During de-novo assembly of a microbial genome with baseline coverage of ~100x, genes with multiple copies in the genome (e.g. 16S rRNA gene) map to a single contig with coverage relative to the number of expected copies (i.e. 4 copies will result in a single contig of ~400x coverage).
Is there any way of separating these out post-assembly, or else re-assemble while maintaining individual copies?
Hi Giuseppe, and thanks for your reply. I do have paired-end reads, yes. I've taken a quick look at gap5. Looks like it has quite a steep learning curve but I can definitely see how its contig editing features could prove useful here. I see it has a 'find repeats' function. Is this suitable for finding entire duplicate genes, or is it more designed for shorter repetitive regions like tandem repeats?
Hi Nathan. First, use something like mpileup to see how variable your repeats are. Tandem repeats of functionally homogenous genes - like rRNA - tend to be subject to concerted evolution, in which they essentially evolve synchronously and remain identical. (In essence, damage is sometimes repaired from the "wrong" copy, causing sequence convergence over time, even whilst different lineages diverge.) If there is little/no variation and your reads are shorter than your repeats, there is not a lot you can do. You current approach - estimating copy number from X coverage - is the norm. You can manually insert the extra copies if you wish, or just make a note (as they did with the 100 rDNA copies in the yeast genome).
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