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Transcriptome analysis revealed that genes oppositely regulated in <jats:italic>WT\u2010GmBIR1<\/jats:italic> and <jats:italic>KD\u2010GmBIR1<\/jats:italic> upon SCN infection were enriched primarily in defense and immunity\u2010related functions. Quantitative phosphoproteomic analysis identified 208 proteins as putative substrates of the GmBIR1 signaling pathway, 114 of which were differentially phosphorylated upon SCN infection. In addition, the phosphoproteomic data pointed to a role of the GmBIR1 signaling pathway in regulating alternative pre\u2010mRNA splicing. Genome\u2010wide analysis of splicing events provided compelling evidence supporting a role of the GmBIR1 signaling pathway in establishing alternative splicing during SCN infection.<\/jats:p><\/jats:list-item>\n<jats:list-item><jats:p>Our results provide novel mechanistic insights into the function of the GmBIR1 signaling pathway in regulating soybean transcriptome and spliceome via differential phosphorylation of splicing factors and regulation of splicing events of pre\u2010mRNA decay\u2010 and spliceosome\u2010related genes.<\/jats:p><\/jats:list-item>\n<\/jats:list><\/jats:p>","DOI":"10.1111\/nph.19087","type":"journal-article","created":{"date-parts":[[2023,6,20]],"date-time":"2023-06-20T08:19:50Z","timestamp":1687249190000},"page":"2335-2352","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["The soybean immune receptor <scp>GmBIR1<\/scp> regulates host transcriptome, spliceome, and immunity during cyst nematode infection"],"prefix":"10.1111","volume":"239","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6669-9430","authenticated-orcid":false,"given":"Tracy E.","family":"Hawk","sequence":"first","affiliation":[{"name":"Department of Plant Sciences University of Tennessee  Knoxville TN 37996 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarbottam","family":"Piya","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences University of Tennessee  Knoxville TN 37996 USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sobhan Bahrami","family":"Zadegan","sequence":"additional","affiliation":[{"name":"Department of Plant Sciences University of Tennessee  Knoxville TN 37996 USA"},{"name":"UT\u2010ORNL Graduate School of Genome Science and Technology University of Tennessee  Knoxville TN 37996 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