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

February 26, 2010

One MORE reason pineapples are awesome

Filed under: Uncategorized — Tags: — James @ 10:00 am

Pineapple plant. photo: CameliaTWU, flickr (click photo to see in original context)

Pineapples use CAM photosynthesis. Normally plants have to open tiny holes in their leaves (called stomata) during the day to let in carbon dioxide that they use during photosynthesis. The problem they face is that when they’re letting carbon-dioxide in, plants also let water out.

CAM plants get around this water loss by collecting all their carbon dioxide at night (when it’s not as hot so they lose less water when they open their stomata) and storing it within their leaves until they need it during the day. This allows them to be much more efficient with water than normal plants (ones carry out plain old vanilla C3 photosynthesis.*)

Why do pineapple plants need to be so frugal when it comes to water? The fact that pineapples are native to paraguay and southern brazil is repeated across the internet, but as you can imagine, that description covers a wide range of climates and habitats some of which are much drier than others. Clearly more research on the subject is called for on my part.

The fact that pineapples do CAM photosynthesis came up in a discussion with another guy in my lab where we discussed the fact that pineapples would make an excellent comparison for grass genomes** and have a reasonably small genome at ~500 megabases***, half the size of the recently published soybean and sorghum genomes and less than a quarter the size of the maize genome.

With all these new third generation sequencing technologies coming out in 2010, hopefully someone will sequence the pineapple genome. If not, maybe the cost of sequencing will drop enough while I’m in grad school that I can sequence the genome myself ( a guy can dream).

For more on my long running admiration for pineapple (second only to my appreciation of corn itself):

Why Pineapples are Awesome.

Phylogeny of Pineapple, an further explanation of awesomeness.

*Let the record reflect that corn does C4 photosynthesis, which another awesome variation on the standard system of photosynthesis.

**In addition to both pineapple  and grasses being monocots, they’re in the same order of plants, Poales, as grasses. The first non-grass monocot to be sequenced will almost certainly be the banana (in fact the process as already begun), but while bananas are monocots they belong to a different order Zingiberales (which includes spice plants like ginger, cardamom, and tumeric).

***526 Megabases as cited in Patterson AH, Freeling M, Sasaki, T “Grains of Knowledge” Genome Research 10.1101/gr.3725905


  1. […] is a good suggestion from an old (2010) blog post by James and the Giant Corn blog said – One MORE reason Pineapples are awesome Pineapples use CAM photosynthesis. Normally plants have to open tiny holes in their leaves (called […]

    Pingback by Various Developments – 11/30/2012 « Homologus — November 30, 2012 @ 10:39 am

  2. Hello,there.
    I’m CJchen from China.
    When I’m searching info about pineapple genome, I found your blog.
    Interesting blog to me…
    Our lab have been conducting tiss” cultu” on pineapple for more than ten years.
    And now I’m do some sequncing data analysis for other students in our lab.
    Have left my blog ..(domain of which was http://www.pineapplechina.com before)
    Hopefully to been contacting with u.

    Comment by CJchen — May 11, 2015 @ 6:11 am

  3. Hi CJchen,

    Thanks for stopping by. Despite my visits to China, I’m afraid I cannot read a lot of your blog. Right now, my chinese vocabulary is still limited to “ni hao”, “xie xie”, and “ganbei.” It looks like right now you are setting up a local blast server for your lab to use? What kind of genomic/transcriptome datasets are you working on with pineapple?


    Comment by James — May 11, 2015 @ 8:33 am

  4. Yeth.
    I have tried to be write in English, however, what i write is seem not so easy to understand for most of my friends in China… Maybe, oneday when my English is good enough, i would rewrite all those posts.
    Before that, if you’re interesting in anything to on my blog, just tell me and i will give the best explaination as i can.
    Thks for visiting my blog and trying to know what I’m doing 🙂
    And you’r right….
    the lastest post on my blog …. setting up a local blast server
    ’cause I will graduate next year and my supervisor asks me to leave thing that might be helpful to my teammates as much as possible.
    mRNA miRNA resuqencing,
    I have just begun learing data-analysis.

    Comment by CJchen — May 12, 2015 @ 6:36 pm

  5. It makes sense to write in whatever language your audience will best understand. The important thing is to keep writing. The more practice you get writing about science (in simple enough terms people outside your own lab can understand what you are talking about) the better you get at it. I credit writing this blog with making me much better at both giving scientific presentations and writing manuscripts.

    I don’t have much experience with microRNAs, but I did lots and lots of work with mRNA analysis when I was a graduate student, and we do lots of it in my lab now, so let me know if you ever have questions you can not figure out the answers to.

    Comment by James — May 12, 2015 @ 6:55 pm

  6. oh….almost forget to ask u …
    So… do u analyse the pineapple genome sequencing data ?
    ’Cau my lab have do several RNAseq on pineapple,, and i wondering when we i access to the genome,,,for which I thought there might have two teams are doing almost the same thing…—one sequence cultivar ‘F13’,,,the other sequence ‘MD2′(the Gold Pineapple,….in Chinese)

    Comment by CJchen — May 12, 2015 @ 7:30 pm

  7. Sadly no. I know one of the groups is based at Fujian Agriculture and Forestry University, but I don’t have any access to their genome assembly. Pineapple is a really useful outgroup for the grasses so I am just eager for a pineapple genome assembly to be published as you are. (Plus once it is published, I will have a good excuse to grow some pineapples in my university’s greenhouses.)

    Comment by James — May 12, 2015 @ 7:46 pm

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