Résumé
Botrytis cinerea stands out for having a wide host range and is qualified as generalist.Nevertheless, recent studies suggest that it actually corresponds to co-existing populationsthat show a certain level of host specialization, as described for the French populations T andG1, specialized on tomato and grapevine, respectively (Mercier et al., 2019, Env. Microbiol.21, 4808–21; Mercier et al., 2021 Phytopathology, 111,2355-66).What are the molecular determinants responsible for such host-specialization? PreviousIllumina sequencing data revealed genes under positive selection encoding cellulases,pectinases and enzymes involved in the oxidative stress response suggesting that theseactivities may contribute to the specialization on tomato. Here, using PacBio sequencing, weproduced complete assemblies and annotation of the genomes of strains Sl3 and Vv3 thatrepresent the T and G1 populations in order to identify all possible genomic correlates of hostspecialization. Both assemblies revealed 16 core chromosomes that were highly syntenic withthose of the reference strain B05.10. The main sources of variation in gene content were thesubtelomeric regions and the accessory chromosomes (ACs), especially the AC BCIN19 of Vv3that was absent in Sl3 and B05.10. The repertoires and density of transposable elements (TEs)were clearly different between the genomes of Sl3 and Vv3 with a larger number ofsubfamilies (26) and a greater genome coverage in Vv3 (7.7%) than in Sl3 (14 subfamilies, 4.5%coverage). An Helitron-like TE was found in almost all subtelomeric regions of the Vv3 genome,in particular in the flanking regions of a highly duplicated gene encoding a Telomere-LinkedHelicase, while both features were absent from the Sl3 and B05.10 genomes. Differentretrotransposons in the Sl3 and the Vv3 strains resulted in the synthesis of distinct sets ofsmall RNAs. Finally, extending the study to additional strains indicated that the AC BCIN19 andthe small RNAs producing TE Copia_4 and Gypsy_7 are common features of the G1 populationthat are scarcely if ever found in strains isolated from other populations. This research revealsthat ACs, TEs and their derived small RNAs differ between populations of B. cinerea specializedon different hosts and paves the way for further studies aiming at investigating the molecularmechanisms underpinning host specialization in a polyphagous pathogen (Simon et al.,BioRxiv, https://doi.org/10.1101/2022.03.07.483234).