Scaffolding a highly repetitive genome

[aharkess]

Hi all,

I'm working through a difficult region in a highly repetitive plant genome. I've got 30 BACs sequenced and assembled into contigs for this region, but the physical map is still incomplete. Using whole genome paired end and mate pair Illumina libraries from 130nt up to 40kb inserts, I'm trying to scaffold these BACs together, but the high transposon content is causing me to have trust issues.

I've used SSPACE to scaffold these before, but when nearly 80% of some BACs is repetitive, I don't trust it. I'm going to use SSPACE again on a repeatmasked version of the BACs, but aside from that, does anyone have suggestions on scaffolding highly repetitive BACs?

Thanks!
Alex

[jimmybee]

What TEs make up the repetitive elements? If you have a library of well-annotated LTRs or some DNA transposons you could use the TSD + terminal sequences to scaffold contigs together. Its painstaking work, but its been shown to work in a few complex genomes like barley and wheat