Biology subjects

Cunnac, S.

Publications and source records attributed to Cunnac, S..

12 recordsLinked to original sources

bioRxiv2026

Two domesticated species of rice shaped the population structure of Xanthomonas oryzae pv. oryzae in Africa

African rice (Oryza glaberrima) was independently domesticated in West Africa around 3000 years ago, and has long been intertwined in the history of the region. The gradual replacement of African rice by Asian rice (Oryza sativa), which was introduced when European settlers arrived, has since dominated rice cultivation in Africa. Domesticated rice species are affected by bacterial leaf blight (BLB), which is caused by the pathogen Xanthomonas oryzae pv. oryzae (Xoo). Here we provide evidence that the bacterial leaf blight pathogen in Africa (AfXoo) belongs to a distinct phylogroup from the one circulating in Asia (AsXoo), and has a different evolutionary history. Analysis of 88 AfXoo genomes identified five groups, one of which is a highly diverse population that might have probably given rise to three independent clonal populations based on multiple genetic tests. Tip-dating analysis revealed that the emergence and expansion of AfXoo coincided with the rise and fall of African rice nearly a thousand years ago, and O. sativa served as a bottleneck in the evolution of AfXoo over time. Although the type III effectors (T3E), proteins that are secreted by the pathogen to evade host resistance or seize control of host nutrients, are highly conserved in AfXoo, we observed some variation in effector families. Different evolutionary modifications in the transcription activator-like effectors (TALEs), especially in repeat variable di-residues (RVDs), likely enabled adaptation to both host species. Previous analyses carried out on samples collected in Burkina Faso have shown that there could be more than one TALE repertoire combination in the field, and genome sequencing data revealed potential TALE evolutionary mechanisms that could happen. Our research provides a comprehensive genetic history of bacterial blight in West Africa, and its past and present impact on rice cultivation in the region. Author summaryFor thousands of years, rice cultivation has been an integral part of African agriculture. However, the cultivation of the locally domesticated African rice cultivar (Oryza glaberrima) has been gradually shifted towards Asian rice varieties (Oryza sativa), which has affected the adaptation of the native pathogen population. One of these pathogens is the causal agent of bacterial leaf blight, Xanthomonas oryzae pv. oryzae (Xoo). Here we performed a population genomics approach to understand the evolutionary history and virulence spectrum of African Xoo (AfXoo), a unique phylogroup within the Xanthomonas oryzae species. Our results suggest that AfXoo were first adapted to African rice at least a thousand years ago. The introduction of O. sativa has shaped the recent population dynamics of AfXoo. TALEs are tightly conserved in AfXoo with multiple sequence variations unique to different populations, which could be explained by different evolutionary forces acting upon both domesticated rice. Our results highlight the interplay between crop domestication and cultivation and pathogen evolution.

genomics↗

bioRxiv2026

eIFiso4G editing confers durable resistance against rice yellow mottle virus

Rice yellow mottle virus (RYMV) is one of the most devastating viral pathogens affecting rice cultivation in Africa. The eukaryotic translation initiation factor 4G isoform eIFiso4G1 plays a pivotal role in rice susceptibility to the virus. Naturally occuring resistance alleles impair infection but are predominantly found in the African cultivated species Oryza glaberrima, whose use in breeding programs is limited by interspecific sterility barriers with the widely grown O. sativa. Here, we used CRISPR-Cas9 to generate knockout (KO) mutations in eIFiso4G1 as well as insertion-deletion (Indel) variants within the region involved in interaction with the viral protein VPg. KO mutations conferred high resistance to RYMV. No resistance-breaking events were observed, suggesting that this resistance may be more durable than that conferred by naturally occuring alleles. However, complete gene KO slightly affected plant growth. Lines carrying Indel mutations in the VPg-interacting region displayed variable resistance levels, with some variants conferring high resistance without compromising plant development. Structural modeling of the eIFiso4G1 variants and their complexes with VPg provided mechanistic insights into how specific Indels modulate the resistance phenotype.

plant biology↗

bioRxiv2025

Symptom observation underestimates co-infections: insight from viral and bacterial diseases in rice fields in Burkina Faso

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. oryzicola, Xoc) in Burkina Faso, and experimental evidence of interactions between the pathogens causing these two diseases, we aimed to monitor the two pathogens more intensively in farmers rice fields. To this purpose, we selected fields showing both types of symptoms to maximize the chance of observing co-infections at the plant scale. We performed observations and sampling in two sites over two consecutive years. Over a global dataset of 1666 samples, 1341 were symptomatic. Although the sampling design aimed to observe co-infections, only 37 of these samples (2.8%) were annotated as presenting both yellow mottle and BLS symptoms. The samples were then subjected to a newly designed molecular detection test that specifically amplifies both the virus (RYMV) and the bacteria (Xo). This revealed that 166 samples, i.e. 12.4% of symptomatic samples, were co-infected by RYMV and Xo, hence showing that symptom observation in the field greatly underestimates co-infection levels. Combining these data with a previously published dataset, we estimated that up to 1-4% of all plants in disease hotspots are simultaneously infected by the two pathogens. Further research on multiple infections would benefit from longitudinal surveys over the crop growing season rather than such a cross-sectional study.

plant biology↗

bioRxiv2024

Comparative transcriptomics reveal a highly polymorphic Xanthomonas HrpG virulence regulon

Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS. IMPORTANCEIn the decades since its discovery, HrpG and its role in the regulation of the type III secretion system (T3SS) and its associated type III effectors (T3Es) in Xanthomonas has been the subject of extensive research. Despite notable progress in understanding its molecular regulatory mechanisms, the full spectrum of processes under control of HrpG, particularly beyond the T3SS and T3Es, and the degree of regulatory conservation across plant-pathogenic Xanthomonas species, remained unclear. To address this knowledge gap, we systematically compared the transcriptomes of 17 Xanthomonas strains, expressing a constitutively active form of HrpG, called HrpG*. We showed that HrpG* regulates different physiological processes other than the T3SS and T3Es and that this regulation shows substantial variation across the different strains. Taken together, our results provide new insights into Xanthomonas-plant interactions through the regulation of different metabolic and virulence pathways by the master response regulator HrpG.

microbiology↗

bioRxiv2023

Rice Yellow Mottle Virus resistance by genome editing of the Oryza sativa L. ssp. japonica nucleoporin gene OsCPR5.1 but not OsCPR5.2

Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (O. glaberrima), however, introgression into O. sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in-frame deletions or replacements in the N-terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single knockout mutants show neither substantial growth defects nor symptoms indicative of programmed cell death, possibly reflecting functional redundancy of the isoforms regarding other important functions. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV-resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits.

plant biology↗

bioRxiv2022

Genome editing of an African elite rice variety confers resistance against endemic and emerging Xanthomonas oryzae pv. oryzae strains

Bacterial leaf blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), threatens global food security and the livelihood of small-scale rice producers. Analyses of Xoo collections from Asia, Africa and the Americas demonstrated surprising continental segregation, despite robust global rice trade. Here, we report unprecedented BB outbreaks in Tanzania. The causative strains, unlike endemic Xoo, carry Asian-type TAL effectors targeting the sucrose transporter SWEET11a and suppressing Xa1. Phylogenomics clustered these strains with Xoo strains from China. African rice varieties do not carry suitable resistance genes. To protect African rice production against this emerging threat, we developed a hybrid CRISPR-Cas9/Cpf1 system to edit six TALe-binding elements in three SWEET promoters of the East African elite variety Komboka. The edited lines show broad-spectrum resistance against Asian and African strains of Xoo, including strains recently discovered in Tanzania. This strategy could help to protect global rice crops from BB pandemics.

plant biology↗

bioRxiv2022

Novel genetic traits in Xanthomonas unveiled by the complete genome sequencing of three clade-1 xanthomonads

Evolutionary early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, and Xanthomonas translucens, which infects small grain cereals, diverse grasses, but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches indicated that this clade likely contains more, yet undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas sp. pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique taxonomic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic traits, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. In addition, strain CFBP 8444 was found to encode a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.

microbiology↗

bioRxiv2021

CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

Using long reads provides higher contiguity and better genome assemblies. However, producing such high quality sequences from raw reads requires to chain a growing set of tools, and determining the best workflow is a complex task. To tackle this challenge, we developed CulebrONT, an open-source, scalable, modular and traceable Snakemake pipeline for assembling long reads data. CulebrONT enables to perform tests on multiple samples and multiple long reads assemblers in parallel, and can optionally perform, downstream circularization and polishing. It further provides a range of assembly quality metrics summarized in a final user-friendly report. CulebrONT alleviates the difficulties of assembly pipelines development, and allow users to identify the best assembly options.

bioinformatics↗

bioRxiv2021

An atypical class of non-coding small RNAs produced in rice leaves upon bacterial infection

Non-coding small RNAs (sRNA) act as mediators of gene silencing and regulate plant growth, development and stress responses. Early insights into plant sRNAs established a role in antiviral defense and they are now extensively studied across plant-microbe interactions. Here, sRNA sequencing discovered a class of sRNA in rice (Oryza sativa) specifically associated with foliar diseases caused by Xanthomonas oryzae bacteria. Xanthomonas-induced small RNAs (xisRNAs) loci were distinctively upregulated in response to diverse virulent strains at an early stage of infection producing a single duplex of 20-22nt sRNAs. xisRNAs production was dependent on the Type III secretion system, a major bacterial virulence factor for host colonization. xisRNA loci overlap with annotated transcripts sequences often encoding protein kinase domain proteins. A number of the corresponding rice cis-genes have documented functions in immune signaling and some xisRNA loci coincide with the coding sequence of a conserved kinase motif. xisRNAs exhibit features of small interfering RNAs and their biosynthesis depend on canonical components OsDCL1 and OsHEN1. xisRNA induction possibly mediates post-transcriptional gene silencing but they do not broadly suppress cis-genes expression on the basis of mRNA-seq data. Overall, our results identify a group of unusual sRNAs with a potential role in plant-microbe interactions.

molecular biology↗

bioRxiv2020

Repeated gain and loss of a single gene modulates the evolution of vascular pathogen lifestyles

Vascular pathogens travel long distances through host veins leading to life-threatening, systemic infections. In contrast, non-vascular pathogens remain restricted to infection sites, triggering localized symptom development. The contrasting features of vascular and non-vascular diseases suggest distinct etiologies, but the basis for each remains unclear. Here, we show that the hydrolase CbsA acts as a phenotypic switch between vascular and non-vascular plant pathogenesis. cbsA was enriched in genomes of vascular phytopathogenic bacteria in the Xanthomonadaceae family and absent in most non-vascular species. CbsA expression allowed non-vascular Xanthomonas to cause vascular blight while cbsA mutagenesis resulted in reduction of vascular or enhanced non-vascular symptom development. Phylogenetic hypothesis testing further revealed that cbsA was lost in multiple non-vascular lineages and more recently gained by some vascular subgroups, suggesting that vascular pathogenesis is ancestral. Our results overall demonstrate how the gain and loss of single loci can facilitate the evolution of complex ecological traits.

microbiology↗

bioRxiv2018

Functional analysis of African Xanthomonas oryzae pv. oryzae TALomes reveals a new susceptibility gene in bacterial leaf light of rice

Most Xanthomonas species translocate Transcription Activator-Like (TAL) effectors into plant cells where they function like plant transcription factors via a programmable DNA-binding domain. Characterized strains of rice pathogenic X. oryzae pv. oryzae harbor 9-16 different tal effector genes, but the function of only a few of them has been decoded. Using sequencing of entire genomes, we first performed comparative analyses of the complete repertoires of TAL effectors, herein referred to as TALomes, in three Xoo strains forming an African genetic lineage different from Asian Xoo. A phylogenetic analysis of the three TALomes combined with in silico predictions of TAL effector targets showed that African Xoo TALomes are highly conserved, genetically distant from Asian ones, and closely related to TAL effectors from the bacterial leaf streak pathogen Xanthomonas oryzae pv. oryzicola (Xoc). Nine clusters of TAL effectors could be identified among the three TALomes, including three showing higher levels of variation in their repeat variable diresidues (RVDs). Detailed analyses of these groups revealed recombination events as a possible source of variation among TAL effector genes. Next, to address contribution to virulence, nine TAL effector genes from the Malian Xoo strain MAI1 and four allelic variants from the Burkinabe Xoo strain BAI3, thus representing most of the TAL effector diversity in African Xoo strains, were expressed in the TAL effector-deficient X. oryzae strain X11-5A for gain-of-function assays. Inoculation of the susceptible rice variety Azucena lead to the discovery of three TAL effectors promoting virulence, including two TAL effectors previously reported to target the susceptibility (S) gene OsSWEET14 and a novel major virulence contributor, TalB. RNA profiling experiments in rice and in silico prediction of EBEs were carried out to identify candidate targets of TalB, revealing OsTFX1, a bZIP transcription factor previously identified as a bacterial blight S gene, and OsERF#123, which encodes a subgroup IXc AP2/ERF transcription factor. Use of designer TAL effectors demonstrated that induction of either gene resulted in greater susceptibility to strain X11-5A. The induction of OsERF#123 by BAI3{Delta}1, a talB knockout derivative of BAI3, carrying these designer TAL effectors increased virulence of BAI3{Delta}1 validating OsERF#123 as a new, bacterial blight S gene.\n\nAuthor SummaryThe ability of most Xanthomonas plant pathogenic bacteria to infect their hosts relies on the action of a specific family of proteins called TAL effectors, which are transcriptional activators injected into the plant by the bacteria. TAL effectors enter the plant cell nucleus and bind to the promoters of specific plant genes. Genes that when induced can benefit pathogen multiplication or disease development are called susceptibility (S) genes. Here, we perform a comparative analysis of the TAL effector repertoires of three strains of X. oryzae pv. oryzae, which causes bacterial leaf blight of rice, a major yield constraint in this staple crop. Using sequencing of entire genomes, we compared the large repertoires of TAL effectors in three African Xoo strains which form a genetic lineage distinct from Asian strains. We assessed the individual contribution to pathogen virulence of 13 TAL effector variants represented in the three strains, and identified one that makes a major contribution. By combining host transcriptome profiling and TAL effector binding sites prediction, we identified two targets of this TAL effector that function as S genes, one previously identified, and one, new S gene. We validated the new S gene by functional characterization using designer TAL effectors. Both S genes encode transcription factors and can therefore be considered as susceptibility hubs for pathogen manipulation of the host transcriptome. Our results provide new insights into the diversified strategies underlying the roles of TAL effectors in promoting plant disease.

plant biology↗

bioRxiv2018

Efficient enrichment cloning of TAL effector genes from Xanthomonas

Many plant-pathogenic xanthomonads use a type III secretion system to translocate Transcription Activator-Like (TAL) effectors into eukaryotic host cells where they act as transcription factors. Target genes are induced upon binding of a TAL effector to double-stranded DNA in a sequence-specific manner. DNA binding is governed by a highly repetitive protein domain, which consists of an array of nearly identical repeats of ca. 102 base pairs. Many species and pathovars of Xanthomonas, including pathogens of rice, cereals, cassava, citrus and cotton, encode multiple TAL effectors in their genomes. Some of the TAL effectors have been shown to act as key pathogenicity factors, which induce the expression of susceptibility genes to the benefit of the pathogen. However, due to the repetitive character and the presence of multiple gene copies, high-throughput cloning of TAL effector genes remains a challenge. In order to isolate complete TAL effector gene repertoires, we developed an enrichment cloning strategy based on O_LIgenome-informed in silico optimization of restriction digestions,\nC_LIO_LIselective restriction digestion of genomic DNA, and\nC_LIO_LIsize fractionation of DNA fragments.\nC_LI Our rapid, cheap and powerful method allows efficient cloning of TAL effector genes from xanthomonads, as demonstrated for two rice-pathogenic strains of Xanthomonas oryzae from Africa.\n\nMETHOD NAMETAL fishing

microbiology↗