Evolution and Expression Divergence of Legume PAL Genes Suggest Associations with Drought Response and Root Nodule Development.

Jianwei Qi; Yongzhong Luo; Songsong Lu; Haixia Huang; Xin Luo; Xiaotong Zhou; Liya Zhang; Shengli Lei; Xia Wang; Jiaqi Zhai; Zhenjia Lu

doi:10.1021/acs.jafc.6c04229

PubMed · 42715939

Evolution and Expression Divergence of Legume PAL Genes Suggest Associations with Drought Response and Root Nodule Development.

Jianwei Qi·Yongzhong Luo·Songsong Lu·Haixia Huang·Xin Luo·Xiaotong Zhou·Liya Zhang·Shengli Lei·Xia Wang·Jiaqi Zhai·Zhenjia Lu

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Abstract

Comparative genomic analyses provide insight into the mechanisms underlying gene-family evolution and crop adaptation. 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 1-3 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.

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Fabaceae Plant Proteins Phenylalanine Ammonia-Lyase Droughts Phylogeny Evolution, Molecular Gene Expression Regulation, Plant Root Nodules, Plant Functional differentiation Gene family identification Nodule development Phenylalanine ammonia-lyase Journal Article

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Jianwei Qi, Yongzhong Luo, Songsong Lu, Haixia Huang, Xin Luo, Xiaotong Zhou, Liya Zhang, Shengli Lei, Xia Wang, Jiaqi Zhai, Zhenjia Lu. 2026-09-09. Evolution and Expression Divergence of Legume PAL Genes Suggest Associations with Drought Response and Root Nodule Development.. https://doi.org/10.1021/acs.jafc.6c04229

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