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Background  Cassava is an important food crop in tropical and sub-tropical regions worldwide. In Africa, cassava production is widely affected by cassava mosaic disease (CMD), which is caused by the African cassava mosaic geminivirus that is transmitted by whiteflies. Cassava breeders often use a single locus,  CMD2 , for introducing CMD resistance into susceptible cultivars. The  CMD2  locus has been genetically mapped to a 10-Mbp region, but its organization and genes as well as their functions are unknown.    Results  We report haplotype-resolved de novo assemblies and annotations of the genomes for the African cassava cultivar TME (tropical  Manihot esculenta ), which is the origin of  CMD2 , and the CMD-susceptible cultivar 60444. The assemblies provide phased haplotype information for over 80% of the genomes. Haplotype comparison identified novel features previously hidden in collapsed and fragmented cassava genomes, including thousands of allelic variants, inter-haplotype diversity in coding regions, and patterns of diversification through allele-specific expression. Reconstruction of the  CMD2  locus revealed a highly complex region with nearly identical gene sets but limited microsynteny between the two cultivars.    Conclusions  The genome maps of the  CMD2  locus in both 60444 and TME3, together with the newly annotated genes, will help the identification of the causal genetic basis of  CMD2  resistance to geminiviruses. Our de novo cassava genome assemblies will also facilitate genetic mapping approaches to narrow the large  CMD2  region to a few candidate genes for better informed strategies to develop robust geminivirus resistance in susceptible cassava cultivars.    Electronic supplementary material  The online version of this article (10.1186/s12915-019-0697-6) contains supplementary material, which is available to authorized users.

Haplotype-resolved genomes of geminivirus-resistant and geminivirus-susceptible African cassava cultivars