FIGURE 4.

Long‐read sequencing allows assembly of complex genomic regions. (a) Coverage plot of a short‐read mapping of a male Populus individual against the (female) reference genome, showing that the genome region with the popARR17 gene exhibits suspicious sequencing coverage. This region, indicated by a red vertical bar, exhibits 1.5‐ to 2‐fold higher coverage than expected. (b) Long‐read assembly of the male‐specific sequence of the Y chromosome (MSY) reveals partial popARR17 duplicates nested within repetitive sequences, readily explaining inconsistencies in short‐read mappings. In this case the regional repeat architecture was resolved largely using ONT sequencing (Müller et al., 2020)