gene synteny analysis without chromosome information

Question

[402374688]

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?

Thank you!

Answer 1

[Jean-Karim Heriche]

Syntenic regions are chromosomal regions derived from a common ancestral region. This usually results in regions in which gene order is conserved. So to determine synteny, one usually looks at gene order after doing multiple sequence alignment of genomic regions. For visualization purposes, it seems that you could show the aligned genomes as lines and genes as blocks as in the figure on this page or figure 5 of this paper or maybe by chromosome like in Ensembl.

[402374688]

Since these three insects don't have chromsome information, can I directly align the assembled scaffolds to obtain synteny blocks?

[Jean-Karim Heriche]

Yes. You may also find this post helpful.

[402374688]

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?

[Jean-Karim Heriche]

You can have a look in EnsEMBL metazoa or in InsectBase if you're species are there.

[402374688]

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.