nod Genes and Nod signals and the evolution of the rhizobium legume symbiosis.

The establishment of the nitrogen-fixing symbiosis between rhizobia and legumes requires an exchange of signals between the two partners. In response to flavonoids excreted by the host plant, rhizobia synthesize Nod factors (NFs) which elicit, at very low concentrations and in a specific manner, various symbiotic responses on the roots of the legume hosts. NFs from several rhizobial species have been characterized. They all are lipo-chitooligosaccharides, consisting of a backbone of generally four or five glucosamine residues N-acylated at the non-reducing end, and carrying various O-substituents. The N-acyl chain and the other substituents are important determinants of the rhizobial host specificity. A number of nodulation genes which specify the synthesis of NFs have been identified. All rhizobia, in spite of their diversity, possess conserved nodABC genes responsible for the synthesis of the N-acylated oligosaccharide core of NFs, which suggests that these genes are of a monophyletic origin. Other genes, the host specific nod genes, specify the substitutions of NFs. The central role of NFs and nod genes in the Rhizobium-legume symbiosis suggests that these factors could be used as molecular markers to study the evolution of this symbiosis. We have studied a number of NFs which are N-acylated by α,β-unsaturated fatty acids. We found that the ability to synthesize such NFs does not correlate with taxonomic position of the rhizobia. However, all rhizobia that produce NFs such nodulate plants belonging to related tribes of legumes, the Trifolieae, Vicieae, and Galegeae, all of them being members of the so-called galegoid group. This suggests that the ability to recognize the NFs with α,β-unsaturated fatty acids is limited to this group of legumes, and thus might have appeared only once in the course of legume evolution, in the galegoid phylum

Medicago sativa cv. Mercedes genome sequence

Note on the methodology used to obtain the genome sequence of Medicago sativa, and results obtained, as a complementary information to the portal containing the data: https://medicago.toulouse.inra.fr/MsatMercedes-NRGENE-20181029/An alfalfa (or lucerne) genome reference sequence is an essential tool for breeding of this major legume species. A clone of Flemish origin has been sequenced and the genome assembly has been carried out with NRGene protocols. A total of almost 190 000 scaffolds have been generated and this genome assembly reaches 2.6 Gb (80% of the 3.2 Gb expected). Genome annotation has provided 233 049 protein-coding genes and 36 752 non-protein coding genes. A genome portal based on JBrowse has been developed for searching the annotated genome (https://medicago.toulouse.inra.fr/MsatMercedes-NRGENE-20181029/)

Genetic variation in host-specific competitiveness of the symbiont Rhizobium leguminosarum symbiovar viciae

International audienceLegumes of the Fabeae tribe form nitrogen-fixing root nodules resulting from symbiotic interaction with the soil bacteria Rhizobium leguminosarum symbiovar viciae ( Rlv ). These bacteria are all potential symbionts of the Fabeae hosts but display variable partner choice when co-inoculated in mixture. Because partner choice and symbiotic nitrogen fixation mostly behave as genetically independent traits, the efficiency of symbiosis is often suboptimal when Fabeae legumes are exposed to natural Rlv populations present in soil. A core collection of 32 Rlv bacteria was constituted based on the genomic comparison of a collection of 121 genome sequences, representative of known worldwide diversity of Rlv . A variable part of the nodD gene sequence was used as a DNA barcode to discriminate and quantify each of the 32 bacteria in mixture. This core collection was co-inoculated on a panel of nine genetically diverse Pisum sativum , Vicia faba , and Lens culinaris genotypes. We estimated the relative Early Partner Choice (EPC) of the bacteria with the Fabeae hosts by DNA metabarcoding on the nodulated root systems. Comparative genomic analyses within the bacterial core collection identified molecular markers associated with host-dependent symbiotic partner choice. The results revealed emergent properties of rhizobial populations. They pave the way to identify genes related to important symbiotic traits operating at this level

<i>cre1</i> mutants show defects in vascular bundle differentiation.

<p><b>A-B</b>. Transversal sections of 7 day-old roots in the Wild-Type (WT) and in the <i>cre1</i> mutant (<i>cre1-1</i> and <i>cre1-2</i> alleles). Sections (80 μm) were made at a 1 cm distance from the root tip. <b>A</b>, bright field images; <b>B</b>, images obtained under UV excitation, revealing the autofluorescence of xylem poles. Bars = 50 μm. <b>C.</b> Number of xylem poles in the Wild-Type (WT) and in the <i>cre1</i> mutant (<i>cre1-1</i> and <i>cre1-2</i> alleles) quantified based on previous sections. <b>D.</b> Stele/root width ratio in the Wild-Type (WT) and in the <i>cre1</i> mutant (<i>cre1-1</i> and <i>cre1-2</i> alleles) quantified based on previous sections. In C and D, error bars represent standard deviation and a Kruskal-Wallis test was used to assess significant differences (letters, α<0.05; n>6).</p

Heat map of <i>Medicago truncatula</i> cytokinin signaling gene expression in roots exposed to various environmental conditions.

<p>Selected Affymetrix array data corresponding to roots under various abiotic and biotic conditions were retrieved from the <i>M. truncatula</i> Gene Expression Atlas (MtGEA) database: “myc.”, mycorrhized roots [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref070" target="_blank">70</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref071" target="_blank">71</a>]; salt stress, two independent experiments (exp. 1 and exp. 2 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref072" target="_blank">72</a>]); <i>Phymatotrichopsis omnivora</i> and <i>Aphanomyces euteiches</i> pathogens (respectively [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref068" target="_blank">68</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref073" target="_blank">73</a>]). All probes corresponding to cytokinin signaling genes were included in the heat map, which was constructed with logarithmic gene expression ratio between the different conditions and their respective controls, based on Euclidean distance and average clustering probes across the experimental conditions included, using the MeV software. Color scale ranges from eight time fold-repression in green (log2 = −3) to eight time fold-induction in red (log2 = 3). Accession numbers correspond to Affymetrix probes (correspondence with gene ID in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.s005" target="_blank">S2 Table</a>), and multiple probes corresponding to a single gene are indicated by a vertical black bar on the right. Colors indicate cytokinin signaling gene families: in blue, CHKs (CHASE domain containing Histidine Kinases); in green, HPTs (Histidine PhosphoTranfert proteins); in orange, RRBs (Type-B Response Regulators); in violet, RRAs (Type-A Response Regulators). MtCRE1, MtCHK2/HK2, MtCHK3/HK3, MtRR1 to MtRR5 gene names were defined in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref013" target="_blank">13</a>]; MtRR8 in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref046" target="_blank">46</a>]; MtRR11 in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0116819#pone.0116819.ref045" target="_blank">45</a>]. For other IDs, no gene name is available in the literature.</p

RMS2 protein can bind Aux/IAA proteins in the presence of IAA and to ASK1 protein IAA-independently.

<p>The lexA DNA-binding domain (lexA) was fused to RMS2 (WT), rms2-1, rms2-2 AtTIR1, AtAFB5, and the cMyc epitope while the B42 activation domain (AD) was fused to Arabidopsis iaa7m (with degron substitutions), IAA7, IAA3, and ASK1. Three independent transformants containing LexA–RMS2/TIR1/AFB5/Myc and B42–Aux/IAAs/ASK1 were spotted in selective media with and without 50 μM IAA. Blue product released by β-galactosidase reporter activity is a measure of protein-protein interactions.</p

List of primers and their sequences used to sequence the pea RMS2 gene.

<p>List of primers and their sequences used to sequence the pea RMS2 gene.</p