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Here, we used the legume phenylalanine ammonia-lyase (PAL) gene family as a model and integrated pan-genomic, phylogenetic, molecular evolutionary, duplication-mode, and transcriptomic analyses, while developing GFtool for gene family identification. Across 45 genomes, we identified 302 PAL genes and classified them into five Groups. Groups 1\u20133 represented ancient lineages shared with outgroups, whereas Groups 4 and 5 were legume-specific. Molecular-clock analyses placed the divergence of Group 2 near the Paleocene-Eocene transition, while Groups 4 and 5 diversified from the middle Eocene to the early Oligocene. WGD\/segmental duplication broadly contributed to PAL copy-number expansion, whereas tandem duplication was enriched in Group 5 of Papilionoideae. Group 2 genes showed drought-induced expression, whereas Group 5 genes were associated with early root nodule development. GFtool provides a scalable framework for gene-family studies.<\/jats:p>","DOI":"10.1021\/acs.jafc.6c04229","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T20:17:23Z","timestamp":1788207443000},"page":"27997-28013","source":"Crossref","is-referenced-by-count":0,"title":["Evolution and Expression\nDivergence of Legume\n                    <i>PAL<\/i>\n                    Genes Suggest Associations\nwith Drought Response and\nRoot Nodule Development"],"prefix":"10.1021","volume":"74","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1656-2871","authenticated-orcid":true,"given":"Jianwei","family":"Qi","sequence":"first","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongzhong","family":"Luo","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Songsong","family":"Lu","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haixia","family":"Huang","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Luo","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaotong","family":"Zhou","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liya","family":"Zhang","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengli","family":"Lei","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xia","family":"Wang","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiaqi","family":"Zhai","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhenjia","family":"Lu","sequence":"additional","affiliation":[{"name":"Forest College of Gansu Agricultural University , , ,","place":["Lanzhou, Gansu, China, 730070"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"key":"2026090917073932000_cit1","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1093\/mp\/ssp106","article-title":"Phenylpropanoid\nBiosynthesis","volume":"3","author":"Vogt","year":"2010","journal-title":"Mol. 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