Today there are a mere 10 published plant genomes out of the more than quarter million named plant species in the world. But even ten genomes is a huge amount of data to deal with for a plant genomics community that largely came of age during the long genome drought of 2002-2006. What is the [...]
Posts under ‘research stories’
Sequenced Plant Genomes
When I was an undergraduate, there were exactly two sequenced plant genomes, rice and arabidopsis. And sure maybe I didn’t have to walk “ten miles to school, barefoot, in the snow, uphill, both ways”* the one way I did have to walk uphill (sometimes in the snow but always with shoes), was very uphill. But [...]
How many maize/corn genes have actually been studied? (Not a lot)
Executive summary: the maize genome project found 32,690 high confidence genes in the maize genome, MaizeGDB records only 1181 named genes in the maize genome (excluding genes carried in the small genomes of chloroplasts and mitochondria), or less than 4% of the number of identified genes.
What does it mean to be a named gene? Why is that number so low? Why are we still able to make reasonable guesses about the functions of genes that have been never been studied? The answers to these questions inside.
Newer Tighter CoGe-MaizeGDB demo
New shorter, tighter, more interesting and all around better CoGe-MaizeGDB walkthrough.
Why to Celebrate the Publication of the Brachypodium Genome
Goes into four answers to why we should celebrate the publication of the genome of the fourth grass ever sequenced (sometimes referred to either affectionately or derisively as the Arabidopsis of the plant world), along with some pretty pictures of the plant itself and a little basic genome analysis.
MaizeGDB and CoGe: A Beautiful Friendship
Editor’s note: I have a new shorter, better, tutorial, here. 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 [...]
How to Give an Interesting Research Talk?
It’s important to not only be able to do breakthrough scientific research, but also turn around and communicate those results to a broader audience who probably isn’t nearly as intrinsically fascinated with your area of research as you are after spending years of your life studying nothing else. Apropos of George Chuck giving a GREAT talk here about the role of microRNAs in regulating phase change in corn (think plant puberty).
The Newly Published Soybean Genome and Fractionation
Here’s the key statistic: The maize genome paper estimated that roughly a quarter of maize genes are currently retained as duplicate pairs from maize’s whole genome duplication, while the soybean paper estimates just over half of soybean genes are similarly retained after soybean’s (apparently slightly older) duplication. <– had it buried at the end of [...]
One of the Joys of Comparative Genomics
I was originally scheduled to fly home yesterday, but was forced to extend my stay by unfortunate chain of events that (among other things) has resulted with me swearing off contact lenses for the foreseeable future. If I worked with arabidopsis or brachypodium, I’d probably have plants flowering this week that I’d be missing. Without [...]
Corn vs Maize
I use the words basically interchangeably on this site. I know it’s confusing and I at least attempt to pick one and use it all the way through a post (often without success, which I’ll catch, and wince at, days later). The problem is that naturally I use one word or the other depending on [...]