<strong>SafePGR: how to limit the risk of spreading viral diseases through the exchange of tropical plant germplasm</strong> <em> Deciphering viral diversity in conserved tropical plant germplasm and refining diagnostic tools</em> Biological Resources Centres (BRCs) conserve and distribute plant germplasm for research and development purposes. They provide breeding programs with genitors that are critical for crop adaptation to ongoing environmental and societal changes. In order to prevent the spread or emergence of diseases, BRCs must guarantee the sanitary status of the resources they distribute. Guadeloupe, Madeira, Azores and Reunion BRCs conserve banana and plantain, sugarcane, yam, sweet potato, garlic and vanilla germplasm. These crops are vegetatively propagated and are prone to the accumulation of viruses, due to the lack of sexual reproduction, which would act as a natural sanitation process since most plant viruses are not seed transmitted. Our knowledge of the viruses infecting these crops is also only partial. Sanitation methods exist for recovering virus-free plants but they require sensitive, polyvalent and reliable diagnosis tests. The general objective of the SafePGR project was to improve the knowledge of the diversity of viruses infecting the crops addressed by the partner’s BRCs, in order to develop or optimize diagnostic techniques, ultimately permitting the safe movement of plants between project partners and beyond. <em>Combining classical molecular biology and next generation sequencing approaches to explore viral diversity</em> To reach its objective, the project combines classical molecular biology and next generation sequencing (NGS) approaches, leading to unprecedented virus discovery in the targeted crops. The NGS-based approaches have the advantage of not assuming any prior information and of therefore very broadly targeting viral genomes, even in the case of novel agents. These NGS-based approaches (so-called metagenomics approaches) are based on random screens of the plant viromes. Because they allow detecting viruses that would have escaped classical detection methods that use known viral sequences as targets, these approaches are complementary to the traditional PCR-based approaches that are widely used in forensics and diagnostics. The innovative approaches developed in the SafePGR project have enabled unprecedented virus discovery in the target crops, from which specific primers were further designed, leading in fine to a systematic, optimized and efficient screening of the plants maintained in the partners BRCs. <em>Beneath the tip of the iceberg: the hidden viral diversity of the conserved tropical plant germplasm</em> A total of 21 new virus species were discovered and their molecular diversity was explored. This led to the establishment of diagnosis methods for these new agents as well as to the optimization of diagnosis for 10 already known viruses. This allowed improving the knowledge of viral status of the germplasm collections. The teams have now a good basis to determine their sanitation and diagnostic strategies, and to revive the associated processes. The results are now transferred on yam collection in Guadeloupe, and are irrigating a project of a quality seed production sector, with economic actors. <em>Scientific production and patents since the beginning of the projects</em> Four papers and one book chapter have been accepted in peer-review journals, concerning virus discovery, and metagenomics. About 6 other are in preparation. This is an important contribution in the field of virology, and plant metagenomics. The complete genome sequences of 8 identified viruses have been integrated in GenBank, including 7 full genome sequences of Sugarcane white streak virus and one full genome sequence of Yam virus X. In addition, 16 partial sequence of Yam virus X RNA-dependent RNA polymerase gene were deposited in GenBank. New and optimized diagnostic protocols are available in the project website, http://www2.antilles.inra.fr/safepgr/ A pipeline has been adapted for bioinformatic analyses, and may be transferred to teams working on similar data sets.Read less <