Nils Poulicard

• PhD Microbiology & Parasitology
• Researcher at Institute of Research for Development

Co-occurrence of multiple diseases and co-infection of individual plants by various pathogens have potential epidemiological and evolutionary implications. Based on previous information on the co-occurrence of the rice yellow mottle disease (caused by the rice yellow mottle virus, RYMV) and bacterial leaf streak (BLS, due to Xanthomonas oryzae pv....

Local co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current context of globalisation. When different phylogenetic lineages co-occur in the same fields, they may be simultaneously present in the same host plant (i.e. mixed infection), with potentially important consequences for disease...

Rice yellow mottle virus (RYMV) is a major pathogen of rice in Africa. RYMV has a narrow host range limited to rice and a few related poaceae species. We explore the links between the spread of RYMV in East Africa and rice history since the second half of the 19 th century. The phylogeography of RYMV in East Africa was reconstructed from coat prote...

Rice is of critical significance regarding food security worldwide, including in Africa. Only two viruses impacting rice production in Africa have been deeply investigated for decades: the rice yellow mottle virus ( Solemoviridae) and the rice stripe necrosis virus ( Benyviridae). Using viral metagenomics, we aimed at broadening knowledge on intera...

The local co-circulation of multiple phylogenetic lineages is particularly likely for rapidly evolving pathogens in the current globalization context. When various phylogenetic lineages co-occur in the same fields, they may simultaneously be present in the same host plant (i.e. mixed infection), with potential important consequences for disease out...

Specificity in plant–pathogen gene‐for‐gene (GFG) interactions is determined by the recognition of pathogen proteins by the products of plant resistance (R) genes. The evolutionary dynamics of R genes in plant–virus systems is poorly understood. We analyse the evolution of the L resistance locus to tobamoviruses in the wild pepper Capsicum annuum v...

Rice is of critical significance regarding food security worldwide including in Africa. Only two viruses impacting rice production in Africa have been deeply investigated for decades: the rice yellow mottle virus ( Solemoviridae ) and the rice stripe necrosis virus ( Benyviridae ). Using viral metagenomics, we aimed at exploring the diversity of vi...

The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at local scale remain scarce, in spite of potential implications for crop...

Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the A...

The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology and phylogeography, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at local scale remain scarce, in spite of potential imp...

Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections con...

Rice yellow mottle virus (RYMV) has persisted as a major biotic constraint to rice production in Africa. However, no data on RYMV epidemics were available in Ghana, although it is an intensive rice-producing country. Surveys were performed from 2010 to 2020 in eleven rice-growing regions of Ghana. Symptom observations and serological detections con...

Viral diseases are a major limitation for crop production, and their control is crucial for sustainable food supply. We investigated by a combination of functional genetics and experimental evolution the resistance of rice to the rice yellow mottle virus (RYMV), which is among the most devastating rice pathogens in Africa, and the mechanisms underl...

Fanleaf degeneration is a complex viral disease of Vitis spp. that detrimentally impacts fruit yield and reduces the productive lifespan of most vineyards worldwide. In France, its main causal agent is grapevine fanleaf virus (GFLV). In the past, field experiments were conducted to explore cross-protection as a management strategy of fanleaf degene...

Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus , family Secoviridae , were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarca...

Since its identification in 2003, grapevine Pinot gris virus (GPGV, Trichovirus) has now been detected in most grape-growing countries. So far, little is known about the epidemiology of this newly emerging virus. In this work, we used datamining as a tool to monitor in-silico the sanitary status of three vineyards in Italy. All data used in the stu...

Since its identification in 2003, little has been revealed about the spread of grapevine Pinot gris virus (GPGV), an emerging grapevine virus. According to studies from Italy, GPGV transmission in the vineyard can be fast but progressive over the years. To gain new insights into the spread of GPGV infections, we tested 67 grapevines in a single vin...

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed alo...

Datamining and metagenomic analyses of 277 open reading frame sequences of bipartite RNA viruses and variants in the genus Nepovirus documented how delicate it can be to unequivocally identify species, in particular subgroup A and C species, based on some of the currently adopted taxonomic demarcation criteria. It suggests a possible need for their...

Rice yellow mottle virus in Senegal is reported here for the first time. The near-complete genomic sequences of two isolates (Se1 and Se5) were obtained. A comparison with 18 sequences from West Africa revealed a new cluster with an isolate from Gambia, located at a basal position in the phylogenetic tree.

The recently described member of the genus Trichovirus grapevine Pinot gris virus (GPGV) has now been detected in most grape-growing countries. While it has been associated with severe mottling and deformation symptoms under some circumstances, it has generally been detected in asymptomatic infections. The cause(s) underlying this variable associat...

Five isolates of Rice yellow mottle virus from western Kenya were fully sequenced. One isolate of strain S4lv had been collected in 1966. Two isolates belonged to the emerging strain S4ug recently described in Uganda. Two isolates collected in 2012 are putative recombinants between the S4lv and S4ug strains.

Appendix S1 Bacterial genomics and soil study. Viral genomic study.

Figure S1 Genes targeted for detection by PCR and qPCR experiments. Figure S2 Microbial diversity comparison between leaf (RNAseq 2 × 150) and soil samples (Miseq sequencing). Figure S3 Phylogenetic relationships of satRNA genomes, GFLV cp gene sequences from RNAseq and from IC‐RT‐PCR NGS‐based dataset obtained from GM rootstock (GMR, in blue), n...

Table S1 Detection of transgenic plant‐derived transcripts from RNAseq (total RNA) and IC‐RT‐PCR‐NGS (virus encapsidated RNA)‐based techniques. Table S2 Sanitary status. Table S3 SNPs quantification. Table S4 F ST values for each sampling category. Table S5 (part A and B): Crossover sites. Table S6 Quality control of DNAseq and RNAseq. Table...

Rice yields in Kenya remain very low due to several constraints with Rice Yellow Mottle Disease (RYMD) caused by Rice Yellow Mottle Virus (RYMV) being the greatest challenge. However, information on pattern of distribution and diversity still remain scanty and hence a hindrance in designing most suitable control measures. A research study was carri...

Rice yields in Kenya remain very low due to several constraints with Rice Yellow Mottle Disease (RYMD) caused by Rice Yellow Mottle Virus (RYMV) being the greatest challenge. However, information on pattern of distribution and diversity still remain scanty and hence a hindrance in designing most suitable control measures. A research study was carri...

Rice yellow mottle virus (RYMV) causes high losses to rice production in Africa. Several sources of varietal high resistance are available but the emergence of virulent pathotypes that are able to overcome one or two resistance alleles can sometimes occur. Both resistance spectra and viral adaptability have to be taken into account to develop susta...

For some crops, the only possible approach to gain a specific trait requires genome modification. The development of virus-resistant transgenic plants based on the pathogen-derived resistance strategy has been a success story for over three decades. However, potential risks associated with the technology, such as horizontal gene transfer (HGT) of a...

Rice (Oryza sativa, L.) yields in Kenya remain very low due to several constraints with rice yellow mottle disease (RYMD) caused by Rice Yellow Mottle Virus (RYMV) being the greatest challenge. However, the distribution pattern and diversity of the virus still remain largely unknown and hence hindrance in designing appropriate interventions. A stud...

Prod 2017-108 EA BIOmE CT ? INRA

This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in...

Chiltepin populations analysed and number of pvr2/eIF4E1 sequences obtained in this study. (DOCX)

Genetic diversity of pvr2/eIF4E1 exons and introns in chiltepin populations according to geographical provinces and habitats. (DOCX)

Zygosity at the pvr2/eIF4E1 locus and identification of susceptible and resistant plants in chiltepin populations. (DOCX)

Effects of the mutations identified in pvr2/eIF4E1 protein on the pvr2/eIF4E1-VPg:PVY interactions evaluated. Yeast growth was evaluated by yeast two hybrid assays and was expressed by percentage of the yeast growth on the selective medium (-LWH) compared to the reference yeast colonies co-transformed with pGADT7::pvr2+ and pGBKT7::VPg-PVY; standar...

Geographic and genetic distance in wild chiltepin populations at the pvr2/eIF4E1 locus. Log-transformed data are presented. (TIF)

Phylogeny of pvr2/eIF4E1 coding sequences in the genus Capsicum based only on the third positions of the codons. The presented phylogeny was reconstructed by the NJ method, bootstrap values (1000 replicates) are indicated on the nodes. hapA to hapQ are pvr2/eIF4E1 haplotypes identified in chiltepin populations; pvr2+ and pvr21 to pvr29 are pvr2/eIF...

Frequency of heterozygous plants for the pvr2/eIF4E1 coding sequences in chiltepin populations according to geographical provinces and habitats. (DOCX)

Genetic differentiation of the pvr2/eIF4E1 coding sequences between biogeographical provinces. (DOCX)

Complementation of yeast strain JO55 with pvr2/eIF4E1 coding sequences identified in chiltepin populations. Control -: negative control corresponding to yeast colonies transformed with empty p424GBP/TRP1 plasmids. (TIF)

Sequence alignment of pvr2/eIF4E1 alleles identified in chiltepin populations and localisation of the polymorphic positions (orange), sites involved in the Potyvirus resistance (purple) and in the m7GTP binding cap recognition (green) and domain of eIF4G interaction (blue). (TIF)

Phylogenetic relationships between Capsicum annuum pvr2+ allele and 4 crystallized eIF4E (A), comparison of the secondary structure of these proteins (B) and disorder prediction in the pvr2/eIF4E1 protein (C). *: localisation of the polymorphic positions identified in the pvr2/eIF4E1 protein of chiltepins. (TIF)

Superposition of the 3D-model generated independently of the pvr2/eIF4E1 alleles identified in chiltepin populations. (A) superposition of the models; (B) pvr2+ (green) and pvr1+ (orange), superposition: RMSDbackbone = 1.050 Å; (C) pvr2+ (green) and pvr21 (orange), superposition: RMSDbackbone = 1.107 Å; (D) pvr2+ (green) and pvr22 (orange), superpo...

Phylogenetic relationships between Potyvirus species and location of the potyviruses infecting chiltepin populations. The presented phylogeny was reconstructed based on partial NIb (304nt) by the NJ method, bootstrap values (1000 replicates) are indicated on the nodes. Grey boxes mentioned the potyvirus sequences identified in chiltepin populations...

Phylogeny of pvr2/eIF4E1 coding sequences in the genus Capsicum. The presented phylogeny was reconstructed by the NJ method, bootstrap values (1000 replicates) are indicated on the nodes. hapA to hapQ are pvr2/eIF4E1 haplotypes identified in chiltepin populations; pvr2+ and pvr21 to pvr29 are pvr2/eIF4E1 haplotypes described in [23]; pvr1+, pvr1 an...

Differences in the VPg protein sequence between TEV and TEV-like potyviruses. TEV (Consensus): Consensus sequence obtained with 20 world-wide TEV isolates (accession numbers: L38714, M11458, M15239.1, NC_001555.1, DQ986288.1, EF470242.2, JN711120.1, EU334794.1, EU334793.1, EU334792.1, EU334791.1, EU334790.1, 334789.1, EU334788.1, EU334787.1, EU3347...

Phylogeny of pvr2/eIF4E1 coding sequences in the genus Capsicum based on the first and the second positions of the codons. The presented phylogeny was reconstructed by the NJ method, bootstrap values (1000 replicates) are indicated on the nodes. hapA to hapQ are pvr2/eIF4E1 haplotypes identified in chiltepin populations; pvr2+ and pvr21 to pvr29 ar...

It has been hypothesized that plant–virus interactions vary between antagonism and conditional mutualism according to environmental conditions. This hypothesis is based on scant experimental evidence, and to test it we examined the effect of abiotic factors on the Arabidopsis thaliana – Cucumber mosaic virus ( CMV ) interaction. Four Arabidopsis ge...

The adaptation of Rice yellow mottle virus (RYMV) to RYMV1-mediated resistance has been reported to involve mutations in the viral protein genome-linked (VPg). In this study, we analysed several cases of rymv1-2 resistance breakdown by an isolate with low adaptability. Surprisingly, in these rarely occurring resistance-breaking (RB) genotypes mutat...

The rymv1-2 and rymv1-3 alleles of the RYMV1 resistance to Rice yellow mottle virus (RYMV), coded by an eIF(iso)4G1 gene, occur in a few cultivars of the Asiatic (Oryza sativa) and African (O. glaberrima) rice species, respectively. The most salient feature of the resistance breaking (RB) process is the converse genetic barrier to rymv1-2 and rymv1...

Amino acid diversity of the VPg of wild type isolates. The amino acid sequence of the isolate CIa - used to construct the CIa infectious clone - is given in the top row. The amino acid at position 49 of the VPg of each isolate is indicated in plain letter. The differences between the VPg sequences of the wild type isolates with that of CIa isolate...

The adaptation of Rice yellow mottle virus (RYMV) to recessive resistance mediated by the rymv1-2 allele has been reported as a model to study the emergence and evolution of virulent variants. The resistance and virulence factors have been identified as eukaryotic translation initiation factor eIF(iso)4G1 and viral genome-linked protein (VPg), resp...

The rymv1-3 allele of the eIF(iso)4G-mediated resistance to Rice yellow mottle virus (RYMV) is found in a few Oryza glaberrima cultivars. The same resistance-breaking (RB) mutations emerged in the central domain of the VPg after inoculation of isolates of different strains. The RB mutations were fixed, often sequentially, at codons 41 and 52 which...

Rice yellow mottle virus (RYMV) reaches a high virus content in rice, is genetically highly variable and evolves rapidly. Nevertheless, only a small proportion of isolates overcome rymv1-2 rice resistance by mutations in the VPg (viral protein genome-linked). The accumulation rates of wild-type (WT) and resistance-breaking (RB) genotypes of the E-...

The diversity of a highly variable RNA plant virus was considered to determine the range of virulence substitutions, the evolutionary pathways to virulence, and whether intraspecific diversity modulates virulence pathways and propensity. In all, 114 isolates representative of the genetic and geographic diversity of Rice yellow mottle virus (RYMV) i...

Polymorphism at Codons 48-49-50 of the VPg Top: Distribution of the nucleotides at codons 48-49-50 in the VPg of 59 RYMV isolates representative of the genetic and geographic diversity of RYMV. The E/T substitution in codon 49 is coded by two nucleotide changes at positions 145 (G to A) and 146 (A to C). The R/K substitution at codon 49 is coded by...

Substitutions over Time Associated to Virulence in the VPg of Isolate Mg16 (S6) Inoculated to Rymv1-2-Resistant Cultivars A total of 19 virulent variants generated from isolate Mg16 and labeled Mg16-1 to Mg16-19 was analyzed. They were inoculated to cv Bekarosaka or Gigante. The last developed leaves of the plants were collected. The VPg of the vir...

Name, Geographical Origin, Strain, and Accession Numbers of the Isolates of Rice yellow mottle virus Whose VPg Was Sequenced In all, 62 isolates were fully or partly sequenced. A total of 59 were wild avirulent isolates collected in the fields. Twenty-two of them were fully sequenced. The VPg of virulent variants derived from seven of them was sequ...

Rice yellow mottle is the most important virus disease of rice in Africa. The disease is a major constraint due to its wide geographical distribution and the extent of yield losses it induces. The role of the causal agent Rice yellow mottle virus (RYMV) in virus–host interactions was studied in relation to the current knowledge of rice genetics. Mo...