Syntenic relationships between fragmented genomes

Question

[jomaco]

Hi,

Is it possible to get and idea of the syntenic relationship between fragmented genomes (or between a fragmented genome and one which has been arranged into linkage groups)?

Many genome papers seem to have a figure such as this (fig. 3A): http://www.nature.com/ncomms/2013/131018/ncomms3640/fig_tab/ncomms3640_F3.html

However, our assembly has hundreds of thousands of contigs.

We wish to compare it with species such as tomato and kiwi, however presumably a diagram like this would get rather messy - as a result my question is whether it would be seen as valid to use only the largest contigs in our assembly for this analysis, to see if synteny is preserved in those larger sequences? (Or should I really be looking into a different approach towards comparing the similarity of the genomes, and stave off syteny analysis until we have a less fragmented assembly?)

Thanks

[brentp]

what analysis do you want to do? what do you want to learn from it? If it's only for visualization then, yes, using large contigs makes sense.

For other things, e.g. finding older duplications, you may want to use as many contigs as possible.