Phylogenetic and population analysis of African Cassava mosaic virus (ACMV) isolates from Cross River State based on the coat protein gene

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African cassava mosaic virus (ACMV) is among the most economically significant begomoviruses affecting cassava (Manihot esculenta Crantz) production in sub-Saharan Africa, however its molecular population dynamics in Cross River State (CRS), Nigeria, have remained poorly characterized. This study presents the phylogenetic and population genetic analysis of cassava begomoviruses ACMV DNA-A isolates from CRS, based on coat protein (CP) gene sequences of 44 begomovirus isolates drawn from five geographic populations namely East/South Africa, Nigeria, Asia, West Africa, and CRS. Sequence alignment was performed using the MUSCLE algorithm in Bioedit, phylogenetic reconstruction was conducted in MEGA 12 under the General Time Reversible model with 1000 bootstrap replicates, and population genetic parameters were estimated using DnaSP v6.01. Phylogenetic analysis placed all three CRS isolates (CRS-P1, CRS-P2, CRS-P3) within the West African clade, with CRS-P1 and CRS-P3 clustering within a Nigerian–Ghanaian subgroup and CRS-P2 forming a distinct Nigerian–Togolese lineage, ruling out Asian or southern/central African origins. The CRS population exhibited the lowest nucleotide diversity (? = 0.010) and the strongest purifying selection (dN/dS = 0.03) across all populations, with only 9 segregating sites among three unique haplotypes. Due to a limited number of segregating sites, neutrality tests could not be performed for the CRS population. In contrast, the remaining populations exhibited significantly negative Tajima’s D statistics, a pattern indicative of either a historical population expansion or the effects of purifying selection. Population differentiation analysis showed that the CRS sequences were significantly differentiated from Asian (Snn = 0.9000), East/South African (Snn = 0.7728), and Nigerian (Snn = 0.4792) populations, but not from West African populations. This suggests possible shared ancestry or ongoing regional gene flow between the CRS and West African populations.These findings indicate the CRS sequences harbors a genetically uniform and highly conserved ACMV lineage of West African origin, with important implications for disease surveillance and resistance breeding in Nigeria.