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

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, Yinglin Ji () and Aide Wang ()
Additional contact information
Yi Wang: Shenyang Agricultural University
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

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: 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.

Date: 2025
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-025-62850-3 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-62850-3

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-025-62850-3

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().