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Old 12-08-2012, 09:53 AM   #1
aharkess
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Location: Georgia

Join Date: Aug 2011
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Default Scaffolding a highly repetitive genome

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
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Alex Harkess
Leebens-Mack Lab
Plant Biology Department
University of Georgia, Athens GA

Last edited by aharkess; 12-08-2012 at 10:01 AM.
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Old 12-08-2012, 05:05 PM   #2
jimmybee
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Default

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
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