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

April 9, 2010

The Peach Genome Is Out

Filed under: biology,genomics — Tags: , — James @ 3:28 pm

1.1 pound peach from the Berkeley Farmer's market.

Here. I had no idea anyone was even considering sequencing the peach genome until I heard a single off-hand comment at the maize meeting last month, and all of the sudden here it is. And in better shape in its first release than some genomes are even after they’re published.

This is a pre-publication release, so the Fort Lauderdale Convention is still in effect,* but the peach genome looks really great from the quick and dirty analysis I have already run. They’ve already got the genome assembled into pseudomolecules (chromosomes), unlike some genomes I could mention that have already been published, and marked the locations and structures of genes in the geneome (there was a weird period last summer when there were pre-release versions of the maize genome organized into chromosomes, and pre-release versions with the genes marked, but none that had both.)

*In short, you or I can download the peach genome, play around and study it to our hearts content, but we can’t publish anything on it until the people who actually sequenced the peach genome publish a paper describing their work.

January 19, 2010

Genome Sequencing vs Genetic Mapping

Filed under: biology,Genetics,Plant breeding,Plants — Tags: , , , , , — James @ 2:17 am

There was a recent paper in Science about the mapping of the Artemisia annua genome. I’ve seen several people interpret this as another genome sequence. It’s hard to blame anyone for this confusion given headlines like “Scientists map the maize genome!” to describe the sequencing of the maize genome. So what’s the difference between a sequenced genome and a mapped genome? I’m glad you asked! (more…)

January 14, 2010

The Newly Published Soybean Genome and Fractionation

Filed under: biology,evolution,Genetics,Plants,research stories — Tags: , , , , — James @ 3:39 pm

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…)

January 12, 2010

Strawberry Genome Sequenced (Correction included)

Filed under: biology,Genetics,Plants — Tags: , — James @ 3:10 pm

After already needing to correct this post, I must now invalidate the whole thing. Seems I’ve been taken in by a premature press release that was turned into reliable sounding articles on news sites and was then picked up by blogs like mine that took the those sites to be credible sources. It’s a big mess. ::sigh::

Among the many things I’m currently missing at the Plant and Animal Genome conference, in addition to an update on the banana genome I’ve just learned (thanks to Mary over at OpenHelix) that the sequencing of the woodland strawberry genome has been completed!

I don’t know yet if the sequence has been released to the public yet. Either way I can’t find the sequence so I can’t yet comment on the quality of the sequence, or any ancient duplications in the lineage (though we already know it must share the ancient hexaploidy of the rosids, possible all eudicots).

Wild diploid strawberry (left) and domesticated octoploid strawberry (right)

What we do know is that modern domesticated strawberries are octoploid, the result of two recent whole genome duplications, but the woodland strawberry doesn’t have any duplications modern enough to be obvious from cytogenetics, visually looking at chromosomes.

Sequencing a genome is a complicated process but it started out with the work of Janet Slovin, a USDA scientist who created the inbred line* used in sequencing and seems to be the front woman from the project (Janet was kind enough to comment and point out the original article was misleading on this point, check out the link she included as well!), she’s quoted in the linked article.
And if you know how I can get my hands on the sequence please PLEASE, drop me a line at jcs98 (at) jamesandthegiantcorn (dot) com.

December 30, 2009

Why I’m so Excited About the Banana Genome

Filed under: biology,evolution,Genetics,Plants — Tags: , , , , — James @ 12:01 pm

The single most consumed fruit in America, yet in the tropics this bananas starchy relatives play an even more vital role in feeding whole nations.

At the Plant and Animal Genome Conference next month (which I really wish I was going to), there will be a workshop on banana genomics, but from the abstract submitted by Carine Charron (h/t to Jeremy at the Agricultural Biodiversity Weblog) I learned that:

The sequencing phase will be completed in early 2010 and automatic annotation will take place during the first semester of 2010.

Why is sequencing the banana genome important? Three reasons: (more…)

November 26, 2009

The Cost of the Turkey Genome

Filed under: Genetics,Link Posts — Tags: , , — James @ 6:52 pm

Just to give you a sense of how fast technology is advancing:

Sequencing the maize genome took four years and 30 million dollars. Today Virginia Tech announced the University of Minnesota and themselves had received a $908,000 grant to sequence the Turkey genome in two years. I don’t know how big or complex the turkey genome is, but the idea of sequencing a whole new species for less than a million dollars is still pretty cool.

h/t to 538 they’ve got more cool turkey statistics over there.

November 21, 2009

Of course plants are more genetically complex!

Filed under: biology,Genetics,Plants — Tags: , , , — James @ 4:12 pm

Let’s remember back to a time before the human genome project published it’s first draft assembly in 2001. The genome of C. elegans a tiny nematode had already been published with ~20,000 genes. The C. elegans genome is one 1/30 the size of the human genome and the tiny worms are so small that biologists have mapped the developmental fate of every single cell in their bodies (an adult C. elegans has exactly 959 or 1031 cells depending on gender), whereas the human body contains tens of trillions. How many genes would you guess humans have?

Estimates at the time ranged from 40,000 to 150,000 genes. (more…)

November 20, 2009

Bloggers on the Maize Genome

Filed under: Genetics,Link Posts,Plants — Tags: , , , , — James @ 3:31 pm

Update: PolITiGenomics just posted a piece on the corn genome as well.

You know I could keep talking about the maize genome all day (and I may very well do just that), but what are other bloggers saying about the most complicated plant genome ever published, of second most important single species for feeding people around the world? (Clearly I’m not at all excited) (more…)

November 19, 2009

Corn Genome

Filed under: biology,Genetics — Tags: , , — James @ 3:25 pm

So I was mixed up and didn’t think this could be publically mentioned until tomorrow, but the finalized corn genome has come out. Edited this link to point to the ISU coverage which seems to be more detailed than the release from Wash U. If Wash U can mention it, so can I. Expect tomorrow to be a day of corn here at Jamesandthegiantcorn (though it would have been more fun if I could had started the day of corn before this news was publically announced.)

Lots of corn … and maybe some genomics. Consider yourselves forwarned!

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