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

Abstract

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, η, k, and π 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 Tajima's D for clade 2 of the TGB. The results of the K<sub>s</sub>*, K<sub>st</sub>*, Z*, and Snn tests suggested that all three phylogroups were divergent to each other for both TGB and CP. The high F<sub>st</sub> on all the clade comparisons for both TGB and CP showed a large gene flow among three clades.

Molecular Analysis of the Global Population of Potato Virus S Redefines Its Phylogeny, and Has Crop Biosecurity Implications

“…Thus, when sequences from other genomic regions are absent, the CP gene can still be used to represent PVS phylogeny. Other members of genus Carlavirus (potato virus M (PVM) [ 53 ] and garlic common latent virus (GCLV) [ 54 ]) also experience a strong negative evolutionary constraint on the CP. Thus, data obtained in this study could also contribute to other evolutionary studies of the genus Carlavirus .…”

Ageratum yellow vein alphasatellite and tomato leaf curl Java betasatellite association with begomoviruses infecting crops and weeds in Indonesia

“…The fixation index (FST) value could be between 0 for panmixia and 1 for fully distinct populations (Hudson et al 1992). Therefore, F ST value > 0.33 usually suggests a rare gene flow and expanding genetic separation among tested populations (Santosa & Ertunç 2021). Plant Protection Science, 59, 2023 (4): 317-324 https://doi.org/10.17221/16/2023-PPS…”

Potato Virus Y and Shallot Latent Virus of Kajoran Horticultural Production Center, Magelang Regency, Indonesia: Molecular Characterization Case Study

“…Its ssRNA genome consists of six ORFs, the CP is encoded by ORF5 (Wang et al, 2018;Li et al, 2023). In the absence of complete genome sequence, the phylogeny of Potyvirus and Carlavirus usually can be constructed using CP sequences, which is the most conserved aspect in the respective genomes (Gibbs and Ohshima, 2010;Santosa and Ertunc, 2021).…”