Functional annotation of the 42,980 protein-coding gene models of Cupressus sempervirens

To evaluate the accuracy of the 42,980 protein-coding sequences, we assigned a score between 0 and 1 to each protein using Psauron V1.0.4 (Sommer et al. 2024). Next, functional annotation was performed on the 42,980 predicted proteins using InterProScan v.5.64-96.0 (Quevillon et al. 2005) for domain and motif searches. We also used the BLASTKoala webservice (http://www.kegg.jp/blastkoala/, September 2024) (Kanehisa et al. 2016) to assign KEGG orthology based on KEGG pathways. The eggNOG-mapper V2.1.12 (Cantalapiedra et al. 2021) was used together with the eggNOG v5 genomes and functional databases of orthologs groups (OGs) (Huerta-Cepas et al., 2019). Finally, the Ensembl Enzyme Prediction Pipeline (E2P2) V.00de829 identified the enzyme codes associated with the 42,980 proteins (https://github.com/carnegie/E2P2) (Chae et al. 2014).