Orthogroup functional annotations and effector candidates

Functional annotations of all predicted proteins in a Parastagonospora nodorum pangenome.Orthogroups were predicted using ProteinOrtho, each gene is annotated with the P. nodorum isolate that it is predicted in and the orthogroup that it belongs to.The column "is_representative" indicates whether the protein was selected as the representative member of the orthogroup. This prefers copies in reference isolates, then copies closest to the average sequence length within the orthogroup.Predicted whole protein functions were found by searching the Swiss-Prot database version 2020_02 (Bairoch & Apweiler, 2000) using MMSeqs2 version 11-e1a1c (--start-sens 3 -s 7.5 --sens-steps 3 -a) (Steinegger & Söding, 2017). Matches were considered reliable for functional annotation if they covered >= 70% of both sequences, with >=60% sequence identity, and an e-value Effector-like sequences were predicted using the Predector pipeline (https://github.com/ccdmb/predector, version: 0.1.0-alpha) (Submitted), which incorporates several software analyses including SignalP versions 3.0, 4.1g, 5.0b (José Juan Almagro Armenteros et al., 2019; Dyrløv Bendtsen et al., 2004; Petersen et al., 2011), DeepSig (Savojardo et al., 2018), TargetP version 2.0 (Jose Juan Almagro Armenteros et al., 2019), DeepLoc version 1.0 (Almagro Armenteros et al., 2017), TMHMM version 2.0c (Krogh et al., 2001), Phobius version 1.01 (Käll et al., 2004), EffectorP versions 1 and 2 (Sperschneider et al., 2016; Sperschneider, Dodds, Gardiner, et al., 2018), ApoplastP version 1 (Sperschneider, Dodds, Singh, et al., 2018), LOCALIZER (Sperschneider et al., 2017), homology searches against dbCAN version 8 using HMMER version 3.3 (Mistry et al., 2013), and sequence matches against PHI-base version 4.9 (Urban et al., 2020) using MMSeqs2 version 11.e1a1c (Steinegger & Söding, 2017).Information from Predector, InterProScan, Pannzer, eggNOG-mapper, positive selection and orthogroup analyses were combined into a single table.Raw orthogroup CDS codon alignments, gene trees, and BUSTED results are also included for all non-singleton orthogroups.