A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses

Brottier, Laurent; Chaintreuil, Clémence; Simion, Paul; Scornavacca, Céline; Rivallan, Ronan; Mournet, Pierre; Moulin, Lionel; Lewis, Gwilym P.; Fardoux, Joël; Brown, Spencer C.; Gomez-Pacheco, Mario; Bourge, Mickaël; Hervouet, Catherine; Gueye, Mamadou; Duponnois, Robin; Ramanankierana, Heriniaina; Randriambanona, Herizo; Vandrot, Hervé; Zabaleta, María Eléxpuru; Dasgupta, Moumita; D’Hont, Angélique; Giraud, Éric; Arrighi, Jean‐François

doi:10.1186/s12870-018-1567-z

Cited by 17 publications

(19 citation statements)

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“…Groups of orthologous genes for A. evenia , related Aeschynomene spp., and several species belonging to different legume clades were then generated using OrthoFinder (Supplementary Table 18 ). A consensus species tree inferred from single-copy orthogroups perfectly reflected the legume phylogeny and, for the Aeschynomene clade, the previously observed speciation with the early diverging species Aeschynomene filosa , Aeschynomene tambacoundensis , and Aeschynomene deamii , and a large group containing A. evenia 16 , 20 (Fig. 2a ).…”

Section: Resultssupporting

confidence: 63%

“…To the single-molecule real-time (SMRT) sequencing technology from PacBio RSII platform was used to obtain a 78× genome coverage (Supplementary Tables 1 – 4 ). The resulting assembly was 376 Mb, representing 94–100% of the A. evenia genome, considering the estimated size of 400 Mb obtained by flow cytometry 12 , 16 or of 372 Mb derived from k -mer frequencies (Supplementary Fig. 1 ).…”

Section: Resultsmentioning

confidence: 99%

“…The present study also reveals that this symbiotic signaling pathway controls not only root but also stem nodulation in A. evenia . This dual nodulation is present in few half-aquatic legume species 16 , 17 such as Aeschynomene spp. and S. rostrata, but the genetics of stem nodulation has remained unknown so far.…”

Section: Discussionmentioning

confidence: 99%

“…A. evenia is also a valuable legume species because: (i) it uses an alternative infection process mediated by intercellular penetration as is the case in 25% of legume species 14 , 15 ; (ii) it is endowed with stem nodulation, a property shared with very few hydrophytic legume species 16 , 17 ; and (iii) it groups with Arachis spp., including cultivated peanut ( Arachis hypogaea ) in the Dalbergioid clade, which is distantly related to L. japonicus and M. truncatula 11 . Previous transcriptomic analysis from root and nodule tissues did not detect expression of several known genes involved in bacterial recognition (e.g., LYK3 and EPR3 ), infection (e.g., RPG and FLOT ), and nodule functioning (e.g., SUNERGOS1 and VAG1) 12 , 18 .…”

Section: Introductionmentioning

confidence: 99%

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Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis

et al. 2021

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Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding remains limited. To overcome such limitations, we conduct genetic studies of nodulation in Aeschynomene evenia, supported by the development of a genome sequence for A. evenia and transcriptomic resources for 10 additional Aeschynomene spp. Comparative analysis of symbiotic genes substantiates singular mechanisms in the early and late nodulation steps. A forward genetic screen also shows that AeCRK, coding a receptor-like kinase, and the symbiotic signaling genes AePOLLUX, AeCCamK, AeCYCLOPS, AeNSP2, and AeNIN are required to trigger both root and stem nodulation. This work demonstrates the utility of the A. evenia model and provides a cornerstone to unravel mechanisms underlying the rhizobium–legume symbiosis.

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Section: Resultssupporting

confidence: 63%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis

et al. 2021

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“…A Cercis genome size of 367 Mbp is tied for smallest in the legume family, and is less than a third the median reported genome size of 1,157 Mbp, across 84 legume genera. We note this result with a caveat, however, that genome sizes can be highly variable, even within a single genus – affected by mechanisms such as bursts of transposon expansions – e.g., variations in Nicotiana (Leitch et al, 2008) or in Aeschynomene (Brottier et al, 2018).…”

Section: Discussionmentioning

confidence: 86%

Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family

et al. 2019

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Based on evolutionary, phylogenomic, and synteny analyses of genome sequences for more than a dozen diverse legume species as well as analysis of chromosome counts across the legume family, we conclude that the genus Cercis provides a plausible model for an early evolutionary form of the legume genome. The small Cercis genus is in the earliest-diverging clade in the earliest-diverging legume subfamily (Cercidoideae). The Cercis genome is physically small, and has accumulated mutations at an unusually slow rate compared to other legumes. Chromosome counts across 477 legume genera, combined with phylogenetic reconstructions and histories of whole-genome duplications, suggest that the legume progenitor had 7 chromosomes – as does Cercis . We propose a model in which a legume progenitor, with 7 chromosomes, diversified into species that would become the Cercidoideae and the remaining legume subfamilies; then speciation in the Cercidoideae gave rise to the progenitor of the Cercis genus. There is evidence for a genome duplication in the remaining Cercidoideae, which is likely due to allotetraploidy involving hybridization between a Cercis progenitor and a second diploid species that existed at the time of the polyploidy event. Outside the Cercidoideae, a set of probably independent whole-genome duplications gave rise to the five other legume subfamilies, at least four of which have predominant counts of 12–14 chromosomes among their early-diverging taxa. An earlier study concluded that independent duplications occurred in the Caesalpinioideae, Detarioideae, and Papilionoideae. We conclude that Cercis may be unique among legumes in lacking evidence of polyploidy, a process that has shaped the genomes of all other legumes thus far investigated.

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An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3

et al. 2022

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N-acetylglucosamine containing compounds acting as pathogenic or symbiotic signals are perceived by plant-specific Lysin Motif Receptor-Like Kinases (LysM-RLKs). The molecular mechanisms of this perception are not fully understood, notably those of lipo-chitooligosaccharides (LCOs) produced during root endosymbioses with nitrogen-fixing bacteria or arbuscular mycorrhizal fungi. In Medicago truncatula, we previously identified the LysM-RLK LYR3 (MtLYR3) as a specific LCO-binding protein. We also showed that the absence of LCO binding to LYR3 of the non-mycorrhizal Lupinus angustifolius, (LanLYR3), was related to LysM3, which differs from that of MtLYR3 by several amino acids and, particularly, by a critical tyrosine residue absent in LanLYR3. Here, we aimed to define the LCO binding site of MtLYR3 by using molecular modelling and simulation approaches, combined with site-directed mutagenesis and LCO binding experiments. 3D models of MtLYR3 and LanLYR3 ectodomains were built, and homology modelling and molecular dynamics (MD) simulations were performed. Molecular docking and MD simulation on the LysM3 identified potential key residues for LCO binding. We highlighted by steered MD simulations that in addition to the critical tyrosine, two other residues were important for LCO binding in MtLYR3. Substitution of these residues in LanLYR3-LysM3 by

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A phylogenetic framework of the legume genus Aeschynomene for comparative genetic analysis of the Nod-dependent and Nod-independent symbioses

Cited by 17 publications

References 47 publications

Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis

Genetics of nodulation in Aeschynomene evenia uncovers mechanisms of the rhizobium–legume symbiosis

Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family

An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3

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