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

Peng Zeng; Hang Zong; Yuwei Han; Weixiong Zhang; Zunzhe Tian; Botong Zhou; Juan He; Yongting Zhang; Xiaonan Liu; Lin Liu; Tinggan Zhou; Qiong Li; Yang Yu; Yingmei Peng; Wenbo Zhu; Simei He; Guanghui Zhang; Huifeng Jiang; Shengchao Yang; Jing Cai

doi:10.1038/s41477-025-02060-3

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

Peng Zeng, Hang Zong, Yuwei Han, Weixiong Zhang, Zunzhe Tian, Botong Zhou, Juan He, Yongting Zhang, Xiaonan Liu, Lin Liu, Tinggan Zhou, Qiong Li, Yang Yu, Yingmei Peng, Wenbo Zhu, Simei He, Guanghui Zhang, Huifeng Jiang, Shengchao Yang, Jing Cai

School of Ecology and Environment

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	1500-1513
Number of pages	14
Journal	Nature Plants
Volume	11
Issue number	8
DOIs	https://doi.org/10.1038/s41477-025-02060-3
State	Published - Aug 2025

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Zeng, P., Zong, H., Han, Y., Zhang, W., Tian, Z., Zhou, B., He, J., Zhang, Y., Liu, X., Liu, L., Zhou, T., Li, Q., Yu, Y., Peng, Y., Zhu, W., He, S., Zhang, G., Jiang, H., Yang, S., & Cai, J. (2025). Two Melanthiaceae genomes with dramatic size difference provide insights into giant genome evolution and maintenance. Nature Plants, 11(8), 1500-1513. https://doi.org/10.1038/s41477-025-02060-3

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title = "Two Melanthiaceae genomes with dramatic size difference provide insights into giant genome evolution and maintenance",

abstract = "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 \textasciitilde{}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.",

author = "Peng Zeng and Hang Zong and Yuwei Han and Weixiong Zhang and Zunzhe Tian and Botong Zhou and Juan He and Yongting Zhang and Xiaonan Liu and Lin Liu and Tinggan Zhou and Qiong Li and Yang Yu and Yingmei Peng and Wenbo Zhu and Simei He and Guanghui Zhang and Huifeng Jiang and Shengchao Yang and Jing Cai",

note = "Publisher Copyright: {\textcopyright} The Author(s), under exclusive licence to Springer Nature Limited 2025.",

year = "2025",

month = aug,

doi = "10.1038/s41477-025-02060-3",

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Zeng, P, Zong, H, Han, Y, Zhang, W, Tian, Z, Zhou, B, He, J, Zhang, Y, Liu, X, Liu, L, Zhou, T, Li, Q, Yu, Y, Peng, Y, Zhu, W, He, S, Zhang, G, Jiang, H, Yang, S & Cai, J 2025, 'Two Melanthiaceae genomes with dramatic size difference provide insights into giant genome evolution and maintenance', Nature Plants, vol. 11, no. 8, pp. 1500-1513. https://doi.org/10.1038/s41477-025-02060-3

TY - JOUR

T1 - Two Melanthiaceae genomes with dramatic size difference provide insights into giant genome evolution and maintenance

AU - Zeng, Peng

AU - Zong, Hang

AU - Han, Yuwei

AU - Zhang, Weixiong

AU - Tian, Zunzhe

AU - Zhou, Botong

AU - He, Juan

AU - Zhang, Yongting

AU - Liu, Xiaonan

AU - Liu, Lin

AU - Zhou, Tinggan

AU - Li, Qiong

AU - Yu, Yang

AU - Peng, Yingmei

AU - Zhu, Wenbo

AU - He, Simei

AU - Zhang, Guanghui

AU - Jiang, Huifeng

AU - Yang, Shengchao

AU - Cai, Jing

PY - 2025/8

Y1 - 2025/8

N2 - 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.

AB - 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.

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U2 - 10.1038/s41477-025-02060-3

DO - 10.1038/s41477-025-02060-3

M3 - 文章

AN - SCOPUS:105012387612

SN - 2055-0278

VL - 11

SP - 1500

EP - 1513

JO - Nature Plants

JF - Nature Plants

IS - 8

ER -

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

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