access to sequencing facility.

ADD REPLYlink written 8.9 years ago by Istvan Albert ♦♦ 79k
3
gravatar for Roderic Page
8.9 years ago by
Roderic Page390
Glasgow
Roderic Page390 wrote:

A good place for information on cicadas is Chris Simon's web site. She maintains Cicada Central which has loads of resources. You might also take a look at a recent PLoS ONE paper from her lab doi:10.1371/journal.pone.0000892. Chris might have some suggestions on possible projects.

ADD COMMENTlink written 8.9 years ago by Roderic Page390
3
gravatar for Jarretinha
8.9 years ago by
Jarretinha3.3k
São Paulo, Brazil
Jarretinha3.3k wrote:

This question is somewhat fortuitous. I have a paper on Physica A with a automata model for Magicicada. Of course, to build the model we discussed a lot the underlying genetic architecture and possible ecological scenarios. It's a fair complicated problem. Despite plentiful cirscunstancial evidence, there are no sound ones for the underlying genetics. No clue about the biological clock, too. And aging and lifecycle are tipically governed by nontrivial QTL. [?] Nevertheless, would be fantastic if you could track down the evolution of this two populations, phylogenetically speaking. This can be done at protein level and/or DNA level with just gels, PCR and Sanger sequencing. It's low resolution, but works. [?] This will be a great opportunity to teach evolutionary theory, ecology and scientific methodology. I can sure help with specific details.

ADD COMMENTlink written 8.9 years ago by Jarretinha3.3k
1

Just follow the citation track of Lloyd & Dybas classical papers on Magicicada. Every subsequent paper on the subject cites them.

ADD REPLYlink written 8.9 years ago by Jarretinha3.3k

I think that would be great! I'll start gathering some more information then!

ADD REPLYlink written 8.9 years ago by Scott70
2
gravatar for Darked89
8.9 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

It is a brainstorming question, so I will just give my 0.02$. There are a number of fairly simple lab techniques producing useful but often not publishable results.

If you want to stick with Magicicada, quick look in Animal Genome Size Database http://www.genomesize.com/ reveals that there are no entries for Cicadidae. So measuring of DNA content, counting chromosomes will be both new and useful for downstream DNA sequencing projects.

Yes, having genomic sequences for species with such life-cycles will be great for chronobiology. But it is a bit over the top as a student project.

At this point NCBI list just 19 nucleotide sequences for all Magicicada. So yes, you can contribute sequencing almost anything from any of these species, but if this is supposed to be more than an exercise in DNA extraction, subcloning and feeding sequencing machines then you will have to pick something interesting.

Like sequencing as many as possible genes responsible for molecular clock. But then you are again on square one: complicated project requiring substantial funding.

ADD COMMENTlink written 8.9 years ago by Darked894.2k
1

I also think that any new data submitable to GenBank is better than sequencing the same plasmid over and over again :-).

What I was trying to say is that sometimes not very sophisticated methods (Feulgen staining is ancient) can produce very useful results. Good if you go for name recognition on a tight budget.

DNA cloning and sequencing is way more widely used in labs so it makes sense to go for it with students.

ADD REPLYlink written 8.9 years ago by Darked894.2k

Thanks for the input. As a community college instructor, it is frustrating to just go over a technique with very little revelevance. Adding something, anything, where they are contributing something, even if it just sequences to various databases is better than nothing! I just want to give my students any type of experience that will make them better prepared for transferring to a university, so even if it is not publishable, but maybe could do a poster presentation would be great.

ADD REPLYlink written 8.9 years ago by Scott70
1
gravatar for Chris Miller
8.9 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

You seem to be going at this a bit backwards. The first step in science is to make a hypothesis, then choose the appropriate tools to answer it. That may include genome sequencing, it may not. It seems like you've got a hammer, and you're looking for a nail.

If you want to study cicadas, start reading up them. Look at the literature and see what other people are studying and what big unanswered cicada questions remain. If you lack access to subscription journals, try your local library, or other online resources. I suspect some of the questions relate to the different cycle lengths - have there been certain genes implicated? Do we know whether it's governed by differential gene expression, genomic factors, or even epigenomics? Has anyone sequenced them already? I'm sure some population geneticists would be interested in divergence patterns between the groups - might help you understand whether they're still the same species, or whether they're slowly splitting apart from each other because of the time differential in emergence.

The same applies for fungi. Find out what some of the big unanswered questions are, then try to figure out what approach you might take to answer some of them. Then narrow it down further to manageable size projects that a new biologist could handle.

ADD COMMENTlink written 8.9 years ago by Chris Miller20k
1

"The first step in science is to make a hypothesis". I wouldn't generalise it like that; not all research is hypothesis-driven.

ADD REPLYlink written 8.9 years ago by Phis1.0k

I admit that this is premature and I have not done my due diligence. All I have done so far (I thought of this last night watching a show where cicada were all over the place) is went to Entrez and only found one article relating to the periodical cicada. I am getting the article through our college library.
My initial thought was dealing with evolution and if we could see any divergence between the populations since they are gentically isolated. How do I know that I have searched enough to comfortably say that these populations have not been sequenced?

ADD REPLYlink written 8.9 years ago by Scott70

To be clear, I don't mean to dig on your idea at all. I think it's fantastic that you want to involve students in some real research. It just seems like you're not even to the point where you know what questions to ask. With any new project, there's a ramp up phase, where you spend some time digging around in the literature to see what's been done and what needs to be done. That should be your first step.

ADD REPLYlink written 8.9 years ago by Chris Miller20k

I didn't think you were slamming my idea and I understand where you were coming from. This is just part of my "digging around" phase - asking experts for their advice. I thought that not only could this save time, but I may find additional information and/or contacts.

ADD REPLYlink written 8.9 years ago by Scott70

Fair enough - best of luck.

ADD REPLYlink written 8.9 years ago by Chris Miller20k

That's a fair critique, PhiS. Still, you should have some idea of what you're getting after. My point was that sequencing an organism without a reason or plan is a bad idea, as the methods you use will depend on what answers you're looking for.

ADD REPLYlink written 8.9 years ago by Chris Miller20k

That's a fair critique, PhiS. Still, you should have some idea of what you're getting after. I guess my point was that sequencing an organism without a reason or plan is a bad idea, as the methods you use will depend on what answers you're looking for

ADD REPLYlink written 8.9 years ago by Chris Miller20k
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