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

• Published in: Nature communications Vol. 16; no. 1; pp. 7463 - 12
• Main Authors: Wang, Yi, Hu, Hongju, Jin, Juntong, Yuan, Hui, Zhang, Jingguo, Wang, Yuqing, Wang, Mingqian, Yin, Shaobo, Zhao, Jiaming, Lin, Shijiao, Liang, Yuling, Wang, Jiayao, Wei, Shipeng, Liu, Weiting, Li, Bin, Ji, Yinglin, Wang, Aide
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 12.08.2025; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/43; 38/91; 45/90; 49/22; 49/23; 631/208/135; 631/208/8; 631/449/1741; 631/449/2653; 96; 96/44; 96/95; Biosynthesis; Chromosomes; Ethylene; Ethylenes - biosynthesis; Ethylenes - metabolism; Fruit - genetics; Fruit - metabolism; Fruits; Gene Expression Regulation, Plant; Genetic analysis; Genome, Plant; Genomes; Genomic analysis; Genomics - methods; Genotype & phenotype; Haplotypes; Humanities and Social Sciences; Maloideae; Malus - genetics; multidisciplinary; Pears; Phylogenetics; Plant Proteins - genetics; Plant Proteins - metabolism; Principal components analysis; Pyrus - genetics; Pyrus - metabolism; Ripening; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; Science; Science (multidisciplinary); China; Japan
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-025-62850-3

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. Based on the ethylene climacteric at the onset of ripening, fleshy fruits can be classified as ethylene-dependent and ethylene-independent. Here, the authors assemble the genomes of both types of pears and reveal genetic basis for their formation.