Genome sequencing of Paris polyphylla var. yunnanensis

To characterize genome size evolution in 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 Hi-C interaction heatmap 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 WGDs since its divergence with V. dahuricum. The gene family analysis showed 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.