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Martinez, Y.

Publications and source records attributed to Martinez, Y..

13 recordsLinked to original sources

Natural habitats are reservoirs of Fusarium lineages highly pathogenic on Triticum aestivum

Fungal plant diseases are a major cause of crop loss worldwide. Understanding the processes driving these diseases is therefore crucial to anticipate and control epidemics while improving crop yield production. Moreover, the new European Green Deal aims to reduce the use of pesticides, while, few alternatives are currently available on the market. There is therefore an urgent need to better track and anticipate fungal crop epidemics in the current context of fungicide reduction. In light of this, our study aims to understand Fusarium spill overs from non-agricultural habitats in order to better characterise potential non-host Fusarium reservoirs that may be implicated in the emergence of Fusarium diseases. To address this question, we isolated Fusarium lineages from natural populations of Brassica rapa. We characterised their phylogenomic affiliation and found that they display high diversity, with a population structure related to the locality of isolation. By inoculation assays, we identified Fusarium strains from non-agricultural habitats that were highly aggressive on wheat. In addition, we observed a strong effect of wheat variety on disease development. We monitored the Fusarium colonisation through a microscopy approach in both wheat and Brassica plants. We observed that while the fungus is mostly on root surface in Brassica plants, it spreads inter-cellularly in wheat roots with vascular colonisation in the wheat shoots. Finally, we showed that most aggressive Fusarium strains were isolated from Brittany, a French region where wheat is vastly cultivated.

ecology↗

A single genetic innovation at the origin of plant terrestrialization

How the functional innovations that enabled plants to first colonize land 450 million years ago evolved remains puzzling. Here, we show that the gain of a single family of enzymes was pivotal in the evolution of two of these innovations, the cuticle that protect plants from dehydration and UV light, and the Arbuscular Mycorrhizal symbiosis promoting water and nutrient uptake. We show that functional phosphatase domain Glycerol-3-Phosphate Acyl Transferase (p-GPATs) evolved in the first land plants, concomitantly with the cuticle and symbiosis. Mutation of two p-GPATs from the liverwort Marchantia paleacea is sufficient to abolish both cuticle formation and AM symbiosis, leading to major developmental defects. We propose that the evolution of p-GPATs in land plants acted as a two birds-one stone innovation, diverting intracellular lipids to the extracellular space and providing a simple path to the evolution of two traits essential for the colonization of land.

plant biology↗

Drosophila pseudoobscura third chromosome inversion arrangements have sex-specific effects on life history traits

Chromosomal inversions can create polymorphic "supergenes" consisting of many alleles in linkage disequilibrium that affect constellations of traits. The coadaptation hypothesis supposes that many alleles within an inversion haplotype have synergistic epistatic interactions, which are maintained by suppressed recombination in inversion heterozygotes, heterozygote advantage, and context-dependent fitness effects. The fitness benefits of chromosomal inversions frequently arise from effects on life history syndromes, including ecotypes and reproductive strategies. Life history syndromes can also be caused by individual pleiotropic alleles in ways that resemble the effects of chromosomal inversions. It is therefore possible that the fitness effects of chromosomal inversions arise because of pleiotropic alleles and not coadaptation. These two hypotheses can be distinguished because pleiotropy predicts greater genetic correlations of traits than coadaptation. To test the coadaptation and pleiotropy hypotheses, we measured three life history traits (lifespan, development time, and body size) in Drosophila pseudoobscura with six different chromosomal inversion genotypes. We assayed males and females raised at multiple temperatures in order to expose phenotype variation. Temperature affected lifespan and development more than any other factor, but we also observed differences in mortality rates and development times that depended on chromosomal inversions and sex. Despite these context-dependent effects on life history traits, we failed to identify genetic correlations that would be evidence for pleiotropic alleles. Our results therefore suggest that the coadaptation hypothesis is better supported.

evolutionary biology↗

A novel pathosystem between Aeschynomene evenia and Aphanomyces euteiches reveals new immune components in quantitative legume root-rot resistance.

Legumes are pivotal for sustainable agriculture, yet their productivity is hindered by soilborne pathogens such as Aphanomyces euteiches. This study introduces Aeschynomene evenia as a novel model to investigate legume immunity and its interplay with Nod factor-independent symbiosis (NFIS). Inoculation of A. evenia accessions with A. euteiches strains revealed a range of quantitative resistance levels. Phenotypic and cytological analyses showed a compatible interaction, including root browning, intracellular colonisation, and oospore production; along with partial resistance traits such as phenolic accumulation at the endodermal barrier. Transcriptomic analyses at 1 and 3 dpi identified 3,403 differentially expressed genes (DEGs), with upregulated genes associated with pathogen perception, immune signalling and specialised metabolite biosynthesis. Kinase-mediated signalling, ROS homeostasis, and WRKY transcription factors were among the most enriched functional categories. Comparative transcriptomics with Medicago truncatula confirmed conserved immune responses, while A. evenia displayed broader transcriptional repression. Integration with symbiotic transcriptomic data revealed overlapping gene signatures, including AeRLCK2 and AeCRK, previously found to be NFIS-specific, as putative dual-function kinases. Aerlck2 and Aecrk mutants exhibited enhanced resistance to A. euteiches, supporting their roles in immune regulation. This work positions A. evenia-A. euteiches as a valuable system to dissect legume quantitative resistance and its intersection with symbiosis.

plant biology↗

Exploring fern pathosystems and immune receptors to bridge gaps in plant immunity

Land plants include angiosperms, bryophytes, lycophytes and ferns, each of which may deploy distinct strategies to resist pathogens. Here, we investigate fern-pathogen interactions by characterizing novel pathosystems and analysing the diversity of fern immune receptors. A collection of fern species was inoculated with a diverse set of microbes, and disease symptoms were assessed. We further leveraged published genome mining tools to analyse the diversity of RECEPTOR-LIKE KINASES, RECEPTOR-LIKE PROTEINS (RLKs/RLPs) and NUCLEOTIDE-BINDING AND LEUCINE-RICH REPEATS (NLRs), along with key immune signalling components, in ferns. Our results reveal that ferns exhibit a range of responses to pathogens, including non-host resistance and specific resistance mechanisms. Among ten ferns tested, Pteris vittata displays the broadest spectrum of pathogen compatibility. Genome mining indicates that ferns encode a diverse repertoire of putative immune receptors, antimicrobial peptides and mediators of systemic acquired resistance. Ferns possess numerous RLKs/RLPs, resembling those required for cell-surface immunity in angiosperms. They also encode diverse NLRs, including a previously undescribed class with a disordered N-terminal domain, termed disN-NLR. These findings provide insights into disease resistance evolution and open promising perspectives for crop protection strategies.

plant biology↗

Horizontal gene transfers and terpene metabolism drive plant-fungal interaction in Marchantia polymorpha

The liverwort Marchantia polymorpha has emerged as a model for studying plant immunity in bryophytes, providing unique insights into conserved defense mechanisms across land plants. By contrast, Marchantia-specific immune mechanisms have not been explored. In this study, we investigated the genetic basis of quantitative resistance in M. polymorpha against the fungal pathogen Colletotrichum nymphaeae, a naturally occurring compatible parasite. Through a combination of phenotypic, cytological and transcriptomic approaches, combined with genome-wide association studies (GWAS), we identified key defense-related genes and pathways. Transcriptomic analyses performed on two lines with contrasting suceptibilities to the pathogen revealed a strong overlap in immune responses between M. polymorpha and angiosperms, including the upregulation of PR proteins, transcription factors typically associated with biotic stresses, and enzymes involved in specialized metabolism. Leveraging the biological and genetic variability present in a collection of natural M. polymorpha accessions, highlight the role of horizontally transferred microbial-like terpene synthase (MTPSL) genes, which may contribute to the exceptional terpene diversity in liverworts and play a role in pathogen resistance. GWAS uncovered candidate loci associated with resistance traits, implicating both core immune components and specialized metabolic pathways. These results provide new insights into the specific molecular underpinnings of bryophyte immunity and underscore the evolutionary significance of horizontal gene transfer and specialized metabolites in shaping plant-pathogen interactions.

plant biology↗

Cold stress involves CBF dependent regulatory pathway to remodel wood formation in Eucalyptus gunnii hybrids.

While being the most planted tree worldwide, most Eucalyptus species are sensitive to frost. Long-term exposure to cold temperatures, among other abiotic cues, triggers modification of secondary xylem differentiation in Eucalyptus, but the molecular mechanisms behind it remain unknown. Overexpression of key players of cold signalling pathway, the CRT-repeat binding factors (CBF), not only causes the expected increase in freezing tolerance but also remodels wood in a similar trend to cold acclimation, making it a good candidate for wood functional adaptation to cold stress. To gain insight in CBF role in cold-induced secondary cell wall (SCW) remodelling, we used both targeted and untargeted methodologies to show that chilling and freezing temperatures induced the deposition of a thick SCW with alterations in lignin and polysaccharides composition as well as modifications of wood anatomy in a Eucalyptus cold-tolerant hybrid. Using co-expression network approaches, we identified CBF transcription factors (TFs) as a regulatory hub in xylem cold response. Direct targets of the CBF TFs were identified by DAPseq and unravelled promising candidates involved in SCW deposition and hormonal signalling pathways. Our results shed new light on the interplay between cold response and wood formation, bringing new evidence for the role of the cell wall in trees tolerance to abiotic stresses.

plant biology↗

Receptor kinase LecRK-I.9 regulates cell wall remodelling and signalling during lateral root formation in Arabidopsis

Assembling and remodelling the cell wall is essential for plant development. Cell wall dynamic is controlled by cell wall proteins and a variety of sensor and receptor systems. LecRK-I.9, an Arabidopsis thaliana plasma membrane-localised lectin receptor kinase, was previously shown to be involved in cell wall-plasma membrane contacts and to play roles in plant-pathogen interactions, but so far, its role in development was unknown. LecRK-I.9 is transcribed at a high level in root tissues including the pericycle. Comparative transcript profiling of a loss-of-function mutant vs wild type identifies LecRK-I.9 as a regulator of cell wall metabolism. Consistently, lecrk-I.9 mutants display an increased pectin methylesterification level correlated with decreased pectin methylesterase and increased polygalacturonase activities. Also, LecRK-I.9 impacts lateral root development through the regulation of genes encoding (i) cell wall remodelling proteins during early events of lateral root initiation, and (ii) cell wall signalling peptides (CLE2, CLE4) repressing lateral root emergence and growth. Besides, low nitrate reduces LecRK-I.9 expression in pericycle and interferes with its regulatory network: however, the control of CLE2 and CLE4 expression is maintained. Altogether, the results show that LecRK-I.9 is a key player in a signalling network regulating both pre-branch site formation and lateral root emergence. HighlightThe lectin receptor kinase LecRK-I.9 regulates the molecular events leading to lateral root formation in both the initiation and emergence processes in Arabidopsis through cell wall remodelling enzymes and signalling peptides.

plant biology↗

TBL38 is an atypical homogalacturonan acetylesterase with a peculiar cell wall microdomain localization in Arabidopsis seed mucilage secretory cells

Plant cell walls are made of complex polysaccharidic/proteinaceous network whose biosynthesis and dynamics implicate several cell compartments and impact plant development. The synthesis and remodeling of homogalacturonan pectins is associated with multiple developmental processes ranging from growth to response to biotic/abiotic stress. It encompasses Golgi-localized methylation and acetylation and subsequent demethylation and deacetylation in the cell wall. In the last decade, our comprehension of plant polysaccharides acetylation has increased significantly thanks to the study of the TRICHOME BIREFRINGENCE-LIKE (TBL) protein family. TBLs are mostly described as Golgi-localized acetyltransferases specifically targeting diverse hemicelluloses or pectins. Various tbl mutants showed altered wall mechanical properties and dynamics. Here, we study TBL38 that is co-expressed with PECTIN METHYLESTERASE INHIBITOR6 (PMEI6) and PEROXIDASE 36 (PRX36) during the development of Arabidopsis seed mucilage secretory cells (MSCs). We demonstrate the atypical TBL38 cell wall localization restricted to the PMEI6/PRX36 MSC cell wall microdomain. A tbl38 mutant displays an intriguing homogalacturonan immunological phenotype in this cell wall microdomain and in a MSC surface-enriched abrasion powder. This fraction was further characterized by mass spectrometry oligosaccharide profiling revealing an increased homogalacturonan acetylation phenotype. Finally, a recombinant TBL38 is shown to display pectin acetylesterase activity in vitro. These results indicate that TBL38 is an atypical cell wall-localized TBL that displays a homogalacturonan acetylesterase activity rather than a Golgi-localized acetyltransferase activity as observed in previously studied TBLs. TBL38 function during seed development is discussed.

plant biology↗

Cell type-specific control of secondary cell wall formation by Musashi-type translational regulators in Arabidopsis

Deciphering the mechanism of secondary cell wall/SCW formation in plants is key to understanding their development and the molecular basis of biomass recalcitrance. Although transcriptional regulation is essential for SCW formation, little is known about the implication of post-transcriptional mechanisms in this process. Here we report that two bonafide RNA-binding proteins homologous to the animal translational regulator Musashi, MSIL2 and MSIL4, function redundantly to control SCW formation in Arabidopsis. MSIL2/4 interactomes are similar and enriched in proteins involved in mRNA binding and translational regulation. MSIL2/4 mutations alter SCW formation in the fibers, leading to a reduction in lignin deposition, and an increase of 4-O-glucuronoxylan methylation. In accordance, quantitative proteomics of stems reveal an overaccumulation of glucuronoxylan biosynthetic machinery, including GXM3, in the msil2/4 mutant stem. We showed that MSIL4 immunoprecipitates GXM mRNAs, suggesting a novel aspect of SCW regulation, linking post-transcriptional control to the regulation of SCW biosynthesis genes.

plant biology↗

Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

Streptomycetes are Gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the presence of Streptomyces in the rhizosphere are mostly unknown but can rely on the ability to release phytohormones, degrade plant cell-wall polysaccharides and produce specialised metabolites. Here we sequenced the genome of the rhizospheric and plant defence-stimulating strain Streptomyces sp. AgN23. We found out that it belongs to the soil and plant root dwelling S. violaceusniger clade. The genome annotation of AgN23 revealed the ability of the bacterium to synthesise auxin, a major regulator of plant development, to degrade plant cell wall with a large repertoire of carbohydrate degrading enzymes and to produce antimicrobials (rustmicin, mediomycin, niphimycin, nigericin) and plant bioactive compounds (nigericin, echosides, elaiophylin) through a set of biosynthetic gene clusters. We also found that these genomic features are well-conserved among members of the S. violaceusniger clade. In addition, AgN23 display original events of biosynthetic gene clusters acquisitions and losses which may account for its beneficial effect on plants. Taken together, our work supports the hypothesis that hydrolytic enzymes and specialised metabolites repertoires underpin the interaction of bacteria belonging to the S. violaceusniger clade with plant roots within the rhizosphere. Impact statementStreptomycetes are filamentous Gram-positive bacteria universally found around and within host plant tissues. These actinobacteria have been extensively investigated for their tremendous ability to produce diverse specialised metabolites (e.g., antibiotics). By contrast their impact on host plant physiology is widely neglected. Whether specific lineage of Streptomyces colonise host plant and what are the underlying molecular mechanisms is poorly documented. Here we report a chromosome-scale assembly of AgN23 genome, a Streptomyces sp. strain previously characterised for its ability to activate the plant immune system. This reference sequence enabled us to position AgN23 in the S. violaceusniger clade from which several representatives have been isolated worldwide from the rhizosphere of unrelated plants. Comparative genomic studies suggest that S. violaceusniger spp. produce a prominent CAZyome with expansion of plant cell wall degrading enzymes families and a conserved specialised metabolism acting on host plant physiology and its rhizospheric microbiota. These genomic features may underly S. violaceusniger spp. adaptation to the rhizopsheric niche. Data summaryThe raw reads sequences of AgN23 genome are available at NCBI on the Sequence Read Archive portal for PacBio and MiSeq data (SRR13990229 and SRR14028548 respectively). The Genome assembly is available on the NCBI nucleotide portal under the accession NZ_CP007153.1. This genome sequence was uploaded on the MicroScope platform for genome annotation and analysis (https://mage.genoscope.cns.fr/microscope/home/index.php) [1]. The RNA-seq raw reads are archived in the NCBI Bioproject PRJNA745930. The following eight supplementary tables are included in the online version of this article. Supplementary Information 1: Genomes used in this study. The accession number used from the NCBI portal, name, size, number of contigs as well as the level of completeness of the assembly are indicated. Supplementary Information 2: List of the single copy core genes used by autoMLST to build the phylogenetic tree in Figure 1. O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/465742v2_fig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@e15f3org.highwire.dtl.DTLVardef@c34218org.highwire.dtl.DTLVardef@1286956org.highwire.dtl.DTLVardef@1bb5b3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Multi-locus sequence typing assigned AgN23 to the S. violaceusniger clade. Phylogenetic tree based on the multiple alignment of 85 single-copy homologous genes selected from genomic sequences with AutoMLST. The green node highlights the isolates considered to be from the same species (ANI>95%). The black node highlights the clade formed by isolates with ANI>90% as compared to AgN23. The black squares highlights the eight strains that were used for the BGC conservation study. The green logo indicates plant-isolated strains. Frankia alni ACN14a was used as outgroup, bootstrap=100. C_FIG Supplementary information 3: Annotation of AgN23 full chromosome. For each gene the frame of translation, sequence length and position on the chromosome are indicated. All genes were annotated according to the Microscope platform, see materials and methods. In addition, the expression for each gene is reported in transcripts per million (TPM) based on the the RNA-seq data from three biological replicates. Supplementary Information 4: Genomes having a Mash-based estimated ANI (Average Nucleotide Identity) superior or egal to 80% according to autoMLST. Supplementary Information 5: Prediction of the CAZyme encoding genes using HMMER dbCAN2. The genes are sorted according their CAZy families. For each gene, the begin position on the chromosome, the CAZy category, the annotation, the expression level in transcripts per million (TPM) and the predicted targets of the putative enzymes are described. Supplementary Information 6: Gene identified by antiSMASH in the region containing a biosynthetic gene cluster. Expression levels in transcripts per million (TPM) are indicated for each gene. Annotated central bioynthetic genes are indicated as Y. Those are the ones used for the calculation of mean BGC expression in Table 2. O_TBL View this table: org.highwire.dtl.DTLVardef@1362f24org.highwire.dtl.DTLVardef@50f792org.highwire.dtl.DTLVardef@1ad9681org.highwire.dtl.DTLVardef@1742e96org.highwire.dtl.DTLVardef@9e9b6c_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2:C_FLOATNO O_TABLECAPTIONantiSMASH annotation of AgN23 chromosomal regions coding for Biosynthetic Gene Clusters. The functional category of each BGCs was determined by antiSMASH. The BGC type, best hit in the MIBiG database as its percentage of similarity to the query are indicated along with the bacterial strain from whom the cluster was described. The expression level of each BGCs was determined by doing the mean of the expression level in Transcripts Per Million (TPM) of the core biosynthetic genes of each BGC from the RNA-seq data (n=3). C_TABLECAPTION C_TBL Supplementary Information 7: Annotation of AgN23 genes putatively involved in biosynthetic pathways for Auxins related phytohomones. Expression levels in transcripts per million (TPM) are indicated for each gene. The genes were detected by blasting reference KEGG sequences for each KEGG ONTOLOGY against AgN23 genes. A cut off of 70% identity and 40% coverage was applied to detect positive hits. These biosynthetic pathways and the KEGG ONTOLOGY are indicated in column F and G. Supplementary Information 8: Inspection of BiG-FAM hits with AgN23 BGCs to identify homologous BGCs found outside the S. violaceusniger clade. BiG-FAM distance higher than 900 were excluded from the analysis. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

genomics↗

Cuban history of CRF19 recombinant subtype of HIV-1

CRF19 is a recombinant form of HIV-1 subtypes D, A1 and G, which was first sampled in Cuba in 1999, but was already present there in 1980s. CRF19 was reported almost uniquely in Cuba, where it accounts for ~25% of new HIV-positive patients and causes rapid progression to AIDS (~ 3 years). We analyzed a large data set comprising ~ 350 pol and env sequences sampled in Cuba over the last 15 years and ~ 350 from Los Alamos database. This data set contained both CRF19 (~ 315), and A1, D and G sequences. We performed and combined analyses for the three A1, G and D regions, using fast maximum likelihood approaches, including: (1) phylogeny reconstruction, (2) spatio-temporal analysis of the virus spread, and ancestral character reconstruction for (3) transmission mode and (4) drug resistance mutations (DRMs). This allowed us to acquire new insights on the CRF19 origin and transmission patterns. We showed that CRF19 recombined between 1966 and 1977, most likely in Cuban community stationed in Congo region. We further investigated CRF19 spread on the Cuban province level, and discovered that the epidemic started in 1970s, most probably in Villa Clara, that it was at first carried by heterosexual transmissions, and then quickly spread in the 1980s within the "men having sex with men" (MSM) community, with multiple transmissions back to heterosexuals. The analysis of the transmission patterns of common DRMs showed mostly acquired drug resistance rather than transmitted one. Our results show a very early introduction of CRF19 in Cuba, which could explain its local epidemiological success. Ignited by a major founder event, the epidemic then followed a similar pattern as other subtypes and CRFs in Cuba. The reason for the short time to AIDS remains to be understood and requires specific surveillance, in Cuba and elsewhere. Author summaryCRF19 is a recombinant form of HIV-1, which causes rapid progression to AIDS (~ 3 years versus 5 - 10 years for other subtypes and CRFs). CRF19 is reported almost uniquely in Cuba, where it is highly prevalent (~ 25%) among newly detected HIV-1 patients. In this study, we found that CRF19 most likely recombined around the 1970s in the Cuban community that was stationed in Democratic Republic of the Congo and Angola at that time. It was introduced very early into the Cuban province of Villa Clara, from where it had several introductions to La Habana in the 1980s and then further spread to other Cuban provinces. The CRF19 epidemic most probably started with heterosexual transmissions, followed in the 1980s by multiple introductions into "men having sex with men" (MSM) community, followed by multiple transmissions back to heterosexuals (often females). The early introduction of CRF19 into Cuba most likely explains its success, not observed in other parts of the world. However, importantly, its rapid progression to AIDS makes it crucial to survey CRF19 sub-epidemics not only in Cuba, but also in other parts of the world having regular exchanges with Cuba.

bioinformatics↗

Global non-animal peroxidases analysis provides insights into the evolutionary study of this gene family in green lineage

The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce the hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, several advances have provided an understanding into the origin and evolutionary history of this family of proteins. Here, we report for the first time an exhaustive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical strategies. Thanks to the availability of numerous genomic sequences from many species belonging to different kingdoms together with expert and exhaustive annotation of peroxidase sequences centralized in a dedicated database, we have deepened our understanding of the evolutionary process underlying non-animal peroxidases through phylogenetic reconstructions. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases can be correlated with the presence or absence of certain organelles or with specific biological processes. Examining a wide range of organisms, we confirmed that ascorbate peroxidases (APx) and cytochromes c peroxidases (CcP) were detected respectively in chloroplast and mitochondria containing organisms. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class III peroxidases (CIII Prx) were only detected in plants and Class II peroxidases (CII Prx) in fungi related to wood decay and plant degradation. Moreover, we demonstrate that biochemical activities (APx, CcP and CIII Prx) assayed in protein extracts obtained from 30 different eukaryotic organisms strongly support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of non-animal peroxidase encoding sequences.

evolutionary biology↗