The following supplementary tables are included as separate sheets in a single Supplementary Tables Excel file. S1 Table.

Information on sampled carrot populations in France and Spain. S2 Table. RT-PCR and RACE primer pairs targeting known and novel viruses in the carrot virome. S3 Table. RNA-dependent RNA polymerase (RdRp) pairwise amino acid identities for carrot umbraviruses 1, 2 and 3 and selected genus Umbravirus members. S4 Table. RdRp pairwise amino acid identities for carrot poleroviruses 1 and 2, carrot enamovirus 1 and selected family Solemoviridae members. S5 Table. Geographical distribution of the various viruses identified in the carrot virome based on merged mapping of HTS data obtained from carrot populations from different regions of France and in Spain. Green squares indicate presence, red squares indicate absence of the virus in the respective locations. Novel viruses are indicated in red. S6 Table. RdRp and capsid protein (CP) pairwise amino acid identities for carrot chordoviruses 3 and 4, carrot vitivirus 1 and selected family Betaflexiviridae members. S7 Table. RdRp, heat-shock protein 70 (hsp70) and CP pairwise amino acid identities for carrot closteroviruses 2 and 3 and selected family Closteroviridae members. S8 Table. Full genome pairwise nucleotide identities and RdRp pairwise amino acid identities for carrot endornavirus 1 and selected family Endornaviridae members. S9 Table. RdRp pairwise amino acid identities for carrot reoviruses 1 and 2 and selected family Spinareoviridae members. S10 Table. RdRp pairwise amino acid identities for carrot cryptic viruses 2 and 3, dill cryptic virus 2 carrot isolate and selected family Partitiviridae members. S11 Table. RdRp fusion protein pairwise amino acid identities for Carrot_amalgaviruses 1 and 2 and selected family Amalgaviridae members. S12 Table. RdRp and CP pairwise amino acid identities for Carrot_associated_toti-like_virus and selected family Totiviridae members. S13 Table. RdRp pairwise amino acid identities for Carrot_associated_RNA_virus_1 and selected family Benyviridae members. (XLSX)