Comparative genomics of diverse African isolates of Cercospora zeina

A serious factor hampering global maize production is grey leaf spot disease. Cercospora zeina is the causative pathogen in Africa, but population genomics analysis of C. zeina is lacking. The literature was reviewed for genomics-based management of African cereal crop pathogens. Whole-genome Illumina sequencing and de novo genome assembly was conducted on a representative set of 30 C. zeina isolates from Kenya and Uganda (East Africa) and Zambia, Zimbabwe and South Africa (Southern Africa). Selection of the diverse set was based on microsatellite data from a larger collection of the pathogen. Pangenome analysis of the assembled genomes and the published long-read C. zeina reference assembly (CMW25467) was done through protein clustering. This revealed 790 non-shared accessory and 10,677 shared core orthogroups (genes) between the 31 isolates. There was a significantly higher proportion of effector genes in the accessory secretome (44%) compared to the core secretome (24%). SNP analysis through PCA, ADMIXTURE, and neighbour-net network phylogeny, revealed a population structure with geographical subdivision between the East African isolates and the Southern African isolates, although gene flow was also evident. Accessory gene content was however largely shared between isolates from all countries, with few genes unique to Southern Africa (32) or East Africa (6). Selective sweep detection revealed selective sweeps in East Africa (20) and Southern Africa (24), within which were six effector genes. The small pangenome and partial population differentiation indicated recent dispersal of C. zeina into Africa, followed by recurrent gene flow owing to widespread maize production across sub-Saharan Africa.