ANI for inter-species analysis and genome tree phylogeny

Question

[blur]

Hi,

I have calculated Average Nucleotide Identity (ANI) for several isolates. All isolates are members of the same species (ANI > 99)

Isolates vary between 99.89 - 99.98

The thing is - the core genome phylogenetic tree is not exactly like the ANI numbers - If I have two isolates that are closest on the tree but have only 99.89 ANI versus a pair that appear more distant on the tree but have 99.97 identity - what does it mean for my tree?

I have been reading a lot about ANI, but most papers focus on the inter-species results not on how to interpert inter-species (inside the species) differences.

Can someone elucidate this point for me - or refer me to a good paper I can read?

Thanks

[5heikki]

Genome A:

AAGGCCTTT

Genome B:

AAGGCCTTA

Genome C:

AAGGCCT

How do you calculate ANI? Does the Genome A - Genome C pair in this example have a higher ANI than Genome A - Genome B? We don't know how your data is. Are you working with closed assemblies? Are you working with organisms that have plasmids? How are you defining your core genome? Etc.

[blur]

I used OrthoANIu algorithm. These are draft genomes that have plasmids. All the isolates are classified into the same species and type and are very close phylogenetically based on every typing methods used (phylogenetic trees, FTIR, MLST etc)

[5heikki]

OrthoANIu doesn't mean anything to me. It's up to you to find out what it does exactly..

[blur]

I know how the OrthoANIu algorithm works I read the paper

[5heikki]

I don't have access to that paper but assuming it works more or less like the original OrthnoAni then it's pretty clear that full genomes are not compared for the final ANI estimate. So whether your ANI result is 99.89% or 99.98% is pretty much up to random chance..

[andres.firrincieli]

Generally speaking, phylogenetic relationship between members of the same species are computed by using MLST of concatenated phylogenetic markers (core genome MLST) or SNP-based phylogeny. ANI does not provide enough power to differentiate between strains of the same species