The way to find shared or unique contents (CDS etc.) between two bacterial genome

Question

[junseob.kim.83]

Hello there,

I got two bacterial strains that are the same specie but showed different phenotypes. I sequenced it by Nanopore and iseq and got the complete circular genome by hybrid assembly. Then, I annotated them by RAST server and got the gb file.

The question is I want to compare these two bacterial genomes to find the reason that they show different phenotypes in the genetic level.

How can I find the shared or unique genes between two complete bacterial genomes?

Is there any recommended tools for doing this?

Thanks,

Jun

Answer 1

[Mensur Dlakic]

You are most likely looking for tools that will perform a pangenome analysis. Starting with a large set of species, they find a core genome they all share, and delineate accessory genes they do not share. In such cases core genome is usually smaller than the accessory set, which won't necessarily be the case here because you have only two genomes that are presumably very similar. Take a pick from several choices below, and there are probably others that would do just as well.

https://academic.oup.com/bioinformatics/article/31/22/3691/240757

https://www.frontiersin.org/articles/10.3389/fmicb.2018.01910/full

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4337-7