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Utricularia from wetlands in Alaska

  • Thread starter Anne-Lise
  • Start date
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 ?



 
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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
 
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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 !
 
We can't see your pictures - it looks like they're set to private on your Google Drive.
 
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.
 
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?
 
[MENTION=10989]nimbulan[/MENTION]: Yes, indeed the pics were on a Google drive. Sorry for that. I edited the post.
[MENTION=10715]Tanukimo[/MENTION]: 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 !
[MENTION=12066]emc2[/MENTION]: 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.
 
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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.
 
Was more thinking in shipping a piece of leaf or better a tube of DNA if you can still perform the extraction locally.

Else, yes, totally agree, these are different use case, I guess a better comparison, for costs, would be with a 10x genomics run. I'm actually quite interested into the sample barcoding, mostly for single cell RNAseq, but anyway that's off topic.
 
  • #10
Another fellow Alaskan!

I've been finding Utricularia in the muskeg ponds around here for years. I've always just assumed that they were U. vulgaris, but to be quite honest I haven't sat down and taken a seriously good look at them/compared them to species descriptions.

It's quite possible that the Utricularia that grow up there are not the same species as ones that grow down here, however the Utricularia here also have very similar looking blooms.
 
  • #11
Bonjour

For me U.vulgaris or U.macrorhiza, these 2 species are very close, just the spur of the corolla is different, so a picture would be more.

The quadrifidal hairs inside the trap could also give information, but it's another story

jeff
 
  • #12
People can't see the pictures that I post. I am using Google Photo (ever since Photobucket held our photos hostage, for $400). How did you edit yours?
 
  • #13
People can't see the pictures that I post. I am using Google Photo (ever since Photobucket held our photos hostage, for $400). How did you edit yours?

She just uploaded them to a different image hosting site. I know there's a way you can make pictures on Google Drive publicly visible, but am not entirely sure how that's accomplished.
 
  • #14
Hello Dexenthes and you all,

Thank you for following up on this ID. The UAF herbarium (ARCTOS: http://arctos.database.museum/SpecimenSearch.cfm) reports Utricularia all over AK ! Once, I get mine IDed, I would love to know if it is the same species than your, Dexenthes !

Jeff 2 wanted to see the spur of this flower but the only picture I've got where we can see one it far from being great and I am not sure that anything could be said from it. For the quadrifidal hairs, I'll need to do another microscopy as I did pics of the wrong hairs, yesterday :blush:

I will open a thread about the genome of this plant. It will in the Utricularia section of the forum.
There, I would like to discuss with you about ideas of what I could look at in this genome, what you would like to see in a paper: for instance a phylogenetic tree of the genus. I bet there are other things that would be great but that I'm not thinking about.

Also, I really ponder about the resistance to the cold of this plant. I mean, the still water gets totally frozen over 2m of depth here during water. Thus, it means that the plant freezes hard every winter, thaw in April/May and keeps going for about 4 months before freezing again. When you think about it, this plant spends more time frozen than not. wow !

I went back to the place where I collected the individual that I sequenced. I wanted to get some water and maybe some mud to prepare an aquarium. Indeed I kept a piece of the individual I sequenced in order to have some material in case I needed to do another run. For about 5 weeks now that my little guy has been in a masson jar, it grows well but it is not strong as the plants from the site or those I transplanted in my landlord's pond (see pics). I guessed that it doesn't like my jar that much.
I just got back from my little field trip. Gosh, the water is super brackish: it stincks and it's crowed with little mosquitoe larvae. It is warm on the surface with the sun. I spotted a giant colony of Utricularia. I put my hand in the middle of it as I wanted to know how deep was the water. I can tell that I went up to my shoulder without reaching the bottom but the layer of Utricularia was also that thick ! On the surface, it is green/nice stems and deeper in is old brown resistant stems. I am amazed: it must be a very old colony. I really cross fingers that nobody will buy this lot and build on it.
I attach a picture I just took on the site. You'll see a very limited part of the big colony and a picure of my landlord's pond with part of the plants I transplanted last year and some new that I brought from the big colony (I took less than 5% of it, no worries). It's my little guy with its super brackish water, in the tank.

0u7l.png



k1o2.png
 
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  • #15
What did you do / edit to make your pictures visible?
 
  • #17
The plant is probably macrorhiza, especially if it is free-floating. Utricularia vulgaris is not native to North America.
 
  • #18
Thank you [MENTION=10715]Tanukimo[/MENTION] for this additional criterium related to the absence of roots.
[MENTION=3500]jeff 2[/MENTION]: Here is a microscopy of a bladder. We can see a bunch of quadrifidal hairs floatting around. Another strong indication of U. macrorhiza it seems.
lrqd.jpg


Yesterday, I participated to a fish survey in the Chena Slough. It is part of the program of Elodea's eradication. I was surprised to find again Utricularia alive and well despite the herbicide disseminated against the invasive plant. I thought that Utricularias were found in bodies of still water only but definitely, they do well in streams ! See the pic bellow.
007y.png
 
  • #19
yes for U.macrorhiza .


On U.macrorhiza : the quadrifids with the longer pair with apex apiculate,parallel or slightly divergent , the shorter pair with apex rounded, slightly to considerably divergent or slightly reflexed, with an included angle of up to 190°


To confirm with a photo of spur :scratch:

jeff
 
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