Orthogroup functional annotations and effector candidates

Functional annotations of all predicted proteins in a <i>Parastagonospora nodorum</i> pangenome.<br>Orthogroups were predicted using OrthoFinder, each gene is annotated with the P. nodorum isolate that it is predicted in and the orthogroup that it belongs to.<br>Predicted whole protein functions were found by searching the Swiss-Prot database version 2020_02 (Bairoch &amp; Apweiler, 2000) using MMSeqs2 version 11-e1a1c (--start-sens 3 -s 7.5 --sens-steps 3 -a) (Steinegger &amp; Söding, 2017). Matches were considered reliable for functional annotation if they covered &gt;= 70% of both sequences, with &gt;=60% sequence identity, and an e-value &lt; 1e-10. Functional domains were predicted using InterProScan (P. Jones et al., 2014; Mitchell et al., 2019). Additionally, GO-terms and predicted product names were predicted using the web-servers of PANNZER (Koskinen et al., 2015) and eggNOG-Mapper (Huerta-Cepas et al., 2017). GO-term predictions from InterProScan, PANNZER, and eggNOG-Mapper were combined and filtered to exclude terms in the GO do_not_annotate “anti-slim” set (available at: http://geneontology.org/docs/download-ontology, downloaded: 2020-05-15) to remove uninformative terms, forming the final GO-term set for the predicted proteomes.<br>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 &amp; Söding, 2017).Information from Predector, InterProScan, Pannzer, eggNOG-mapper, positive selection and orthogroup analyses were combined into a single table.