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Thread: Ongoing project: sequencing the genome of an Alaskan Utricularia

  1. #9

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    I was where you are a few years ago, it's definitively interesting to learn, but takes a lot of time!

    I will MP you my pipeline, mostly using SLURM scheduler commands and bash to launch the actual tools.

  2. #10
    Anne-Lise's Avatar
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    Quote Originally Posted by patrickntd View Post
    Hi Anna,

    Re: sequencing, I think you may also need to deal with DNA from fungi and algae in your resultant dataset, since they are commonly live together with Utrics in the nature.
    Excellent point ! I found this paper a couple of days ago and I am definitely keeping my eyes open on Tetrahymena and its algae: https://www.ncbi.nlm.nih.gov/pubmed/27613221
    A month ago when I wasn't aware of this paper, I blasted some reads reads and I remember seeing some ciliophora hits which looks promissing now. These past couple of days I looked at taxonomic assignations of my contigs within prokaryotes (BuzyBee does that quickly and nicely). I've got an almost complete genome of a Flavobacterium but there are also some pseudomonas, comamonadales, methanococcales... But definitely, my interest now shifted on the ciliophora and its algae. Fingers crossed, I should know pretty soon !

    Quote Originally Posted by patrickntd View Post
    Re: point to explore:
    I think phylogeny and comparison to gibba should be done which is straightforward and informative. It will be even more interesting if you can correlate that to the geographic information. In addition, I am interested to know how this specie adapt to the specific environment in AK (freezing cold and short daytime in winter) based on the genome. For examples, do the proteins in energy utilization, digestion, reproduction have SNP to make them adapt to cold temperature?
    Also, an interest of mine and I am glad that you share my interest in cold adaptation. I understand that the turions helps from one year to the other but still, they stay hard frozen for 8 months a year (like the woodfrogs, lol) ! It worth to look at anti-freeze proteins and such. My lab does that with bacteria isolated from sea ice. Hopefully, I'll find a way to adapt this search to the plant.
    Regarding a comparison to gibba, I was a bit afraid of it as I never compared genomes but if you say that it is easy, I am willing to give it a try ! Hence, I might need suggestions for the tool(s) to use. I can definitely find that in litterature but if you have some experience, I would really appreciate your insight to pick an efficient one that doesn't take days to install and figure out. Thank you, Patrick !

  3. #11

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    Anne,

    Unfortunately, I don't have hand-n experience of bioinformatics that can provide you technical advice. I think you may not need whole genome comparison. Instead, you can compare those protein or gene family of interest. Good luck.

  4. #12
    Anne-Lise's Avatar
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    Thank you @patrickntd. I hope that you're doing okay in Houston. My thoughts are going to you and your dears.

  5. #13

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    Thank you very much.

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