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comparative genomics

Why to Celebrate the Publication of the Brachypodium Genome

Brachypodium distachyon (photo courtesy of Devin O'Conner)

Sorry this is late going up. -James

This morning Nature officially published the paper* describing the sequence of the Brachypodium distachyon genome. This publication brings the number of grass genomes available for comparative analysis to four. In celebration I’m going to list four reasons to be excited about the publication of this genome.

The location of Brachypodium within the grass family tree.

Brachy (as I will refer to the species from here on) is a member of the Pooideae a sub-family of grasses from which no sequenced grasses have come. For the work we do in my lab this is exciting because it adds more depth to our analysis of changes in the grass genomes. The more distantly related grasses we can compare at the whole genome level, the better we can infer what the ancestral species that gave rise to all the grasses might have been like at a genome level. The most we know, or can make educated guesses about that species, the better position we are in to say what changed along the evolutionary paths leading to grasses like maize, rice, and sorghum. The choice of the Pooideae wasn’t at random, or even because of the sub-family’s distant relationship to other sequenced grasses. (more…)

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 this, but figured it’d be more fun to start out with something cool.

But first of all, let’s do this the right way this time. Here’s the paper in Nature describing the soybean genome. Here’s one of the places you can download the entire sequence from. Hopefully that establishes, beyond a reasonable doubt, that the soybean genome has, in fact, been published. (more…)