Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species

Premise – Orthology inference is crucial for comparative genomics, and multiple algorithms have been developed to identify putative orthologs for downstream analyses. Despite the abundance of proposed solutions, including publicly available benchmarks, it is difficult to assess which tool to best use for plant species, which commonly have complex genomic histories.
Methods – We explored the performance of four orthology inference algorithms – OrthoFinder, SonicParanoid, Broccoli, and OrthNet – on eight Brassicaceae genomes in two groups: one group comprising only diploids and another set comprising the diploids, two mesopolyploids, and one recent hexaploid genome.
Results – Orthogroup compositions reflect the species’ ploidy and genomic histories. Additionally, the diploid set had a higher proportion of identical orthogroups. While the diploid+higher ploidy set had a lower proportion of orthogroups with identical compositions, the average degree of similarity between the orthogroups was..., We tested seven variations of four orthology inference algorithms - OrthoFinder, SonicParanoid, Broccoli, and OrthNet. We used publicly available genomes and associated protein files from eight Brassicaceae species and compared the results from these algorithms on two sets of species: one consisting of five diploid species and one consisting of eight species - five of the diploids, two mesopolyploids, and one hexaploid. We examined the similarities and differences in the results to understand the performance of these algorithms in inferring orthologs and orthogroups with and without genomically complex species., , # **Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species**

[https://doi.org/10.5061/dryad.8sf7m0cw8](https://doi.org/10.5061/dryad.8sf7m0cw8)

# Description of the data and file structure

Primary data, scripts, and outputs are found on GitHub: [https://github.com/itliao/OrthologyComparison](https://github.com/itliao/OrthologyComparison)

The first page outlines the types of files in each of the directories, and each directory has a separate README that walks through the steps of the analyses, important scripts, inputs for the scripts, and outputs generated from the scripts.

Some of the input/output files are too large to host on GitHub, and thus are found in this repository:

## Gene\_Composition\_Comparison\_Orthogroups - OUTPUTS

The following files are outputs from making comparisons between the orthogroup gene compositions from two different orthology inference algorithms. The \"diploid set\" refers to orthogroup inferences made...