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.

Many genomes are released before their publication under the conditions of an agreement called the Ford Lauterdale Policy (a name I think sounds ridiculously ominous). It boils down to the idea that as genomes are sequenced and assembled, the pre-publication data is made available to other research groups, but any publications that take advantage of whole genome analysis (the kind of science I do now) cannot be published until after the people who sequenced the genome publish it. That doesn’t mean other scientists can’t do their research and even write their papers beforehand though.

The result is something called simultaneous publication. On the same time the maize genome paper came out, a minimum of 14 other papers on maize were published in journals like PLoS Genetics, Plant Physiology, Proceedings of the National Academy of Sciences, and even the same issue of Science as the maize genome paper itself. These are just the first of hundreds more research publications that will be made possible by the sequencing of the maize genome (hopefully including some written by me!) each adding incrementally (or sometimes drastically) to our understanding of the world around us and our ability to change it for the better.*

If you’re interested in checking out  some of those papers, this edition of PLoS genetics has been completely taken over by maize genome papers, and the whole PLoS series of journals are open access which means you don’t have to buy a subscription or belong to a university or company that has already purchased access to read them.

*Based on the my current scientific-political theories, people on the left will consider the first of those two achievements worthy and the second unsafe and arrogant, while people on the right will consider the first a huge waste of money, but hopefully with be excited about the possibilities of the second. Myself I’m excited beyond belief about every bit of it.

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. 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.

The definition of ortholog boils down to being the same gene in different species. Scientists (like me!) can identify orthologs not just by looking for the most similar gene in another species’ genome, but also looking at synteny, the order of genes on chromosomes. Orthologous genes are in the genomes of two species descended from a common ancestor*, and the genes themselves can both trace their history back a gene sitting on a chromosome in that ancestral species. After the two species went their separate ways, each of their genomes began to accumulate differences (mutations). Eventually it can be hard to tell which genes are most closely related to each other, but one of the things that lasts a long time is orthologous genes will has some or many of the same genes nearby on the chromosome, in a similar order to each other, since many genes are still in the same places in the genome as they were in the genome of the common ancestor of both the species being studied.

That’s a huge mouthful. And it gets even more complicated when plants start holding on to extra genomes (something that isn’t too uncommon in plants, see my discussion on the genetics of wheat). Maize (corn) went through such a genome doubling, estimated to have happened ~10 million years ago. So when we compared the genome of corn (which should be getting officially published really REALLY soon) to that of other grass species like rice and sorghum (all the grains we grow (wheat, rice, corn, sorghum, barley, rye, oats, etc) are grasses) there are actually two separate maize regions that are equally related to every sorghum or rice region.**

This figure shows a gene conserved between all four regions and the dna surrounding it. The lines connect blast hits, regions a program (called BLAST) used by lots of biologists as identified as having similar DNA sequences between the the segments from the different genomes.

*One of the reasons comparative genomics is a field that wouldn’t exists if the people who don’t believe in evolution were right.

**That doesn’t mean maize has two copies of every gene present in sorghum and wheat. Right after getting an extra genome copy (technically two extra copies, since normal diploid organisms have two, one from each of their parents to start with, and maize doubled both) it did. Over the past ten million years the extra copies of many genes were lost, either deleted from the genome or accumulating so many mutations that they stopped functioning.