Recently we sequenced a genome of an insect. To examine the quality og the genome with related species, we aim to compare synteny relationship among them. I have obtained single copy orthologs that are present in all three insects. I want to know how to show this relationship, some kinds of circular visualization or some other figures? To make it clear, what I have is three insect genoms, single copy genes present in three species (including their position and correspondence). How can I present the synteny relationship among them?
Since these three insects don't have chromsome information, can I directly align the assembled scaffolds to obtain synteny blocks?
Yes. You may also find this post helpful.
Thank you. It's really helpful. In addition, I wanna know since I've got certain gene locations present in all three species, is there some tools that can directly show the relationship of these genes in three insects?
You can have a look in EnsEMBL metazoa or in InsectBase if you're species are there.
Unfortunatly no. All my three insects are recently sequenced. I just want to find if there is some synteny regions with scaffold information or rearrangement to genes I mentioned above.