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Comparative genomic analyses reveal different genetic basis of two types of fruit in Maloideae

Author

Listed:
  • Yi Wang

    (Shenyang Agricultural University
    Chinese Academy of Sciences)

  • Hongju Hu

    (Hubei Academy of Agricultural Sciences)

  • Juntong Jin

    (Shenyang Agricultural University)

  • Hui Yuan

    (Shenyang Agricultural University)

  • Jingguo Zhang

    (Hubei Academy of Agricultural Sciences)

  • Yuqing Wang

    (Shenyang Agricultural University)

  • Mingqian Wang

    (Shenyang Agricultural University)

  • Shaobo Yin

    (Shenyang Agricultural University)

  • Jiaming Zhao

    (Shenyang Agricultural University)

  • Shijiao Lin

    (Shenyang Agricultural University)

  • Yuling Liang

    (Shenyang Agricultural University)

  • Jiayao Wang

    (Shenyang Agricultural University)

  • Shipeng Wei

    (Shenyang Agricultural University)

  • Weiting Liu

    (Shenyang Agricultural University)

  • Bin Li

    (Shenyang Agricultural University)

  • Yinglin Ji

    (Shenyang Agricultural University)

  • Aide Wang

    (Shenyang Agricultural University)

Abstract

Fleshy fruits are classified as ethylene-dependent or ethylene-independent according to the ethylene climacteric at the onset of ripening. However, the mechanism forming these two types of fruits is unclear. Pears (Pyrus spp.) contain the both types, thus can serve as a model system to answer this question. Here, we assemble haplotype-resolved and chromosome-level genomes for ethylene-dependent and ethylene-independent accessions, and re-sequence 118 pear accessions. Two long noncoding RNAs named Ethylene Inhibiting Factor 1 (EIF1) and EIF2 are identified, which suppress the transcription of ethylene biosynthesis gene ACS1 and ethylene biosynthesis, generating ethylene-independent fruit. Comparative genomic analyses reveal that allele-specific structural variations result in the loss of EIF1 and/or EIF2, removing the suppression on ACS1 transcription and generating ethylene-dependent fruit. Further study reveals that, in most common fleshy fruits of Maloideae, EIF homologue exits in ethylene-independent pear and loquat and is transcribed; while in ethylene-dependent apple and hawthorn, EIF homologue does not exist in their genomes.

Suggested Citation

  • Yi Wang & Hongju Hu & Juntong Jin & Hui Yuan & Jingguo Zhang & Yuqing Wang & Mingqian Wang & Shaobo Yin & Jiaming Zhao & Shijiao Lin & Yuling Liang & Jiayao Wang & Shipeng Wei & Weiting Liu & Bin Li &, 2025. "Comparative genomic analyses reveal different genetic basis of two types of fruit in Maloideae," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62850-3
    DOI: 10.1038/s41467-025-62850-3
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    References listed on IDEAS

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    1. Liyi Zhang & Jiang Hu & Xiaolei Han & Jingjing Li & Yuan Gao & Christopher M. Richards & Caixia Zhang & Yi Tian & Guiming Liu & Hera Gul & Dajiang Wang & Yu Tian & Chuanxin Yang & Minghui Meng & Gaope, 2019. "A high-quality apple genome assembly reveals the association of a retrotransposon and red fruit colour," Nature Communications, Nature, vol. 10(1), pages 1-13, December.
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