Phylogenetic and diversity analyses of Garlic common latent virus based on the TGB and CP gene sequence

Garlic common latent virus (GarCLV, Carlavirus), in co-infection, often worsens the severity of other Allium viruses on the garlic (Allium sativum Linnaeus). The nucleotide (nt) and amino acid (aa) sequences of the TGB and CP genes were analysed to get the first deep insight into the genomic variations and population structure of GarCLV. Global recombinant-free isolates were clustered into three clades in both the nt-based phylogenetic trees of TGB and CP. The clade 3 isolates shared low similarity percentages among themselves, as well as to the clade 1 and 2 isolates. Most major aa changes in the CP were observed on its 5' and 3' ends. Clade 2 obtained the lowest S, eta, k, and TE values for both the TGB and CP, which indicated low variations among its isolates. Both TGB and CP have undergone a negative selection, with CP being under stronger negative pressure than TGB. Neutrality tests estimated the non-significant negative values to all clades for TGB and CP, except Tajimas D for clade 2 of the TGB. The results of the Ks*, Kst*, Z*, and Snn tests suggested that all three phylogroups were divergent to each other for both TGB and CP. The high Fst on all the clade comparisons for both TGB and CP showed a large gene flow among three clades.

Automated summary

GarCLV exhibits genetic diversity with three distinct clades identified based on the nucleotide and amino acid sequences of the TGB and CP genes. Clade 2 shows the lowest variability and most major amino acid changes are found in the CP gene at its 5' and 3' ends. Neutrality tests suggest that all clades are divergent from each other, with high gene flow observed among them.