Dent D, Cocking E. Establishing symbiotic nitrogen fixation in cereals and other non-legume crops: The Greener Nitrogen Revolution. Agric Food Secur. 2017;6:1–9.

Article  Google Scholar 

Jhu M-Y, Oldroyd GED. Dancing to a different tune, can we switch from chemical to biological nitrogen fixation for sustainable food security? PLoS Biol. 2023;21: e3001982.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Soltis DE, Soltis PS, Morgan DR, Swensen SM, Mullin BC, Dowd JM, Martin PG. Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms. Proc Natl Acad Sci USA. 1995;92:2647–51.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sprent JI, Ardley J, James EK. Biogeography of nodulated legumes and their nitrogen-fixing symbionts. New Phytol. 2017;215:40–56.

Article  CAS  PubMed  Google Scholar 

Libourel C, Keller J, Brichet L, Cazalé A-C, Carrère S, Vernié T, Couzigou J-M, Callot C, Dufau I, Cauet S, et al. Comparative phylotranscriptomics reveals ancestral and derived root nodule symbiosis programmes. Nat Plants. 2023;9:1067–80.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang H, Moore MJ, Soltis PS, Bell CD, Brockington SF, Alexandre R, Davis CC, Latvis M, Manchester SR, Soltis DE. Rosid radiation and the rapid rise of angiosperm-dominated forests. Proc Natl Acad Sci USA. 2009;106:3853–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kates HR, O’Meara BC, LaFrance R, Stull GW, James EK, Liu S-Y, Tian Q, Yi T-S, Conde D, Kirst M, et al. Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants. Nat Commun. 2024;15:4262.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Albalat R, Canestro C. Evolution by gene loss. Nat Rev Genet. 2016;17:379–91.

Article  CAS  PubMed  Google Scholar 

Guijarro-Clarke C, Holland PWH, Paps J. Widespread patterns of gene loss in the evolution of the animal kingdom. Nat Ecol Evol. 2020;4:519–23.

Article  PubMed  Google Scholar 

Merenyi Z, Krizsan K, Sahu N, Liu XB, Balint B, Stajich JE, Spatafora JW, Nagy LG. Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits. Nat Ecol Evol. 2023;7:1221–31.

Article  PubMed  PubMed Central  Google Scholar 

Puttick MN, Morris JL, Williams TA, Cox CJ, Edwards D, Kenrick P, Pressel S, Wellman CH, Schneider H, Pisani D, et al. The interrelationships of land plants and the nature of the ancestral embryophyte. Curr Biol. 2018;28:733–45.

Article  CAS  PubMed  Google Scholar 

Harris BJ, Clark JW, Schrempf D, Szollosi GJ, Donoghue PCJ, Hetherington AM, Williams TA. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat Ecol Evol. 2022;6:1634–43.

Article  PubMed  PubMed Central  Google Scholar 

Ferrandez-Roldan A, Fabrega-Torrus M, Sanchez-Serna G, Duran-Bello E, Joaquin-Lluis M, Bujosa P, Plana-Carmona M, Garcia-Fernandez J, Albalat R, Canestro C. Cardiopharyngeal deconstruction and ancestral tunicate sessility. Nature. 2021;599:431–5.

Article  CAS  PubMed  Google Scholar 

Cai L, Arnold BJ, Xi Z, Khost DE, Patel N, Hartmann CB, Manickam S, Sasirat S, Nikolov LA, Mathews S, et al. Deeply altered genome architecture in the endoparasitic flowering plant Sapria himalayana Griff. (Rafflesiaceae). Curr Biol. 2021;31:1002–11.

Article  CAS  PubMed  Google Scholar 

Timilsena PR, Barrett CF, Pineyro-Nelson A, Wafula EK, Ayyampalayam S, McNeal JR, Yukawa T, Givnish TJ, Graham SW, Pires JC, et al. Phylotranscriptomic analyses of mycoheterotrophic monocots show a continuum of convergent evolutionary changes in expressed nuclear genes from three independent nonphotosynthetic lineages. Genome Biol Evol. 2023;15: evac183.

Article  PubMed  Google Scholar 

Hottes AK, Freddolino PL, Khare A, Donnell ZN, Liu JC, Tavazoie S. Bacterial adaptation through loss of function. PLoS Genet. 2013;9: e1003617.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schopfer CR, Nasrallah ME, Nasrallah JB. The male determinant of self-incompatibility in Brassica. Science. 1999;286:1697–700.

Article  CAS  PubMed  Google Scholar 

Stein JC, Howlett B, Boyes DC, Nasrallah ME, Nasrallah JB. Molecular cloning of a putative receptor protein kinase gene encoded at the self-incompatibility locus of Brassica oleracea. Proc Natl Acad Sci USA. 1991;88:8816–20.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shimizu KK, Shimizu-Inatsugi RIE, Tsuchimatsu T, Purugganan MD. Independent origins of self-compatibility in Arabidopsis thaliana. Mol Ecol. 2007;17:704–14.

Article  PubMed  Google Scholar 

Hoballah ME, Gübitz T, Stuurman J, Broger L, Barone M, Mandel T, Dell’Olivo A, Arnold M, Kuhlemeier C. Single gene-mediated shift in pollinator attraction in Petunia. Plant Cell. 2007;19:779–90.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zufall RA, Rausher MD. Genetic changes associated with floral adaptation restrict future evolutionary potential. Nature. 2004;428:847–50.

Article  CAS  PubMed  Google Scholar 

Griesmann M, Chang Y, Liu X, Song Y, Haberer G, Crook MB, Billault-Penneteau B, Lauressergues D, Keller J, Imanishi L, et al. Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science. 2018; 361:eaat1743.

Article  PubMed  Google Scholar 

van Velzen R, Holmer R, Bu F, Rutten L, van Zeijl A, Liu W, Santuari L, Cao Q, Sharma T, Shen D, et al. Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen-fixing rhizobium symbioses. Proc Natl Acad Sci USA. 2018;115:E4700–9.

PubMed  PubMed Central  Google Scholar 

Cathebras C, Gong X, Andrade RE, Vondenhoff K, Hayashi M, Keller J, Delaux PM, Griesmann M, Parniske M. A novel cis-element enabled bacterial uptake by plant cells. bioRxiv. 2022. https://doi.org/10.1101/2022.03.28.486070.

Legume Phylogeny Working Group (LPWG). A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny. Taxon. 2017;66:44–77.

Article  Google Scholar 

Aarabi F, Kusajima M, Tohge T, Konishi T, Gigolashvili T, Takamune M, Sasazaki Y, Watanabe M, Nakashita H, Fernie AR, et al. Sulfur deficiency–induced repressor proteins optimize glucosinolate biosynthesis in plants. Sci Adv. 2016;2: e1601087.

Article  PubMed  PubMed Central  Google Scholar 

Schumacher K, Schmitt T, Rossberg M, Schmitz G, Theres K. The Lateral suppressor (Ls) gene of tomato encodes a new member of the VHIID protein family. Proc Natl Acad Sci USA. 1999;96:290–5.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Greb T, Clarenz O, Schafer E, Muller D, Herrero R, Schmitz G, Theres K. Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation. Genes Dev. 2003;17:1175–87.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li X, Qian Q, Fu Z, Wang Y, Xiong G, Zeng D, Wang X, Liu X, Teng S, Hiroshi F, et al. Control of tillering in rice. Nature. 2003;422:618–21.

Article  CAS  PubMed  Google Scholar 

Cenci A, Rouard M. Evolutionary analyses of GRAS transcription factors in angiosperms. Front Plant Sci. 2017;8:273.

Article  PubMed  PubMed Central  Google Scholar 

Mizzotti C, Galliani BM, Dreni L, Sommer H, Bombarely A, Masiero S. ERAMOSA controls lateral branching in snapdragon. Sci Rep. 2017;7: 41319.

Article