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Article|02 Apr 2026|OPEN
Evolution and diversification of PAL-mediated salicylic acid biosynthesis in Rosaceae
Qiao-Ling Zhang1,2 ,† , Tong-Jian Liu3,4,5 ,† , Yi-Bing Wang3,4,5 ,† , Tian Feng3,4,5 and Lin Chen1,2 , Bo-Zhi Xiao6 , Han-Xiang Li3,4,5 , Hai-Bo Tan3,4,5 , Hui-Run Huang3,4,5 , Xue-Jun Ge3,4,5 , Hai-Fei Yan3,4,5 , , Xin-Feng Wang,3,4,5 ,
1Hangzhou Xixi National Wetland Park Service Center (Hangzhou Xixi National Wetland Park Ecology & Culture Research Center), Hangzhou 310013, China
2Zhejiang Xixi Wetland Ecosystem Observation and Research Station, Hangzhou 310013, China
3State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China
4Key Laboratory of National Forestry and Grassland Administration on Plant Conservation and Utilization in Southern China, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
5South China National Botanical Garden, Guangzhou 510650, China
6Guangzhou Dublin International College of Life Sciences and Technology, South China Agricultural University, Guangzhou 510642, China
*Corresponding author. E-mail: yanhaifei@scbg.ac.cn,wangxf@scbg.ac.cn
†Qiao-Ling Zhang and Tong-Jian Liu,Yi-Bing Wang contributed equally to the study.

Horticulture Research 13,
Article number: uhag108 (2026)
doi: https://doi.org/10.1093/hr/uhag108
Views: 65

Received: 29 Sep 2025
Accepted: 18 Mar 2026
Published online: 02 Apr 2026

Abstract

Salicylic acid (SA) is a central phytohormone in plant immunity and stress responses, yet the evolutionary dynamics of its phenylalanine ammonia-lyase (PAL)-mediated biosynthetic route remain poorly understood despite recent biochemical advances. As the original source of SA, Spiraea (Rosaceae) holds historical and evolutionary significance for studying SA biosynthesis. Here, we generated a chromosome-level genome assembly of Spiraea chinensis and integrated comparative genomics, transcriptomic, and targeted metabolite profiling to investigate the evolutionary diversification of SA biosynthesis across Rosaceae. Phylogenomics places S. chinensis in the subfamily Amygdaloideae, diverging from other genera ~57.8 Mya. Extensive chromosome fission–fusion events and lineage-specific whole-genome duplication (WGD) have driven karyotype diversification across Rosaceae. Comparative analyses revealed the PAL-mediated route as the dominant SA biosynthetic pathway across Rosaceae, with WGD-driven expansion in Amygdaloideae and combined WGD- and small-scale duplication (SSD)-derived origins in Rosoideae. WGD-derived PAL-route genes largely retained synteny and stable high expression, whereas lineage-specific SSD-derived paralogs exhibited reduced synteny and variable expression, consistent with post-duplication regulatory divergence and subfunctionalization. Transcriptome analyses revealed pronounced tissue-specific expression of PAL-route genes across Rosaceae, and UPLC–MS/MS profiling further demonstrated differential SA accumulation in S. chinensis, with the highest levels in branches (606–1038 ng/g FW), followed by leaves (183–432 ng/g FW) and flowers (42–56 ng/g FW), supporting active SA biosynthesis in both vegetative and reproductive tissues. Collectively, our results establish the PAL-mediated pathway as the primary and evolutionarily conserved route of SA biosynthesis in Rosaceae and demonstrate how genome dynamics and regulatory diversification jointly drive the evolutionary innovation within this pathway.