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  • Hello

    Hello,

    My name is Taylor. I work at the University of Guelph, in Ontario Canada. I work on glyphosate resistant giant ragweed. We just sent out four samples for RNAseq analysis to look at differences in gene expression between sprayed and unsprayed susceptible and resistant plants.

    Our biggest problem is that we have little to no genetic data available on our species; no reference genome (and only about 40 entries in NCBI).

    Glad to be a part of the community,
    Taylor

  • #2
    If this genome is important, why not go for a de novo assembly to actually have a reference genome? This way you'll have genomic data with RNA-Seq (plus a very nice project and probably a thesis to go with it). I am guessing that ragweed is somewhere between 100-200 Mbp in size. The best de novo assembly strategy is lots of throughput and coverage with Illumina short reads, plus some long PacBio reads to span repeats and join contigs. My best guess is that this will cost $10K (all in at service lab) This doesn't seem out of reach for an important contribution to the field.

    Mike Schatz at CSHL has done a lot of work in this area: http://schatzlab.cshl.edu/presentati...%20Genomes.pdf

    Genome Quebec can provide service and has informatics experience on hybrid de novo assemblies. http://gqinnovationcenter.com/servic...acBio.aspx?l=e

    **Disclaimer: I work for a sequencing company.

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