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  • how to sequencing a new plant

    Now we have a new plant and we want to get it's whole genome sequence. But we don't know the complexity of the genome(repetitive sequence and heterozygosity). Is there anyone who can do this? Thank you!

  • #2
    Have you looked for your plant or a relative in the Plant C-Value database? That would give you a size estimate, and my guess is size is a good estimator of complexity.

    Given the cost of sequencing, for a few thousand dollars you could just do a shotgun library of the genome on Illumina and start estimating from that -- both by looking directly for coding fragments & comparing against other plant genomes. Depending on what you are interested in scientifically, RNA-Seq may serve your goals better and in any case is pretty valuable for interpreting the genome. RAD-Seq may be a method to get quickly at the question of the heterozygosity (and I'm guessing one could infer ploidy as well).

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    • #3
      Originally posted by krobison View Post
      Have you looked for your plant or a relative in the Plant C-Value database? That would give you a size estimate, and my guess is size is a good estimator of complexity.

      Given the cost of sequencing, for a few thousand dollars you could just do a shotgun library of the genome on Illumina and start estimating from that -- both by looking directly for coding fragments & comparing against other plant genomes. Depending on what you are interested in scientifically, RNA-Seq may serve your goals better and in any case is pretty valuable for interpreting the genome. RAD-Seq may be a method to get quickly at the question of the heterozygosity (and I'm guessing one could infer ploidy as well).
      Thank you for your advice. It is useful to me. I didn’t look for the C-value of it and now I will go to certain it first.
      My goal is just want to get the whole genome sequence of the plant. But I am afraid just use Illumina can’t assemble to a good result when the genome is complexity (there are many repetitive sequence and so on just as grape).

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      • #4
        As an aside. There is no one single technology that will assemble a new plant, especially a repetitive one, to a "good result". At least at what we would now consider to be a reasonable cost. I suppose that you could always go back to good old Sanger sequencing if you want a single technology solution and if you have boat-loads of money. :-)

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        • #5
          Originally posted by westerman View Post
          As an aside. There is no one single technology that will assemble a new plant, especially a repetitive one, to a "good result". At least at what we would now consider to be a reasonable cost. I suppose that you could always go back to good old Sanger sequencing if you want a single technology solution and if you have boat-loads of money. :-)
          Thank you!

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