2.7. Orthology identification

To identify orthologs between A. majus and L. vulgaris, Orthofinder v.2.2.7 was used with the following species included in the analysis (Emms and Kelly, 2015): L. vulgaris, A. majus, Arabidopsis thaliana, Solanum lycopersicum, S. tuberosum and Erythranthe guttata. The full transcriptome assemblies of L. vulgaris and A. majus were also included in Orthofinder analysis. The annotated protein sequences of the other species were downloaded from publicly available sources: the A. thaliana protein sequences were extracted from (https://ftp.uniprot.org/pub/databases/uniprot/previous_releases/release-2019_04/knowledgebase/uniprot_sprot-only2019_04.tar.gz) using the keyword for species name ARATH, S. lycopersicum (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG3.2_release/ITAG3.2_proteins.fasta), S. tuberosum (ftp://ftp.ensemblgenomes.org/pub/plants/release-44/fasta/solanum_tuberosum/pep/Solanum_tuberosum.SolTub_3.0.pep.all.fa.gz), A. majus (http://bioinfo.sibs.ac.cn/Am/download_data_genome_v2/02.gene_predict/snapdragon_IGDBV1.pros.fasta.gz) and E. guttata (ftp://ftp.ncbi.nih.gov/genomes/Erythranthe_guttata/protein/protein.fa.gz).