CRESS domain-based molecular characterization of Begomovirus gossypimultanense

Cotton leaf curl disease (CLCuD) is a serious threat to cotton production across the Indian subcontinent, especially in Rajasthan, Haryana, and Punjab. The disease is caused by monopartite single-stranded DNA begomoviruses along with their associated satellite DNAs. Among these viruses, Begomovirus gossypimultanense (Cotton leaf curl Multan virus; CLCuMuV) is one of the primary viruses responsible for widespread infections and significant yield losses.

Twenty-six symptomatic cotton leaf samples collected from diverse agro-ecological regions of northwestern India were screened and confirmed as CLCuMuV through molecular analyses. Given that the full-length replication-associated protein (Rep) is widely used as a representative phylogenetic marker across ssDNA viruses, we hypothesized that the conserved CRESS domain (~ 300 bp) within the Rep protein, which is functionally indispensable, could serve as an alternative molecular marker for molecular characterization of CLCuMuV. To test this hypothesis, in addition to sequences generated from field samples, a dataset of 278 publicly available CLCuMuV CRESS domain sequences retrieved from the NCBI database was assembled. Comparative phylogenetic analyses showed that both the full-length Rep and the CRESS domain resolved five major groups (Group 1-5) with consistent clustering, and tanglegram analysis demonstrated one-to-one correspondence between group compositions, indicating strong phylogenetic congruence. Population genetic analyses revealed high haplotype diversity in both regions, while neutrality and selection pressure analyses indicated predominant purifying selection, with stronger functional constraint in the CRESS domain.

Our findings demonstrate that the conserved CRESS domain within the Rep gene reliably recapitulates the phylogenetic and population genetic structure inferred from the full-length Rep protein. The strong topological congruence, high haplotype resolution, and evidence of functional constraint support the CRESS domain as a robust, reliable, and cost-effective molecular marker for epidemiological characterization and evolutionary studies of CLCuMuV.