Ears segregating for the colored aleurone mutant phenotype. Image courtesy of MG Neuffer via MaizeGDB.

Purple plant1's phenotype is highly variable depending on the genetic background the mutant is in. Images courtesy of MG Neuffer via MaizeGDB.

The two genes are also duplicates (homeologs) resulting from the maize whole genome duplication. From the picture below you can also see both the two genes and the regions they are in match up to single regions in rice and sorghum, two grasses that haven’t gone though a whole genome duplication since the great radiation of grass species that took place an estimated 50 million years ago (well after dinosaurs stopped walking the earth).

More interesting, at least to me, is the fact that there is NO gene equivalent to colored aleurone1 and purple plant1 in the region we’d expect to find such a gene in Brachypodium (the only other grass species with a sequenced genome)*. From all the genes that line up perfectly on either side we can predict the exact location the gene equivalent to colored aleurone1 and purple plant1 should be found in the Brachypodium genome. But the gene isn’t there…

The GEvo panel shown here can be regenerated at: http://tinyurl.com/yddlwor

The original version of this image had Pl1 mislabeled as C1. This version corrects that error.

For a couple more examples of comparisons between the four sequences grass genomes check out the Cogepedia post I spent this morning pulling together.

*The publication of which I celebrated just a little while ago.

One of the earliest fruits of my work to define relationships between syntenic genes* was a list of sorghum genes and corn genes in one or both of the two related regions of the corn genome (each region in sorghum corresponds to two in corn because the ancestors of corn completely doubled their genome in the time after the ancestors of corn and sorghum went their separate ways.)

But this is not the post where I explain my research projects. That post would be confusing and densely written at the best of times, which two AM in the morning certainly isn’t. Tonight my goal is simply to introduce the embedded video below, which explains how any researchers who want to can check out the relationships I’ve identified between genes in the two duplicate regions of maize, and the genes of the sorghum genome can do so using the MaizeGDB genome browser, and CoGe’s own GenomeViewer application. Video below. If you’re going to watch, I recommend selecting the highest resolution youtube offers you.

To play around with the panel of genes shown at the end of the video, click here. Note that I misspoke during the video voice over, saying the Brachypodium genome hadn’t been sequenced (obviously it has since I ran a BLAST search of it during the video), what I meant to say was that the paper describing the Brachypodum distachyon genome has not yet been published.

The video itself was more an experiment than anything else. At a bare minimum it has convinced me that I need to either invest money in better video editing software, or invest time in checking out the best open source video editors. I did the editing on an ancient version of iMovie that was choking on the high resolution videos I was trying to edit (why many of the transitions are less smooth than I would like.) Ideally I’d also like to hire voice actors to read my lines more clearly, and with fewer ‘uhhs’ than I can manage myself. Since I wasn’t able to do that, please forgive the times when my voice becomes unintelligible, the voice overs were primarily recorded between midnight and 2 am local time.

If you’re interested in using the particular aspect of CoGe I’m advertising today, check out the written tutorial on CoGepedia, or ask me any questions you have directly.

*Genes arranged in the same order in different genomes, or different parts of the same genome