Fig. 1: D. alata genome structure and recombination.

a HiC contact matrix of TDa95/00328 chromosomes 4 and 5. Within chromosomes, the band of high contact density along the diagonal reflects the well-ordered underlying assembly. The checkerboard pattern observed between 75 and 85 Mb indicates chromatin domain A/B compartmentalization¹⁵⁶ within chromosome 4. The winged pattern observed within chromosomes, particularly chromosome 5, showing elevated contact densities between chromosome ends is typical of Rabl-structured chromosomes in the nucleus²⁹. Chromosomes are outlined with cyan boxes. Each pixel represents the intersection between a pair of 50 kb loci along the chromosomes. The density of contacts between two loci is proportional to pixel color, with darker pixels representing more contacts and lighter representing fewer. b A composite genetic linkage map (black points), integrating five mapping populations (colored points, legend), is shown for chromosome 5. The maps exhibit highly concordant marker orders (Kendall’s tau correlations between 0.9091 and 0.9626) and validate the large-scale correctness of the chromosome-scale assembly. The sigmoidal shape of the maps along the physical chromosome reflects suppressed recombination within the pericentromere. Individual component maps were scaled and shifted vertically to display their marker-order concordance. c The D. alata chromosome landscape is shown. Transposable elements (TEs; tan lines, left Y-axis) are enriched within the pericentromeres; while low-complexity repeat (LCR; brown, right Y-axis), protein-coding gene (dark blue line, left Y-axis), and meiotic recombination (cyan lines, right Y-axis) densities are elevated nearer the chromosome ends. Densities were computed using 500 kb bins. Composite map marker positions are shown as black ticks under the X-axis, with A/B chromatin compartment structure drawn below (A compartment domains in gold; B domains in dark cyan). cM centiMorgan, Mb megabase. Source data are provided as a Source Data file.