DOI: 10.5061/dryad.8sf7m0cw8
title: Different orthology inference algorithms generate similar predicted orthogroups among Brassicaceae species

description: 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
 not different from the diploid set. Discussion – Three algorithms –
 OrthoFinder, SonicParanoid, and Broccoli – are helpful for initial
 orthology predictions. Results from OrthNet were generally an outlier but
 could provide detailed information about gene colinearity. With our
 Brassicaceae dataset, slight discrepancies were found across the orthology
 inference algorithms, necessitating additional analyses, such as tree
 inference to fine-tune results.
description: 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.
description: # **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 with only the diploid species, and the "diploid+higher ploidy set" refers to orthogroup inferences made with all eight species comprising diploid and polyploid species. ### diploid set * diploid_pairwiseMetrics_240212.csv * initial output of the pairwise metrics (RS, ARS, Jaccard) from the script when comparing orthogroup gene compositions. However, there are duplicate orthogroup comparisons that need to be removed and/or combined * diploid_newMetrics_noDup_240221.csv * output after correcting for the duplicate pairwise metrics (RS, ARS, Jaccard) in orthogroup comparisons. Used for generating summary heatmap figures * geneOutput_230929.zip - 26499 separate files * zipped folder that includes the table summary of the gene composition of the orthogroups based on the *Arabidopsis* gene. For instance, to generate and compare the orthogroup compositions anchored by gene AT1G01010, we found the orthogroup that included AT1G01010 from each orthology inference algorithm. We created a table merged the information from all the orthology inference programs (except OrthNet) together, where all the genes found in the corresponding orthogroups that included AT1G01010 were included. Empty cells indicate that the gene was missing or not included in any orthogroup/cluster in that specific orthology inference algorithm. * table columns include: * gene copy found in the orthogroup * each orthology inference algorithm: BR (Broccoli), OFb (OrthoFinder-BLAST), OFd (OrthoFinder-DIAMOND), OFm (OrthoFinder-MMseqs), SPd (SonicParanoid-DIAMOND), SPm (SonicParanoid-MMseqs). OrthNet was not included. * each cell indicates the particular orthogroup/cluster that the gene (row name) was found. Empty cells indicate that the gene was missing or not included in any orthogroup/cluster in that specific orthology inference algorithm. ### diploid+higher ploidy set * full_pairwiseMetrics_240209.csv * initial output of the pairwise metrics (RS, ARS, Jaccard) from the script when comparing orthogroup gene compositions. However, there are duplicate orthogroup comparisons that need to be removed and/or combined * full_newMetrics_noDup_240221.csv * output after correcting for the duplicate pairwise metrics (RS, ARS, Jaccard) in orthogroup comparisons. Used for generating summary heatmap figures * geneOutput_230928.zip - 26602 separate files * zipped folder that includes the table summary of the gene composition of the orthogroups based on the *Arabidopsis* gene. For instance, to generate and compare the orthogroup compositions anchored by gene AT1G01010, we found the orthogroup that included AT1G01010 from each orthology inference algorithm. We created a table merged the information from all the orthology inference programs (except OrthNet) together, where all the genes found in the corresponding orthogroups that included AT1G01010 were included. Empty cells indicate that the gene was missing or not included in any orthogroup/cluster in that specific orthology inference algorithm. * table columns include: * gene copy found in the orthogroup * each orthology inference algorithm: BR (Broccoli), OFb (OrthoFinder-BLAST), OFd (OrthoFinder-DIAMOND), OFm (OrthoFinder-MMseqs), SPd (SonicParanoid-DIAMOND), SPm (SonicParanoid-MMseqs). OrthNet was not included. * each cell indicates the particular orthogroup/cluster that the gene (row name) was found. Empty cells indicate that the gene was missing or not included in any orthogroup/cluster in that specific orthology inference algorithm. ## Gene\_Composition\_Comparison\_Species\_Pairs - OUTPUTS The following files are outputs from making comparisons between the orthogroup gene compositions from the BASELINE comparison (OrthoFinder-BLAST-MCL) and one of the orthology inference algorithms for each pair of species. The "diploid set" refers to orthogroup inferences made with only the diploid species, and the "diploid+higher ploidy set" refers to orthogroup inferences made with all eight species comprising diploid and polyploid species. ### diploid set * diploid_speciesPairsJIvalues_toCorrect_240222.csv * initial output from script when comparing SPECIES PAIRS orthogroup gene compositions. However, there are duplicate comparisons that need to be removed and/or combined. The metric calculated was the Jaccard Index (or JI). * spPairs_diploid_newMetrics_noDup_240223.csv * after correcting for the duplicate orthogroup comparisons. Used for generating summary heatmap figures. ### diploid+higher ploidy set * mixed_speciesPairsJIvalues_toCorrect_240226.csv * initial output from script when comparing SPECIES PAIRS orthogroup gene compositions. However, there are duplicate comparisons that need to be removed and/or combined. The metric calculated was the Jaccard Index (or JI). * spPairs_mixed_newMetrics_noDup_240227.csv * after correcting for the duplicate orthogroup comparisons. Used for generating summary heatmap figures.