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

March 14, 2010

And the list gets better!

Filed under: genomics,Site Business — James @ 4:02 pm

Based on e-mails and responses to my previous post I’ve made the following additions to the sequenced plant genomes page:

  • Added an entry on Columbine, a member of an early diverging group of eudicots. As far as I can tell this sequence is currently unreleased, but from the JGI website it looks like the initial assembly is already complete, so if you know of a way for people to get ahold of that let me know.
  • Added an entry on the Castor Bean. The sequencing group has released a 4x coverage genome assembly. (The castor bean is the source of the deadly toxin ricin, and is not grown in the US, we import our castor oil from other countries.)
  • Split the entry on Arabidopsis into “Arabidopsis species and allies“. This gives the Arabidopsis lyrata its own heading, and will be important since there are another 7 species from the Arabidopsis genus and its close relatives in the JGI sequencing pipeline.
  • Added an entry on v2 of the date palm genome generated by Weill Cornell Medical College in Qatar. This definitely should still be considered an “in progress” genome, but at least until the banana genome comes out it’s the best non-grass monocot genome available.
  • Added an entry on the genome of Physcomitrella patens, which, as a moss, is the descendant of an evolutionary lineage that split from all the other genomes I’ve listed on the page around 450 million years ago.
  • Added the recently announced sunflower genome project to the list of planned, in-progress, and private genome efforts. (Apparently the genome of the cultivated sunflower is more 3 gigabases. Bigger than corn!) That’ll be a cool genome to see when it comes out.
  • Added information on the woodland strawberry genome project, which aims to have an assembled genome of Fragaria vesca by sometime this year. You may remember the woodland strawberry genome from the mix up back in January.
  • Added the various groups that have announced they have private genome sequences of the oil palm genome to the same section.

Particular thanks to Greg, Jeff, and Eric whose suggestions where behind most of these additions.

Completely unrelated, you may have noticed I switched the RSS feed back to full length entries. I recently tried out Google Reader (I’m way behind the times I know), and it is SO MUCH nicer to see the full entries there than have to click through from a brief summary. The downside, as I know from previous experiences, is that when I send out the full entries by RSS I get a lot less traffic.

I don’t earn any income from traffic to this site, but it is a nice feeling to know people are reading and enjoying something I wrote, and I have no way of tracking how many people (if any) read an article from the RSS feed.

Anyway I’ll keep sending out full entries for at least the next week (I expect I’ll be too busy to worry about ego stroking traffic statistics until at least a week from Tuesday.)


  1. Awesome list James.

    Any chance you’ll get a pool together as to the date that there will be so many plant genomes being sequenced that you can’t manually track them any more? I’d like to put $5 on a year from now. Perhaps a plot of new plant genomes for each year since 2000 will help out. . .

    Comment by Eric — March 14, 2010 @ 10:20 pm

  2. It’s a good question. If there was a pool, I’d put my money at closer to two years out, but let me generate that graph…

    Comment by James — March 15, 2010 @ 12:23 am

  3. I would not want to take that bet. Its going to get out of hand very fast. Which is one reason why its going to be so important to have good resources… like a list of ones that are done.

    Comment by Greg — March 15, 2010 @ 12:16 am

  4. Glad you switched to full length feeds! And if you are curious about your traffic, try feedburner — you can route your RSS feed through it, and it will show you how many people have subscribed to your feed (through any feed reader) each day.

    Comment by Joseph Tychonievich — March 15, 2010 @ 8:40 am

  5. I’ve heard about feed burner. The extra data is very tempting, although I’m afraid to find out how many more readers I’d lose if I switched the RSS feed out from under them.

    Comment by James — March 15, 2010 @ 8:57 pm

  6. We feel all warm and fuzzy when we read your posts, too, James. Happiness goes both ways.

    Comment by Liza — March 15, 2010 @ 4:28 pm

  7. Well thank you Liza. Seeing web traffic is nice, but people who actually take the time to post comments bring a smile to my face every time.

    Comment by James — March 15, 2010 @ 9:02 pm

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