Two Melanthiaceae genomes with dramatic size difference provide insights into giant genome evolution and maintenance

To characterize genome size evolution in the Melanthiaceae family, we sequenced the genomes of Paris polyphylla var. yunnanensis (54.58 Gb/1C) and Veratrum dahuricum (Turcz.) O. Loes. (3.93 Gb/1C). Using a hierarchical bottom-up chromosome assembly strategy, we successfully assembled the five giant chromosomes of P. polyphylla, with the largest chromosome reaching 14.14 Gb. We observed widespread secondary diagonal signals in a Hi-C interaction heat map of P. polyphylla, which suggests a higher-order helical structure (with ~250 Mb per turn) of interphase chromatin. Our genome assemblies reveal that P. polyphylla has not undergone recent whole-genome duplications since its divergence from V. dahuricum. Gene family analysis showed that the five DNA repair pathways are all significantly enriched in the expanded gene families in P. polyphylla. Our results not only report a giant, high-quality plant genome, but also reveal how giant chromosomes evolved and were retained.