Filling in inverted repeat gaps (chloroplast)

Question

[lisakim2017]

Hello, I was wondering if anyone could help me figure out how to map inverted regions. I have made my assembly of contigs, and have determined the genetic content of almost the entirety of the chloroplast genome except for one inverted repeat region. Other than going into the lab, is there any software could help me span the gap, or could you direct me to any journals where I could read up on it? Thank you!

[lisakim2017]

Thanks for responding so quickly!

What i meant by spanning was, is there anything that would help me build or piece together contigs near the inverted region, then fill in the gap. But I will try what you suggested, thank you!

Answer 1

[SES]

It is very difficult to span the IR regions with de novo assembly because they are large and identical, or nearly so. I have gotten the best results from mapping to a closely related plastid genome to get the gap size/sequence. The good news is that there are many thousands of plastid genomes published and they are highly conserved, so you can likely find a good reference.

I have also heard of people masking one of the IRs and trying to span the gap by assembling only one region, and then scaffolding the contigs together. Though, I haven't done this myself, or seen this method demonstrated.

Answer 2

[Biomonika (Noolean)]

You may map reads back to your assembled contigs and expect doubled coverage for contigs representing collapsed inverted repeats. Could you please be more specific what you mean by spanning?

[lisakim2017]

Yeah I think someone else in my lab was trying the mapping assembly first so I will look toward trying that next, thank you!