Phylogenetic analysis based on full genome sequencing of Italian tomato spotted wilt virus isolates identified in “Roggianese” sweet pepper and chilli pepper

Abstract

A study aimed at defining population structure of Italian tomato spotted wilt virus (TSWV) isolates was performed. Full genome sequencing of six TSWV isolates found in two Italian regions (two from Latium: Lazio 17 and Tarquinia; and four from Calabria: PepCal 10, 12, 22 and 24) were assembled. Identity percentages in nucleotide sequence among these TSWV isolates are here provided. The six full length genome sequences were compared with other two Italian isolates (p105 and p202/3WT) already fully sequenced, as well as full TSWV genomes that could be retrieved from GenBank. Phylogenetic analysis, performed in concatenated sequences and for each gene of each genome segment (L, M and S), confirmed the presence of two clades, namely A‐like and D‐like. In particular, the phylogenetic tree based on segment L grouped all the newly sequenced TSWV isolates in D‐like clade. In the M segment phylogenetic tree, all our TSWV isolates shifted in the A‐like clade. Isolates separation was not correlated to their geographical origin in phylogenetic study of distinct ORFs encoded by the RNA S segment. In fact, in nucleocapsid‐encoding phylogenetic tree, PepCal 10 and 22 grouped in an A‐like clade with p105, PepCal 12 and 24 in a D‐like clade with p202/3WT, whereas Lazio 17 and Tarquinia in a third well distinct group. NSs tree displayed only PepCal 10 with p105 in A‐like clade, whereas PepCal 12, 22, 24 with p202/3WT in D‐like subclade; and isolates from Latium grouped a separated clade adjacent to D‐like isolates. Additional analysis on putative reassortment events showed that TSWV Calabrian isolates likely originated from a reassortment event in M RNA and other in S RNA with p105 as major parent. Recombination events were detected in isolates from Latium in L and S RNAs with Chinese isolates as putative major parent.