Fig. 1

Assembly of the B73-Ab10 genome. a Whole-genome view. For each chromosome, the top to bottom tracks are gene density, Cinful-Zeon retrotransposon density, Gypsy superfamily retrotransposon density in 10 Kb sliding windows, repeat location (knob180 in blue, TR-1 in red, 45S rDNA in teal, CentC in magenta), and the distribution of gapless contigs. CENH3 ChIP-seq peaks identifying centromeres are marked by orange rectangles. The inset shows the centromere on chromosome 3, TR-1-rich knob on chromosome 4, and knob180-rich knob on chromosome 7. The five most common retroelement families are shown for each panel, along with centromeric retrotransposons (CRM) for the centromere. CENH3 enrichment in chromosome 3 is displayed in a heatmap. b The impact of assembly merging over a CentC-rich region on chromosome 9. Seven contigs (orange, above) from the PacBio assembly were originally misassembled, as can be seen in the alignment to the Bionano map (connecting lines show matching sites). CentC tracts and gaps are annotated. Assembly merging corrected the output, leaving an 11-Kb gap that was filled with nanopore reads. c Sequence alignment between normal chromosome 10 from B73 (N10) (140–152 Mb) and Ab10 (140–195 Mb) from B73-Ab10. Annotation is as in a, with Kindr genes marked with black bars in the top track. Links show homologous regions larger than 500 bp