A Novel Method to Classify and Study Chickpea Chlorotic Dwarf Virus (CpCDV) Strains Based on Evolutionary Diversity and Cis-Regulatory Elements (CRE)

Chickpea chlorotic dwarf virus (CpCDV) is a primary virus belonging to the Mastrevirus genus that infects dicotyledonous crops like chickpeas and cotton. The current study investigates the evolutionary and regulatory activities of CpCDV strains utilising phylogenetic and recombination analysis. The objective of this research is to uncover a potential Cis-regulatory element (CRE) that will allow us to classify different strains based on the functions they govern in various plant parts. NCBI provided 268 full-length sequences of the CpCDV genome, and the Sequence Demarcation Tool generated the homology graph. Only 36 sequences were used, with homology ranging from 94% to 100%. Phylogenetic analysis utilising the neighbour-joining method revealed the various strains in clades and their surrounding strains. Recombination analysis identified strain CpCDV21 as the potential major parental strain involved in evolutionary and recombination events, along with 11 other recombinant variants. These analyses helped to predict the genomic modelling, divergence, and rate of exchange. Furthermore, CRE analysis identified the distinct strains that are linked to various categorical elements, such as hormone-responsive strains CpCDV17 and CpCDV20, which are dominantly present in the Sudan region and control major HREs, such as ABRE and TGACG. The stress-responsive elements, such as WUN motifs and MYB, are dominant in the promoter region of strain CpCDV13 that originated in Burkina Faso. Other stress-responsive elements, such as WRE3, STRE and light-responsive, including GT1 and G-box, while tissue-specific O2-site element present in major amounts. Such elements are crucial not only for plant growth and development but also for defence. CpCDV strains employ these elements to control the genomic machinery and therefore regulate plant function. These findings improve our knowledge of CpCDV's cis-regulatory components, recombination patterns, and genetic composition. In the future, this information can be used to develop resistance and improve crop quality through a CRE-mediated strategy.