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International audience; In Guadeloupe, a French overseas territory located in the Eastern Caribbean, infectious and non-infectious diseases, loss of biodiversity, natural disasters and global change threaten the health and well-being of animals, plants, and people. Implementing the “One Health” (OH) approach is crucial to reduce the archipelago's vulnerability to these health threats. However, OH remains underdeveloped in Guadeloupe, hampering efficient and effective intersectoral and transdisciplinary collaborations for disease surveillance and control. A multidisciplinary research group of volunteer researchers working in Guadeloupe, with collective expertise in infectious diseases, undertook a study to identify key attributes for OH operationalization by reviewing past and current local collaborative health initiatives and analyzing how much they mobilized the OH framework. The research group developed and applied an operational OH framework to assess critically collaborative initiatives addressing local health issues. Based on a literature review, a set of 13 opinion-based key criteria was defined. The criteria and associated scoring were measured through semi-directed interviews guided by a questionnaire to critically evaluate four initiatives in animal, human, plant, and environmental health research and epidemiological surveillance. Gaps, levers, and prospects were identified that will help health communities in Guadeloupe envision how to implement the OH approach to better address local health challenges. The methodology is simple, generic, and pragmatic and relies on existing resources. It can be transposed and adapted to other contexts to improve effectiveness and efficiency of OH initiatives, based on lessons-learned of local past or current multi-interdisciplinary and intersectoral initiatives.

International audience; Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene ( R1 ) of brinjal eggplant ( Solanum melongena ) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena , whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum , the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum .

Endogenous viral elements (EVEs) are widespread in plant genomes. They result from the random integration of viral sequences into host plant genomes by horizontal DNA transfer and have the potential to alter host gene expression. We performed a large-scale search for co-transcripts including caulimovirid and plant sequences in 1,678 plant and 230 algal species and characterized 50 co-transcripts in 45 distinct plant species belonging to lycophytes, ferns, gymnosperms and angiosperms. We found that insertion of badnavirus EVEs along with Ty-1 copia mobile elements occurred into a late blight resistance gene (R1) of brinjal eggplant (Solanum melongena) and wild relatives in genus Solanum and disrupted R1 orthologs. EVEs of two previously unreported badnaviruses were identified in the genome of S. melongena, whereas EVEs from an additional novel badnavirus were identified in the genome of S. aethiopicum, the cultivated scarlet eggplant. Insertion of these viruses in the ancestral lineages of the direct wild relatives of the eggplant would have occurred during the last 3 Myr, further supporting the distinctiveness of the group of the eggplant within the giant genus Solanum.

International audience

International audience; The family Geminiviridae contains viruses with single-stranded DNA genomes that have been found infecting a wide variety of angiosperm species. The discovery within the last 25 years of endogenous geminivirus-like (EGV) elements within the nuclear genomes of several angiosperms has raised questions relating to the pervasiveness of EGVs and their impacts on host biology. Only a few EGVs have currently been characterized and it remains unclear whether any of these have influenced, or are currently influencing, the evolutionary fitness of their hosts. We therefore undertook a large-scale search for evidence of EGVs within 134 genome and 797 transcriptome sequences of green plant species. We detected homologues of geminivirus replication-associated protein (Rep) genes in forty-two angiosperm species, including two monocots, thirty-nine dicots, and one ANITA-grade basal angiosperm species (Amborella trichopoda). While EGVs were present in the members of many different plant orders, they were particularly common within the large and diverse order, Ericales, with the highest copy numbers of EGVs being found in two varieties of tea plant (Camellia sinensis). Phylogenetic and clustering analyses revealed multiple highly divergent previously unknown geminivirus Rep lineages, two of which occur in C.sinensis alone. We find that some of the Camellia EGVs are likely transcriptionally active, sometimes co-transcribed with the same host genes across several Camellia species. Overall, our analyses expand the known breadths of both geminivirus diversity and geminivirus host ranges, and strengthens support for the hypothesis that EGVs impact the biology of their hosts.

International audience; Endogenous viral elements (EVEs) are viral sequences that were captured in the genomes of their hosts through active or passive horizontal gene transfer (HGT). In plants, most characterized EVEs originate from viruses in the family Caulimoviridae. EVEs from a yet unknown genus in the family Caulimoviridae were discovered recently and found to be distributed widely in almost all tracheophytes spanning ferns, gymnosperms and angiosperms. This new genus was named Florendovirus and there is so far no evidence that any of its member still exists under an infectious form.The potential role of florendovirus EVEs in plant biology was investigated using a transcriptomic-based approach. A systematic search for transcripts containing florendovirus coat protein, movement protein, reverse transcriptase or RNAse H domain and host plant domains was performed on a total of 973 assembled transcriptomes originating from algae, ferns, club mosses, gymnosperms, monocots and dicots, using an annotation pipeline based on tblastx. Fused transcripts containing viral and host plant domains were found in 390 plant species, providing evidence that florendovirus genes are co-transcribed with host genes, including several genes involved in plant defense mechanisms. The results of these analyses will be presented and their implication on our understanding of the roles of florendovirus in plant.

Edible banana arose from combinations of species Musa acuminata, whose genome is denoted A, and M. balbisiana, whose genome is denoted B. The nuclear genome of all known diploid BB genitors harbors infectious alleles of endogenous Banana streak viruses (eBSV). Their activation by abiotic stresses leads to spontaneous infections by cognate viruses in diploid AB, triploid AAB and tetraploid AAAB interspecific hybrids. Banana streak viruses are naturally transmitted by several species of mealybug. A comprehensive risk assessment study of the activation of infectious eBSV alleles was undertaken in Guadeloupe. Firstly, a large scale prevalence survey was carried out for viral species BSOLV, BSGFV and BSIMV among the main cultivated banana types. Overall prevalence levels were low for BSOLV (0.85%) and BSGFV (0.99%). No sample was found infected by BSIMV. No impact of BSV in infected plants could be observed, with only one infected sample displaying typical BSV leaf streak symptoms. The comparison of prevalence levels monitored in AAB genotypes and in AAA genotypes suggests that BSOLV and BSGFV infections in AAB genotypes result preferentially from the activation of eBSV infectious alleles rather than from vector-borne transmission. Statistical analyses showed a positive correlation between prevalence levels and altitude. Secondly, the activation of eBSOLV and eBSGFV infectious alleles was monitored under field conditions over two production cycles in triploid plantains French Clair (AAB genotype) and Pelipita (ABB genotype), using a random block assay and plants originating from either cell culture or horticultural multiplication. Activation rates were significantly higher for infectious allele GF7 than for infectious allele OL1 and also higher in French Clair than in Pelipita. Results pointed to an influence of the mode of production of planting material on activation, and to an absence of impact of BSGFV and BSOLV infection on production.

Endogenous viral elements (EVE) can be used as 'fossil records' to reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. Most of the EVEs that have been characterized so far belong to family Caulimoviridae. However the first plant EVEs to be discovered were geminivirus derived sequences in the nuclear genomes of various Nicotiana species. Since then, endogenous geminivirus-like elements (EGV) have also been identified in the genomes of several plants, including yam (several Dioscorea species), apple (Malus domestica), lettuce (Lactuca sativa), cottonwood (Populus trichocarpa) and coffee (Coffea canephora). We therefore search for evidence of EGVs within 134 plant genome sequences and 797 plant transcriptome sequences. We detected homologues of geminivirus replication-associated protein (rep) genes from 17 genomes and 39 transcriptomes from angiosperms. Copy numbers of EGVs within these genomes varied widely with the highest copy numbers, approximately 1000, being found in two varieties of tea (Camellia sinensis). Phylogenetic and similarity-based analyses revealed multiple taxonomically novel geminivirus lineages, including two in Camellia species which might represent novel genera. We found that some of the Camellia and Dioscorea EGVs are transcriptionally active, and display evidence of purifying selection, suggesting that expressed geminivirus proteins were, and may still be, functionally active in certain host plants. Collectively our analysis expands the known breadth of past geminivirus diversity, provides a first large-scale view of EGV prevalence, and strengthens support for the hypothesis that EGVs impact the biology of their hosts.

Banana streak viruses (BSV) are mealybug-transmitted badnaviruses. The genomes of interspecific banana varieties, including plantains, harbor infectious alleles of endogenous BSV sequences (eBSV), whose activation by abiotic stresses leads to spontaneous BSV infections. In Guadeloupe, activation of infectious alleles OL1 and GF7 is the main source of infections by BSOLV and BSGFV, respectively, in banana interspecific varieties, including widely cultivated French Clair plantain. The first multi-site survey of the activation of eBSV infectious alleles is being carried out in Guadeloupe. It focuses on infectious alleles OL1 and GF7. Nine experimental plots with 222 to 376 French Clair plants each were designed and deployed throughout Guadeloupe's south Basse Terre area at altitudes ranging from 15 to 300m. Planting material originated from two batches of vitroplants. Activation of OL1 and GF7 infectious alleles are monitored by immuno capture PCR (IC-PCR), using a polyclonal antiserum and BSOLV- or BSGFV-specific primers. Indexings were performed on vitroplants at the end of the weaning stage, prior to planting, on a 1:10 sampling. They showed that cell culture resulted in 12% and 15% activation levels for OL1 infectious allele for each batch of vitroplants, respectively. Activation levels of infectious allele GF7 was only 1% for both batches. These results confirm previous observations made on other AAB plantains. Indexings were also performed on all plants of the nine plots at the end the flowering stage. Activation levels varied between plots, from 0.3 to 6% for infectious allele OL1, and from 0% to 3% for infectious allele GF7. Overall, only one infected plant displayed leaf symptoms and no visible impact of BSV infections on plant growth and fruit production was noted. Activation rates will be monitored again at the end (flowering stage) of the second cycle. This experiment helps formulating a BSV risk management strategy.

Endogenous viral elements (EVEs) are viral sequences that are integrated in the nuclear genomes of their hosts and are signatures of viral infections that may have occurred millions of years ago. The study of EVEs, coined paleovirology, provides important insights into virus evolution. The Caulimoviridae is the most common group of EVEs in plants, although their presence has often been overlooked in plant genome studies. We have refined methods for the identification of caulimovirid EVEs and interrogated the genomes of a broad diversity of plant taxa, from algae to advanced flowering plants. Evidence is provided that almost every vascular plant (tracheophyte), including the most primitive taxa (clubmosses, ferns and gymnosperms) contains caulimovirid EVEs, many of which represent previously unrecognized evolutionary branches. In angiosperms, EVEs from at least one and as many as five different caulimovirid genera were frequently detected, and florendoviruses were the most widely distributed, followed by petuviruses. From the analysis of the distribution of different caulimovirid genera within different plant species, we propose a working evolutionary scenario in which this family of viruses emerged at latest during Devonian era (approx. 320 million years ago) followed by vertical transmission and by several cross-division host swaps.