Duplication and sub‐functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution

• DOI: 10.1111/jipb.13743
• Publication Date: 2024-08-02T11:31:22Z
• Authors: Tengfei Liu; Haiyue Liu; Wenfei Xian; Zhi Liu; Yaqin Yuan; Jingwei Fan; Shuaiying Xiang; Xia Yang; Yucheng Liu; Shulin Liu; Min Zhang; Yanting Shen; Yuannian Jiao; Shifeng Cheng; Jeff J. Doyle; Fang Xie; Jiayang Li; Zhixi Tian
• Keywords: Flavonoids; 0303 health sciences; Glycine max; Fabaceae; Genes, Plant; Plant Root Nodulation; Evolution, Molecular; 03 medical and health sciences; Gene Expression Regulation, Plant; Gene Duplication; Medicago truncatula; Symbiosis; Root Nodules, Plant; Intramolecular Lyases; Phylogeny; Plant Proteins

ABSTRACTGene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2‐fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae‐gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae‐gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon–intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae‐gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae‐gain genetic innovation and sub‐functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.