Nuclear Phylotranscriptomics/Phylogenomics Support Numerous Polyploidization Events and Hypotheses for the Evolution of Rhizobial Nitrogen-Fixing Symbiosis in Fabaceae

Fabaceae, with 765 genera and ∼19,500 species, are the third-largest angiosperm family and important both economically and ecologically, with global crops intensively studied in part for their nitrogen-fixing ability. However, resolution of Fabaceae phylogeny and divergence times at intrasubfamilial levels have been elusive, precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae. Here, we report a highly resolved phylogeny using >1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species along with other datasets for a total of 463 legumes spanning all six subfamilies and 333 of 765 genera. The subfamilies are maximally supported as monophyletic, with the clade comprising subfamilies Cercidoideae and Detarioideae being the sister of remaining legumes, and Duparquetioideae and Dialioideae being successive sisters to the clade of Papilionoideae and Caesalpinioideae. Molecular clock estimation revealed early radiation of subfamilies near the K/Pg boundary marked by mass extinction and subsequent divergences of most tribe-level clades within ∼15 million years. Phylogenomic analyses of thousands of gene families support 28 proposed WGD/WGT events across Fabaceae, including those at the ancestors of Fabaceae and five of the subfamilies, with support from further analyses for the Fabaceae ancestral polyploidy. The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was examined through ancestral character reconstruction and phylogenetic analyses of related gene families, providing support for hypotheses of one or two switch(es) to rhizobial nodulation followed by multiple losses. These results form a foundation for further morphological and functional evolutionary analyses across Fabaceae.