Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypothes

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Fabaceae are the third largest angiosperm family,with 765 genera and~19500 species.They are important both economically and ecologically,and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability.However,resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained 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 le-gumes spanning all 6 subfamilies and 333 of 765 genera.The subfamilies are maximally supported as mono-phyletic.The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining le-gumes,and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae.Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary,marked by mass extinction,and subsequent divergence of most tribe-level clades within~15 million years.Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae,including those at the an-cestors of Fabaceae and five of the subfamilies,and further analyses supported the Fabaceae ancestral polyploidy.The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral char-acter reconstruction and phylogenetic analyses of related gene families and the results support the hypoth-eses of one or two switch(es)to rhizobial nodulation followed by multiple losses.Collectively,these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.
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