Question about expected chloroplast coverage

Question

[jal]

Hi

I'm trying to recover whole chloroplast sequence data from paired-end Illumina reads from a pool-seq project (25 individuals per pool). We have access to a close reference but not a species-specific chloroplast reference. Following alignment and filtering of reads from one lane (basically following the Popoolation pipeline), I'm getting coverage of about 10% of chloroplast genome at a read depth of 10. This seems very low to me...I expected that because there are many more copies of the cp genome than the nuclear genome, I would get higher cp coverage (our nuclear coverage is at about 70% at a read depth of 25-500). Does anyone have any numbers that I can compare to (e.g. cp coverage from paired-end Illumina data, not necessarily pooled)?

Thanks!

Answer 1

[Istvan Albert]

I just want to make the note that the chloroplast sequence is also much shorter than that of the nuclear genome. So it could have hundreds or thousands of copies and still be much shorter than the nuclear DNA.