The evolutionary dynamics of ancient and recent polyploidy in the African semiaquatic species of the legume genus Aeschynomene

Abstract

SummaryThe legume genus Aeschynomene is notable in the ability of certain semiaquatic species to develop nitrogen-fixing stem nodules. These species are distributed in two clades. In the first clade, all the species are characterized by the use of a unique Nod-independent symbiotic process. In the second clade, the species use a Nod-dependent symbiotic process and some of them display a profuse stem nodulation as exemplified in the African Aeschynomene afraspera.To facilitate the molecular analysis of the symbiotic characteristics of such legumes, we took an integrated molecular and cytogenetic approach to track occurrences of polyploidy events and to analyze their impact on the evolution of the African species of Aeschynomene.Our results revealed two rounds of polyploidy: a paleopolyploid event predating the African group and two neopolyploid speciations, along with significant chromosomal variations. Hence, we found that A. afraspera (8x) has inherited the contrasted genomic properties and the stem-nodulation habit of its parental lineages (4x).This study reveals a comprehensive picture of African Aeschynomene diversification. It notably evidences a history that is distinct from the diploid Nod-independent clade, providing clues for the identification of the specific determinants of the Nod-dependent and Nodindependent symbiotic processes, and for comparative analysis of stem nodulation.

The role of rhizobial (NifV) and plant (FEN1) homocitrate synthases in Aeschynomene/photosynthetic Bradyrhizobium symbiosis

“…By PCR, cloning, sequencing and transriptomic data analysis (see material and method section SI) using this A. evenia (CIAT22838) FEN1 sequence as basis, we obtained four different sequences of putative FEN1 genes for A. afraspera and one sequence for another A. evenia line, PI 225551. This difference in the number of FEN1 homologs between these two species is not surprising considering that A. evenia is diploid whereas A. afraspera is octoploid 16 . Phylogenetic analysis showed that all the gene products clustered in a clade containing L. japonicus FEN1 (Fig.…”

“…Using the obtained sequences a phylogenetic analysis was performed as described in 16 and data are presented as rooted trees using the Cucumis IPMS as outgroup. GenBank/EMBL and Gene_ID numbers for sequences obtained and used for phylogenetic analysis can be found in Table S4 of the Supplementary information section.…”

Legumes versus rhizobia: a model for ongoing conflict in symbiosis

“…For instance, some legumes have evolved the capacity to form nodules on stem tissues, in some cases with rhizobia that do not even secrete the canonical NFs (e.g. Aeschynomene; Chaintreuil et al, 2016). Variation in the legume-rhizobia interaction reflects divergent biogeographic histories (Sprent et al, 2017), independent origins of nodulation within legumes (Werner et al, 2014), and the evolution of novel plant mechanisms to better control symbionts .…”

Pure polyploidy: Closing the gaps in autopolyploid research

“…Autopolyploidy has also been inferred through coalescent modeling in Capsella bursa‐pastoris (St. Onge et al, ) and through phylogenetic analysis of orthologous transcripts in the conifer Sequoia sempervirens (Scott et al, ). Unfortunately, extensive genomic rearrangements after WGD, as well as more recent WGDs, can obscure the nature of an ancient WGD to a point where multiple lines of evidence either cannot resolve an auto‐ or allopolyploid origin or produce conflicting results (e.g., Chaintreuil et al, ).…”