Genetic Diversity and Evolutionary Relationships of Faba Bean Necrotic Yellows Virus in Lentil and Chickpea from Western Iran

Articles in Press

Document Type : Research Article

Authors

1 Department of Plant Protection, SR. C., Islamic Azad University, Tehran, P.O. Box 1451-5775, Iran

2 Department of Plant Virus Research, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran

3 Foulad Institute Technology, Fouladshahr, Isfahan, Iran

Abstract

Faba bean necrotic yellows virus (FBNYV, genus Nanovirus, family Nanoviridae) is an economically important nanovirus associated with severe yellowing disease in chickpea (Cicer arietinum L.) and lentil (Lens culinaris Medik). In this study, we determined the complete genome sequences of six Iranian FBNYV isolates collected from chickpea and lentil fields in western Iran. The genetic distance, genetic differentiation, gene flow and selection pressure of the Iranian populations, which studied, and global populations of this virus were also analyzed, using population genetic and statistical approaches. Pairwise sequence comparisons revealed that the Iranian isolates shared the highest nucleotide identity with the isolates from Azerbaijan. Phylogenetic analyses, which were based on full-length genome sequences, confirmed a close relationship between the Iranian isolates and Azerbaijani FBNYV isolate [AZ; Lahic12]. The isolates clustered according to geographical origin rather than host species. To investigate evolutionary forces shaping FBNYV diversity, isolates were divided into three geographical populations. The Caspian Sea population (Iran and Azerbaijan) exhibited higher genetic diversity compared to Mediterranean populations (Syria/Egypt and Tunisia/Morocco/Spain). Selection pressure analysis indicated that, except for DNA-C (encoding the C-link protein), all genomic components were under purifying (negative) selection, suggesting functional constraints and coordinated genome evolution. The DNA-C component showed an evidence of positive selection. Gene flow analysis (Fst) revealed limited genetic exchange among the three populations, which indicated significant population differentiation. Neutrality tests suggested possible population expansion events, although results were not statistically significant. Overall, our findings suggest that FBNYV populations may share a common geographical origin but have evolved independently in distinct regions, with founder effects contributing to their current genetic structure.

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References

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Available Online from 17 July 2026

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