Ploidy, heterozygosity and the assembly graph. (a) Schematic representation of a tetraploid genome, such as apple, cotton or cabbage, consisting of haploid chromosomes A to D with homozygosity/heterozygosity shown as different colored blocks. (b) Even without repeats or sequencing error, the assembly graph of the homozygous and heterozygous segments of the genome branch and intertwine in complex patterns. A plant-specific assembler would need to recognize these branching patterns and attempt to reconstruct the individual sequences for chromosomes A to D.
Schatz et al. Genome Biology 2012 13:243 doi:10.1186/gb-2012-13-4-243