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Thread: Utricularia from wetlands in Alaska

  1. #1
    Anne-Lise's Avatar
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    Utricularia from wetlands in Alaska

    Hello everyone,

    I noticed last year that an Utricularia grows in the wetlands around here in Fairbanks, AK. It blooms in early July.
    The wetlands I'm talking about are actually some lots for sale that I surveyed for woodfrogs.

    For my job I started to work with an innovative device that sequences DNA in a friendly manner.
    The device is called minION. It is used in diverse areas of Research but still very little in Conservation while I think it has a huge potential as it is portable (smaller than an iPhone), fun and efficient.

    Last month, I decided to try this new technology with the Utricularia that grows around here. I sequenced its genome and I am currently working on the informatic to release it to the public along with a publication.

    I don't know what species it is. I'll be able to tell with the genome when my work will be done but I wanted to take a guess with you before to use the "hard-core" data.
    The herbarium of the University reports observations of a couple of species growing around here: U. vulgaris, U. minor, U. macrorhiza and a couple of others.

    I attach a couple of pictures I made of the plant I sequenced. My guess is U. macrorhiza. What do you think ?



    Last edited by Anne-Lise; 08-09-2017 at 10:42 AM.

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    jeff 2's Avatar
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    Bonjour

    no picture

    have you a spur picture ?

    U.macrorhiza and U.vulgaris are very close

    this system minION interest me , for the genus pinguicula my speciality .

    jeff
    Last edited by jeff 2; 08-08-2017 at 11:54 PM.

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    Anne-Lise's Avatar
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    Hi Jeff,

    I saw somewhere that there's a couple of pinguicula growing in Alaska and I would like to find them before winter (that is kind of like in 6 weeks - LOL).

    The minION is user-friendly compared to the other sequencing technologies but it still requires lab skills in molecular biology and some material. I don't know what is your profession. If you're a researcher, I would definitely encourage you to give it a shot. I would be more than happy to send you my protocoles. However, if you don't work in a lab already, it would be a real challenge.
    Briefly, minION is portable and controlled from a laptop. It still requires pipettes, diverse lab consumables (enzymes and reaction kit) and some computational power to process the large amount of data that represents a run.
    People have been using minION in extreme environments for research: on sea ice in Arctic and Antarctic and even on the ISS station !
    Currently a couple of herpetologists are using it in the middle of the Equator rainforest. They're the only one I know of, whom are using this device for Conservation. It's amazing and opens great avenues for endangered species for instance. I'm professionally moving into this direction.

    I hope this help. Let me know if you have more questions !

    If people are interested in this Utricularia genome project, I would be very happy to open a thread about it where I could give more details about the technology, the results and hopefully integrate people's thoughts and requests into my work.

    Thank you for your interest !

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    nimbulan's Avatar
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    We can't see your pictures - it looks like they're set to private on your Google Drive.

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    Are the shoots dimorphic? Do you see stems with only foliage and stems with only bladders? If you don't it should be Utricularia macrorhiza, since the other aquatic Utricularia species in Alaska (minor, intermedia, and ochroleuca) all have dimorphic growth.

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    I would be interested on your feedback and you protocols over the nanopore sequencing.
    Send me a MP if you don't mind sharing.

    Depending the output, coverage, etc it seems quite a steep price by sample. The device is cheap, but then with kit and flowcell it seems each sample will run around ~$1500 versus ~$400 on a regular agilent+multiplexed HiSeq lane.
    Sure you can't do that in-situ, but I would assume that extracting DNA and shipping to a lab would not be too bad?

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    Anne-Lise's Avatar
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    @nimbulan: Yes, indeed the pics were on a Google drive. Sorry for that. I edited the post.
    @Tanukimo: that is a very efficient criterion of identification for macrorhiza. With the pictures now available, we can see that there is bladders and foliage on the same stem. However, I've got more individuals that grow now in a pond on the property of my landlord and I'll take a closer look. That is great, thanks !
    @emc2: Hi ! What you say makes total sense. If you work in a lab and never go into the field, yes, Illumina makes sense but it also leaves you with fragmented genomes as repeats regions don't get resolved with short reads. For instance, right now I also work on the genome of an arctic "fungi". The thing was first sequenced on one lane of Hiseq by my colleage. He deposited 44000 contigs that were > 500bps while in fact his assembly was way above 44 000 contigs with <500kps contigs included. I did a run of minION on it and I came down right away to ~800 contigs. I see Illumina and minION complementary. In Conservation, minION offers possibilities that others technologies never will as long as they do not create a portable device. Think about endangered species. There is a demand from federal agencies to sequence locally DNA from endangered species because it is so difficult to do all the paperwork to ship this kind of samples out of state/country.
    Also, you can barcode your libraries which decrease the cost per sample. I think I saw total cost/sample <$1000 in a recent paper published about the sequencing of A. thaliana with minION.
    As you can see I am a fan :-) I'll MP you.
    Last edited by Anne-Lise; 08-09-2017 at 11:06 AM.

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    nimbulan's Avatar
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    U. macrorhiza seems likely, though oddly my field guide does not contain U. vulgaris. I'm pretty sure it's not any other species.

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