Investigation of phylogenetic relationships and genetic structure of Iranian isolates of Cotton leaf curl Gezira virus

Document Type : Research Paper

Authors

1 1- Department of Plant Protection, Faculty of Agriculture, Agricultural Sciences and Natural Resources University of Khuzestan, Mollasani, Iran.

2 1- Department of Agriculture, Minab Higher Education Center, University of Hormozgan, Bandar Abbas, Iran.

3 Agricultural Engineering Department, Minab Higher Education center, University of Hormozgan, Bandar abbas.

10.22092/ijcr.2024.367077.1226

Abstract

Background and objectives: Cotton leaf curl Gezira virus (CLCuGeV) is a significant pathogen that annually reduces cotton yields in regions where the crop is cultivated. The virus genome consists of a single-stranded circular DNA, encapsidated as a 2.8-kilobase segment in twin particles. It contains six genes, two of which are located on the virion strand (V1 and V2), and four on the complementary strand (C1–C4). This study aims to investigate the phylogenetic relationships among Iranian isolates of CLCuGeV, reported from different hosts and geographical locations, as well as to analyze the genetic structure of the virus population by examining nucleotide polymorphisms within the complete genome of these isolates.
 
Materials and methods: Eight nucleotide sequences of Iranian CLCuGeV isolates were extracted from the GenBank database and analyzed. Sequence alignment was performed followed by the construction of a phylogenetic tree. Nucleotide polymorphism analysis was conducted to identify insertion-deletion polymorphisms (InDels) among the sequences. Additionally, non-synonymous (dN) and synonymous (dS) substitution rates, along with the dN/dS ratio, were calculated to assess the natural selection pressure on the nucleotide sequences.
 
Results: Phylogenetic analysis revealed that the Iranian CLCuGeV isolates clustered according to their host and geographical origin. Nucleotide polymorphism analysis identified eight haplotypes, with 247 polymorphic loci. Haplotype and nucleotide diversity were calculated as 1 and 0.03633, respectively, while the average number of nucleotide differences was 99.429. No InDel polymorphism was observed among the sequences, and the dN/dS ratio was -0.08779, indicating negative selection pressure. Furthermore, nine recombination events were detected at various nucleotide positions.
 
Conclusion: The findings suggest that genetic variability in the genome sequences of Iranian CLCuGeV isolates may influence key viral processes such as transcription, replication, and pathogenicity. This genomic diversity could potentially expand the virus’s host range in the future or enable the virus to overcome resistance in current cotton cultivars.

Keywords

Main Subjects

References

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Iranian Journal of Cotton Researches
Volume 12, Issue 1 - Serial Number 20
September 2024
Pages 29-40

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