The rhizosphere microbiota of the zinc and cadmium hyperaccumulators Arabidopsis halleri and Noccaea caerulescens is highly convergent in Prayon (Belgium)

The Prayon site is known as a zinc-polluted area where two zinc and cadmium hyperaccumulator plant species currently coexist, although Arabidopsis halleri was introduced more recently than Noccaea caerulescens . While soil microorganisms may influence metal uptake, the microbial community present in the rhizosphere of hyperaccumulators remains poorly known. Plants of both species were sampled with their bulk and rhizosphere soil from different plots of the Prayon site. Soil components (ionome, pH, water composition, temperature) were analyzed, as well as shoot ionome and expression levels of metal transporter genes ( HMA3 , HMA4 , ZIP4 / ZNT1 , ZIP6 , MTP1 ). The taxonomic diversity of the microorganisms in soil samples was then determined by 16S rRNA metabarcoding and compared at the Operational Taxonomy Unit (OTU) level and across different taxonomic levels. Our elemental analyses confirmed that the site is still highly contaminated with zinc and cadmium and that both plant species indeed hyperaccumulate these elements in situ . Although the pollution is overall high, it is heterogenous at the site scale and correlates with the expression of some metal transporter genes. Metabarcoding analyses revealed a decreasing gradient of microbial diversity, with more OTUs discovered in the rhizosphere than in the soil bulk, especially at the bottom of the cores. However, the variability gradient increases with the distance from roots. Using an ad hoc pseudo-taxonomy to bypass the biases caused by a high proportion of unclassified and unknown OTUs, we identified Chloroflexi, Armatimonadetes, Pirellulaceae, Gemmatimonadetes and Chitinophagaceae as the drivers of the differences in the gradient along the cores. In contrast, no significant difference was identified between the rhizosphere composition of A. halleri and N. caerulescens . This suggests that, despite their distinct colonization history in Prayon, the two plant species have now recruited highly convergent microbial communities in the rhizosphere

Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes

International audienceBackground: Transposable elements (TEs) are genomic parasites with major impacts on host genome architecture and host adaptation. A proper evaluation of their evolutionary significance has been hampered by the paucity of short scale phylogenetic comparisons between closely related species. Here, we characterized the dynamics of TE accumulation at the micro-evolutionary scale by comparing two closely related plant species, Arabidopsis lyrata and A. halleri. Results: Joint genome annotation in these two outcrossing species confirmed that both contain two distinct populations of TEs with either 'recent' or 'old' insertion histories. Identification of rare segregating insertions suggests that diverse TE families contribute to the ongoing dynamics of TE accumulation in the two species. Orthologous TE fragments (i.e. those that have been maintained in both species), tend to be located closer to genes than those that are retained in one species only. Compared to non-orthologous TE insertions, those that are orthologous tend to produce fewer short interfering RNAs, are less heavily methylated when found within or adjacent to genes and these tend to have lower expression levels. These findings suggest that long-term retention of TE insertions reflects their frequent acquisition of adaptive roles and/or the deleterious effects of removing nearly neutral TE insertions when they are close to genes. Conclusion: Our results indicate a rapid evolutionary dynamics of the TE landscape in these two outcrossing species, with an important input of a diverse set of new insertions with variable propensity to resist deletion

Homology modeling and in vivo functional characterization of the zinc permeation pathway in a heavy metal P-type ATPase

The P1B ATPase Heavy Metal ATPase 4 (HMA4) is responsible for zinc and cadmium translocation from roots to shoots in the plant Arabidopsis thaliana. It couples ATP hydrolysis to cytosolic domain movements enabling metal transport across the membrane. Thanks to high conservation level within the P-type ATPase family, the role of the HMA4 cytoplasmic catalytic domains can be inferred from well characterized pumps. In contrast, the function of its terminal cytosolic extensions as well as the metal permeation mechanism through the membrane remains elusive. Here, homology modeling of the HMA4 transmembrane region was conducted based on the crystal structure of a ZntA bacterial homolog. The analysis highlighted amino acids forming a metal permeation pathway, whose importance was subsequently investigated functionally through mutagenesis and complementation experiments in plants. Although the zinc pathway displayed overall conservation among the two proteins, significant differences were observed, especially in the entrance area with altered electronegativity and the presence of a salt bridge/H-bond network. The analysis also newly identified amino acids whose mutation results in total or partial loss of the protein function. In addition, comparison of zinc and cadmium accumulation in shoots of A. thaliana complemented lines revealed a number of HMA4 mutants exhibiting different abilities in zinc and cadmium translocation. These observations could be instrumental to design low cadmium accumulating crops, hence decreasing human cadmium exposure

Development of a bioinformatic tool for the treatment of WGS data for dermatophytes typing and characterization: Focus on squalene epoxidase mutations and terbinafine resistance.

peer reviewedObjectives: The present work aims to use the Whole Genome Sequencing (WGS) as a tool to characterize dermatophytes strains. Data generated by WGS are analyzed by using a bioinformatic tool called “WGS typer” and several markers are highlighted, such as genes implicated in resistance to antifungals or genes linked with high virulence in dermatophytes. The tool will also permit to analyze dermatophytes following their genetic diversity and provide similarity dendrograms. The present work focus on squalene epoxidase (SQLE) gene characterization among T. rubrum and T. indotineae strains by the WGS typer. Material and methods: 15 strains of T. rubrum (7 resistant to terbinafine and 8 susceptible) and 19 strains of T. indotineae (8 resistant to terbinafine and 11 susceptible) from a multicenter study, previously characterized by Eucast E.Def.11.0 method (Arendrup et al., 2020) were used for SQLE characterization by WGS.WGS has been performed by the GIGA genomics platform using the Illumina technology. The WGS Typer is a commercial bioinformatics tool developed by Hedera-22 (http://www.hedera22.com) and licensed to the Department of Clinical Microbiology of the University of Liège. This tool enables high-throughput typing of pathogen isolates based on raw sequencing data and a collection of relevant markers (single genes, gene variants, gene clusters, MLST). The analysis reports the presence/absence of targeted markers or genotypes from a sequence homology search against the assembled sequencing data according to a set of sequence identity/coverage thresholds. Results: We evaluated the ability of the tool to detect mutations in the SQLE gene that are responsible for terbinafine resistance in dermatophytes. Seven T. rubrum showed a resistant profile to terbinafine (MIC values >0.25µg/µl) with the microdilution method. Among these, four shared the F397L mutation on SQLE, one was wearing L393F mutation while two other shared the L393S mutation. All these mutations were efficiently highlighted by the WGS typer. Among the eight strains presenting a MIC value under 0.25µg/µl, no mutation was found on SQLE gene. Regarding T. indotineae, 8 strains were previously characterized to be resistant to terbinafine with the microdilution method (MIC values >0,25µg/µl). Among them, the WGS typer detected seven strains with the mutation F397L and one strain with the mutation L393F on the SQLE gene. Among the eleven strains presenting a MIC value under 0.25µg/µl by microdilution, no mutation was found on SQLE. The study was completed with genetic similarity comparisons and dendrogram creation. No clear separation into clusters was observed between resistant/susceptible strains neither in the T. rubrum group nor in the T. indotineae group. T. rubrum and T. indotineae species were well separated into two distinct clusters. Conclusion: We present here a valuable and innovative tool for the analysis of dermatophytes. The tool permits to easily and accurately detect mutations on the SQLE gene responsible for terbinafine resistance. A dendrogram of similarity based on WGS data can also be generated

The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

Insights into the Evolution of Multicellularity from the Sea Lettuce Genome

We report here the 98.5 Mbp haploid genome (12,924 protein coding genes) of Ulva mutabilis, a ubiquitous and iconic representative of the Ulvophyceae or green seaweeds. Ulva’s rapid and abundant growth makes it a key contributor to coastal biogeochemical cycles; its role in marine sulfur cycles is particularly important because it produces high levels of dimethylsulfoniopropionate (DMSP), the main precursor of volatile dimethyl sulfide (DMS). Rapid growth makes Ulva attractive biomass feedstock but also increasingly a driver of nuisance “green tides.” Ulvophytes are key to understanding the evolution of multicellularity in the green lineage, and Ulva morphogenesis is dependent on bacterial signals, making it an important species with which to study cross-kingdom communication. Our sequenced genome informs these aspects of ulvophyte cell biology, physiology, and ecology. Gene family expansions associated with multicellularity are distinct from those of freshwater algae. Candidate genes, including some that arose following horizontal gene transfer from chromalveolates, are present for the transport and metabolism of DMSP. The Ulva genome offers, therefore, new opportunities to understand coastal and marine ecosystems and the fundamental evolution of the green lineage