James and the Giant Corn Genetics: Studying the Source Code of Nature

May 25, 2010

Selaginella moellendorffii genome

Filed under: Uncategorized — Tags: — James @ 12:26 pm

Public domain image of selaginella from wikimedia commons.

Added another genome to our sequenced plant genomes wiki, Selaginella moellendorffii, better known as as a spikemoss. Selaginella is a vascular non-seed plant which split from the lineage that gave rise to most of the plants you seed around you every day hundreds of millions of years ago. At 110 megabases, Selaginella is currently the smallest sequenced plant genome (smaller than Arabidopsis!).

Un-related to genomics, did you know plants recognizably belonging to the Selaginella genus can be found in fossils 335-350 million years old? This is a plant that has remained mostly unchanged since BEFORE dinosaurs walked the earth! This was just one of the many interesting facts I learned from reading Jo Ann Bank’s review: Selaginella 400 Million Years of Separation.

As far as I could tell the Selaginella genome paper has not yet been published (I couldn’t find it anyway). The good news is that according the the Selaginella wiki (Yes, Selaginella gets its own wiki … I kind of wish maize had a wiki… ), the paper was submitted back in August of 2009, so it’s possible that any day now this genome will move from the fun-to-play-with category into the awesome-to-publish on one.

November 20, 2009

About the Maize Genome Paper

Filed under: biology,Genetics,research stories — Tags: , , , — James @ 11:23 am

Looking at the maize genome paper in isolation it’d be easy to wonder what all the fuss was about. The paper itself is only four pages long with (plus a page of citations), with two figures, and as awesome as figure 1 is (and it really is very, VERY awesome), it doesn’t seem like an lot for a project that represents the work of more than 150 authors over four years. But the real fruits of the maize genome project are the sequences that can be found on either maizesequence.org or maizegdb.org and additional exciting research it is already enabling. And as the result of a quirk the way genome sequence is released to the research community, we can already get a sense of some of that other research. (more…)

November 7, 2009

Figure from my Research Proposal

Filed under: biology,research stories — Tags: , , , , , — James @ 7:17 pm

“My budget…triples the number of National Science Foundation graduate research fellowships.  This program was created as part of the space race five decades ago. In the decades since, it’s remained largely the same size –- even as the numbers of students who seek these fellowships has skyrocketed.  We ought to be supporting these young people who are pursuing scientific careers, not putting obstacles in their path.” – President Obama

I’m still feeling brain dead after the final push for submitting.

Speaking of NSF, here’s the one figure I managed to shoehorn into my research proposal.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy.

Blast hits between an orthologous quartet of gene spaces, one in rice, one in sorghum and the two copies created by the maize tetraploidy. As usual click the picture to see it fullsized

If you’d like you can even click here to be able to play around with the figure yourself using the CoGe interface. Now I’ve got to try to explain what this figure is about. (more…)

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