Tissue-resolved comparative developmental transcriptomics reveals auxin-associated regulatory shifts underlying divergent fruit tissue origins in pomes and drupes

Jiakai Liang; Qiaoming Yu; Yan Wang; Man Xie; Xiangxiang Chen; Peien Feng; Yunxiao Liu; Mingjun Li; Yaqiang Sun; Jia-Long Yao; Fengwang Ma; Yangjun Zou; Tao Zhao

doi:10.1016/j.jgg.2026.06.006

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Tissue-resolved comparative developmental transcriptomics reveals auxin-associated regulatory shifts underlying divergent fruit tissue origins in pomes and drupes

doi: 10.1016/j.jgg.2026.06.006

a. State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China;
b. The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand

Funds:

This work was financially supported by National Key R&D Program of China (2023YFD1202400), National Natural Science Foundation of China (32102338), and the Chinese Universities Scientific Fund (2452021133).

Received Date: 2026-01-12
Accepted Date: 2026-06-11
Rev Recd Date: 2026-06-10

Available Online: 2026-06-22

Abstract

Abstract

Fruit type divergence in closely related species offers a powerful lens into the evolution of plant developmental programs. Within the Rosaceae family, pomes (e.g., apple) and drupes (e.g., peach) share a common ancestry but exhibit a fundamental difference: pomes recruit the hypanthium to form fleshy tissue, while drupes develop flesh solely from the ovary wall. To uncover the regulatory basis of this divergence, we conduct a comparative tissue-resolved developmental transcriptomic analysis across these fruit types. We identify distinct patterns of auxin-related networks, with pomes showing preferential activation of auxin signaling, transport, and biosynthetic pathways within the hypanthium, accompanied by differences in gibberellin responses. Through integrated network analysis, we identify a set of candidate regulators, including MADS-box, YABBY, and AP2 family genes, that interface with auxin signaling in a tissue-specific manner. Furthermore, we delineate a putative regulatory axis in which upstream transcription factors (FIL, ANT, AP1), potentially modulated by DOF3.2, are differentially associated with the auxin biosynthesis framework (e.g., YUC6) between pomes and drupes. Our findings suggest that fruit type divergence is associated with the spatial redeployment of auxin-related regulatory modules across tissues, providing a molecular framework for understanding fleshy fruit diversification and a basis for future evolutionary-developmental studies.
- Comparative transcriptomics,
- Auxin signaling,
- Fruit development,
- Evolutionary-developmental biology (Evo-Devo),
- Rosaceae

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