Guru Yes please include, in fact they may be all that is needed? They represent the assembled contigs and scaffolds that were linked to the genetic map and this represent the chromosomes... I believe that they contain most of the contigs and scaffolds so there is redundancy. there is one Tc0 that represents the unassembled contigs and scaffolds left over after assembling the 10 pseudochromosomes that represent each of the 10 cacao chromosomes. Yopu could see how this is on the gbrowse at the below website. Regards Mark On Jan 26, 2012, at 10:39 AM, Guru Ananda wrote:

Dear Mark,

Sorry for the delay in response. We're wondering whether or not to include pseudomolecules (along with contigs and scaffolds) as genomic sequence for cacao genome. Can you kindly clarify this?

Thanks, Guru.

On Thu, Oct 27, 2011 at 4:08 PM, Mark Guiltinan <mjg9@psu.edu> wrote: Hello Galaxy,

Would you please perform the following new genome load?

Theobroma cacao

All the necessary resource files can be found and downloaded at:

http://cocoagendb.cirad.fr/gbrowse/download.html

Thank you

Mark Guiltinan

Mark Guiltinan Professor of Plant Molecular Biology Penn State University Department of Horticulture 422 Life Sciences Building University Park, PA 16802-5807 Phone 814 863-7957 mjg9@psu.edu Web Site: http://guiltinanlab.cas.psu.edu

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