Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

Abstract

Unresolved questions about evolution of the large and diverse legume family include the timing of polyploidy (whole-genome duplication; WGDs) relative to the origin of the major lineages within the Fabaceae and to the origin of symbiotic nitrogen fixation. Previous work has established that a WGD affects most lineages in the Papilionoideae and occurred sometime after the divergence of the papilionoid and mimosoid clades, but the exact timing has been unknown. The history of WGD has also not been established for legume lineages outside the Papilionoideae. We investigated the presence and timing of WGDs in the legumes by querying thousands of phylogenetic trees constructed from transcriptome and genome data from 20 diverse legumes and 17 outgroup species. The timing of duplications in the gene trees indicates that the papilionoid WGD occurred in the common ancestor of all papilionoids. The earliest diverging lineages of the Papilionoideae include both nodulating taxa, such as the genistoids (e.g., lupin), dalbergioids (e.g., peanut), phaseoloids (e.g., beans), and galegoids (=Hologalegina, e.g., clovers), and clades with nonnodulating taxa including Xanthocercis and Cladrastis (evaluated in this study). We also found evidence for several independent WGDs near the base of other major legume lineages, including the Mimosoideae-Cassiinae-Caesalpinieae (MCC), Detarieae, and Cercideae clades. Nodulation is found in the MCC and papilionoid clades, both of which experienced ancestral WGDs. However, there are numerous nonnodulating lineages in both clades, making it unclear whether the phylogenetic distribution of nodulation is due to independent gains or a single origin followed by multiple losses.

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

“…As we confirmed the ploidy level of the sequenced individuals to diploid, we assume that the rather high level of putative paralogy observed in this study comes from a high level of repeated sequences in the genome of R. pseudoacacia . This hypothesis is congruent with the ancestral whole genome duplication events which occurred within the Fabaceae (Cannon et al., ; Soltis et al., ). However, it may also be influenced by the fact that we considered all types of paralogous RAD loci, whereas we tested only considered those loci identified by reads 2 snp as true paralogs (“para”).…”

Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism

“…By duplicating genes or whole genomes, redundant copies of key genes regulating the symbiosis can be created (92,93). Because mutations are less likely to disrupt key symbiosis genes, duplication could result in a lower rate of symbiosis loss and higher retention of symbiotic capacity (36,94). The potential link between symbiosis persistence and gene duplication is an interesting research avenue.…”

Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms

“…These results are in accordance with what was already described for these species. Indeed, it was found that soybean contains a very large number of retained genes from this WGD (Cannon et al, 2015). Additionally, recent studies on large gene families in G. raimondii indicate that their copy number is driven either by retention after the last WGD (e.g.…”