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.


  1. […] isn’t everything, genome […]

    Pingback by Nibbles: Peach genome, P, Marine protected areas — April 10, 2010 @ 3:35 am

  2. […] isn’t everything, genome […]

    Pingback by Nibbles: Peach genome, P, Marine protected areas | Science Report | Biology News, Economics News, Computer Science News, Mathematics News, Physics News, Psychology News — April 10, 2010 @ 4:27 am

  3. Hey James–that’s an interesting question about whether Ft. Lauderdale applies to blogs. In fact, I’m going to ask my contacts at NHGRI next week. My impression was that it was formal publication. But I think it’s worth asking.

    I have restricted data in my ENCODE training presentation. But the ENCODE team is aware of that. Still…I think I’ll check.

    Comment by Mary — April 11, 2010 @ 5:31 am

  4. Thanks Mary!

    Comment by James — April 11, 2010 @ 9:34 am

  5. Turns out (at least for ENCODE) that blogs are covered as a publication type for data restriction policy. The overview page here on the policy has several links: http://www.genome.gov/27528022

    Specifically the current ENCODE data policy (warning, PDF) says:
    “The publication and presentation moratorium is expected to extend to all
    forms of public disclosure, including meeting abstracts, oral presentations, and formal electronic submissions to publicly accessible sites (e.g., public websites, web blogs).”

    It may vary slightly by project, but I think that’s likely to be pretty consistent across these types of projects. The initial Ft. Lauderdale was way too long ago to have covered blogs, so this is actually interesting to know.

    I’m glad I looked that up….Thanks for the prompt on that.

    Comment by Mary — April 12, 2010 @ 9:10 am

  6. Hmmm. Well I can’t say I blame them as once a genome is sequenced (at great cost and with the sacrifice of much sweat and tears on the part of the research team), there’s a lot of simple stuff I could do in a couple of days that would steal a lot of thunder out of what’s in the usual genome paper.

    Do I hope they publish soon though, because I was practically jumping up and down when I did my initial analysis!

    Comment by James — April 12, 2010 @ 10:54 am

  7. Cool, fruit genetics, now that’s the way to go! The stone fruits are a pretty interesting lot what with all the crosses they’ve got between peaches/nectarines, plums, and apricots. The first thing that comes to mind for me is how awesome would it be, when we’ve got a good handle on what does what in the peach, if someday someone could use this to produce a parthenocarpic peach (or other stone fruit) variety with only a vestigial pit, not that big hard thing? I wonder how that would affect public perception of GE; if it gave them peaches & nectarines they could just bite right through, with no more paying by the pound for something that has a large part you’re just going to spit out. Wouldn’t that be pleasant? I wonder what people would think it, knowing the instant they bit into it that it was GE? It’d be interesting to see how that would play out.

    I’ve got a peach tree. I hope it produces well this year, it’s nice and pruned, good mushroom shape, didn’t bear last year, might be ready to go now. I should graft a nectarine or nectaplum on to it someday.

    Comment by Party Cactus — April 11, 2010 @ 9:59 pm

  8. Instead of getting rid of the peach pits, what if we could make those pits edible and tasty like almonds, another closely related species?

    But yes, once genetic engineering reaches the point where it provides cool new things for people to eat (like a seedless peach) I think it will drastically change how the public perceives the technology. Unfortunately right now, with the cost of getting a single GM trait approved at over 100 million dollars. Even if I had a seedless peach tree growing in my greenhouse right now, if it had been created with genetic engineering I doubt I could convince a company it would be profitable to pay to have it approved for human consumption.

    Best of luck with your (seeded) peach tree yielding this year, that’s awesome!

    Comment by James — April 12, 2010 @ 10:49 am

  9. a virus-resistant plum variety was approved this past year: http://www.nature.com/nbt/journal/v28/n4/box/nbt0410-306_BX3.html

    have you heard anything about this? It totally flew under my radar.

    Comment by Amy — April 14, 2010 @ 12:43 pm

  10. I hadn’t read anything about it either. Nice catch Amy! I’ll definitely look into those further, see if I can figure out if they’ve been released to growers yet.

    Virus resistance in fruit trees is a great example of the sort of research that’d probably never make a company rich, but reliably provide real benefits for fruit growers. (For those who can’t access the above link, the virus resistant plums were developed by the USDA.)

    Comment by James — April 14, 2010 @ 8:59 pm

  11. ooo more on GM fruit trees!

    Comment by Amy — April 15, 2010 @ 3:33 pm

  12. Dear James,

    I’m glad that you are appreciative of the release of the peach genome, and recognize the high quality of this genome. The peach genome v1.0 represents a major effort by numerous labs around the globe. Please rest assured that we are aware of the unique and special nature of the peach genome, and what it has to offer the plant community.

    As such, we are gratified that you are restraining yourself from “a lot of simple stuff I could do in a couple of days that would steal a lot of thunder out of what’s in the usual genome paper”. Having said that, those types of analyses and the material in this blog, while it does not seem to jeopardize any planned publications, is not in the spirit of the Fort Lauderdale agreement. The comparative analyses on CoGe are blatantly violating that spirit, and I have requested that it be removed from the public domain. I hope that you and other scientists will respect the International Peach Genome Initiative’s desire to make the data available to the research community, while simultaneously keeping certain analyses protected for the researchers who produced the data.

    Now that that’s out of the way, to Party Cactus: the diversity that exists in peach is very broad, and includes genotypes that do not produce a stone. Unfortunately this trait has not been incorporated into developed varieties. There are also varieties that produce a “sweet” pit not unlike almond (sister species), but I don’t believe anybody has worked on incorporating that trait into a peach variety, the stones are rather tough after all. Regardless, these traits are likely to be incorporated into accepted peaches without GM in the future. Other interesting traits that occur in peaches that you may not be aware of: weeping form (like the willow), doubled flowers (like the rose), I could go on. To make a long story short, it is amazing that so many forms and biotypes can exist with so little DNA!

    I wish the same could be said for plum pox virus. I am not aware of any resistant peach germplasm to that disease, and the US is in continued danger of having the disease occur. The USDA plum that is mentioned above is highly promising and will hopefully be successfully field tested in Europe in the coming years for durable PPV resistance. If the mechanism for resistance is robust, it will likely be incorporated into other stone fruits and into US germplasm to protect against any future US PPV outbreaks.

    In closing, thanks for your interest in peaches and the peach genome, and rest assured we are working on the publication!

    Best regards,
    Bryon Sosinski
    Co-coordinator for the International Peach Genome Initiative

    Comment by Bryon Sosinski — April 16, 2010 @ 1:33 pm

  13. I have cut my post back to the bare minimum that the peach genome has been released and is obviously of high quality. Now that I’ve heard from Eric that he and you were already in communication, it’s probably best to let the two of you handle the issues with Cogepedia.

    Thank you for sharing your expertise on peaches and other stone fruits, I was unaware that seedless and sweet pitted peaches are already present in peach germplasm and was fascinated to learn that. Being able to take non-transgenic approaches (perhaps using marker assisted selection based on your work?), mean we might actually see those traits in grocery stores at some point in the foreseeable future!

    I look forward to the genome paper and certainly plan to highlight its publication, and it would be awesome if you’d be willing to come back and comment further at that time (when reserved analysis is no longer at stake).

    Comment by James — April 16, 2010 @ 3:30 pm

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