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Old 03-21-2015, 11:01 AM   #1
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Default Include heterochromatin in genome size estimates?

I am planning on sequencing several entire drosophila (fruit fly) genomes for an upcoming project. The published length of the drosophila genome is ~150 Mbp, up to ~175 Mbp including known heterochromatin. However, there is supposedly another 25-50 Mbp of heterochromatin in the form of large peri-centromeric and per-telomeric DNA satellites that is not included in these estimates.

My question is, how much does heterochromatin factor in to coverage calculations for NGS? When I am calculating my estimated genome coverage and figuring out how many lanes we need, should I be using 150 Mbp (eurchromatin only) or ~200 Mbp (euchromatin+heterochromatin)? I know that large tandem repeats and "structural" DNA (i.e. satellites) will not be properly amplified or sequenced, but I'm assuming they will still consume reagents and take up some space in the lane. Any advice you can provide would be much appreciated.

The sequencing will be done on an illumina HiSeq 2500, most likely using 2*100 bp reads.

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drosophila, heterochromatin, illumina, whole genome sequencing

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