Fig. 4.

Assembly of haplophases. Diploid plant genomes have a maternal (a) and a paternal haplotype (c), which differ at specific positions (b). Long reads belong to one or the other haplotype (d). The assembly graph separates haplophases in regions with sufficient differences between both parental haplotypes, but collapses them in identical (homozygous) regions (e). Resolving the assembly graph into final sequences is possible in four different ways (f): It is possible that both haplophases are resolved by connecting the two divergent blocks correctly (1), identical regions could be assigned to one haplophase leading to a less continuous second haplophase (2 and 3), or the identical region can cause an erroneous connection of the flanking distinct sequences (4). This illustration shows the analysis of a diploid genome, but the concept is generalisable to polyploids.