Video Tip of the Week: Browsing Butterflies with GBrowse and Ensembl

A couple of months back when the Heliconius (Postman) Butterfly genome paper was released, we got to see another example of how the new sequencing technologies are giving us access to more and more genome data–in species that are not the main model organisms. Monarch butterfly genome data had been released prior to that as well. And you may not know that there’s a huge effort to get thousands of insect genomes–the i5k project. I think that’s my favorite thing about where we are today: we can examine more species in more detail than we ever have before.  Not only do we get interesting details from the genome sequence framework, but interesting info about species evolutionary relationships, and intriguing and novel biology features can be explored as well. I mean–the human genome and its variations are great–but Monarch butterflies have a sun compass! How cool is that??

And like most genome papers today, only a fraction of the data that was obtained is in the main body of the paper. The “compelling examples” might be there. But of the “12,699 predicted protein-coding genes” of the Heliconius genome, only a handful are really addressed in the text. A few more handfuls in some figures. The earlier Monarch butterfly paper delivered “a set of 16,866 protein-coding genes” (and 10 supplements beyond the paper!). But to access the data yourself and compare to your genes and species of interest you need to turn to the browsers that accompany the papers.

In this case you have two choices for browser styles: the Heliconius Genome Consortium (authors of the paper) maintain a GBrowse installation at their Butterflygenome.org site. The Monarch group has a GBrowse at MonarchBase. In addition, the data for both is also now included in Ensembl as of the July 2012 release 15. [note: see administrative details in the comments --mm]

For this week’s tip we fly around from the species-specific GBrowsers to the collected sets at Ensembl. It’s great to have the species-specific sites for depth of information about the projects and resources, but it’s also nice to have the additional tools and displays of the larger genome browsers. Community browsers can offer very current and new data that might not yet be included in the super-browsers, and the super-browsers may offer additional tools and infrastructure that is not available from the community browsers. Your best bet is to be aware of both, and to get comfortable with the main software features and their strengths and weaknesses.

The bugs are coming–and thousands of them. Be ready. And beware: look for the right superhero

Note: I have been unable to locate the Mothra genome that’s been all atwitter for the last couple of days.

Quick links:

Heliconius GBrowse: http://butterflygenome.org/

MonarchBase: http://monarchbase.umassmed.edu/genome.html

Ensembl Metazoa: http://metazoa.ensembl.org/

i5k Insect and other Arthropod Genome Sequencing Initiative http://arthropodgenomes.org/wiki/i5K

If you came looking for butterfly photos, try this: http://www.butterfliesandmoths.org/ This is also a citizen science site where you can submit your own sightings–I have done that in the past.

References:

Dasmahapatra, K.K., Walters, J.R., Briscoe, A.D., Davey, J.W., Whibley, A., Nadeau, N.J., Zimin, A.V., Hughes, D.S.T., Ferguson, L.C., Martin, S.H. & (2012). Butterfly genome reveals promiscuous exchange of mimicry adaptations among species, Nature, DOI: 10.1038/nature11041

Zhan, S., Merlin, C., Boore, J. & Reppert, S. (2011). The Monarch Butterfly Genome Yields Insights into Long-Distance Migration, Cell, 147 (5) 1185. DOI: 10.1016/j.cell.2011.09.052

Stensmyr, M. & Hansson, B. (2011). A Genome Befitting a Monarch, Cell, 147 (5) 972. DOI: 10.1016/j.cell.2011.11.009

Kersey, P.J., Staines, D.M., Lawson, D., Kulesha, E., Derwent, P., Humphrey, J.C., Hughes, D.S.T., Keenan, S., Kerhornou, A., Koscielny, G. & (2011). Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species, Nucleic Acids Research, 40 (D1) D97. DOI: 10.1093/nar/gkr895

2 thoughts on “Video Tip of the Week: Browsing Butterflies with GBrowse and Ensembl

  1. Mary Post author

    Well, technically you can…If you go to ENSEMBL main site and click the “full list” link, that page also offers the link to the Metazoa set.

    But the other thing is that for us that allows us to tag the post so it matches ENSEMBL tutorial in our database, and will appear in the searches that way. Since the software foundation is the ENSEMBL framework, that tutorial will help people to use that interface.

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