OrthoANI: An improved algorithm and software for calculating average nucleotide identity

TLDR

Species demarcation in Bacteria and Archaea relies on genome relatedness, and average nucleotide identity (ANI) has replaced DNA‑DNA hybridization but suffers from asymmetry between reciprocal calculations. The study introduces OrthoANI, an algorithm that fragments genomes, identifies orthologous fragment pairs, and computes symmetric ANI values. OrthoANI is implemented as freely available standalone software that performs these calculations efficiently. Across 63,690 genome pairs, reciprocal ANI differences exceeded 1 %, while OrthoANI values were ~0.1 % higher than ANI, correlating strongly and providing a more robust, faster means for taxonomic purposes.

Abstract

Species demarcation in Bacteria and Archaea is mainly based on overall genome relatedness, which serves a framework for modern microbiology. Current practice for obtaining these measures between two strains is shifting from experimentally determined similarity obtained by DNA-DNA hybridization (DDH) to genome-sequence-based similarity. Average nucleotide identity (ANI) is a simple algorithm that mimics DDH. Like DDH, ANI values between two genome sequences may be different from each other when reciprocal calculations are compared. We compared 63 690 pairs of genome sequences and found that the differences in reciprocal ANI values are significantly high, exceeding 1 % in some cases. To resolve this problem of not being symmetrical, a new algorithm, named OrthoANI, was developed to accommodate the concept of orthology for which both genome sequences were fragmented and only orthologous fragment pairs taken into consideration for calculating nucleotide identities. OrthoANI is highly correlated with ANI (using BLASTn) and the former showed approximately 0.1 % higher values than the latter. In conclusion, OrthoANI provides a more robust and faster means of calculating average nucleotide identity for taxonomic purposes. The standalone software tools are freely available at http://www.ezbiocloud.net/sw/oat.