Spiraea genome reveals how Rosaceae evolved a key defense hormone
image: Floral morphology and genomic features of S. chinensis. (a and b) Representative flower morphology. (c) Circos plot of the chromosome-level genome assembly. Tracks (from outer to inner) show: (i) nine pseudo-chromosomes with lengths in megabases (Mb), centromeres highlighted in red; (ii) gene density; (iii–v) densities of LTRs, TIRs, and Helitrons; (vi–vii) Illumina and HiFi read coverage; (viii) GC content; and (ix) intra-genomic synteny. All statistics were calculated in 250-Kb sliding windows with a 100-Kb step.
Credit: Horticulture Research
A chromosome-level genome of Chinese spiraea reveals how the rose family conserved and remodeled a major route for producing salicylic acid, a hormone central to plant immunity and environmental stress responses. By combining genome assembly, comparative genomics, transcriptome analysis, and targeted metabolite profiling, the study identifies the phenylalanine ammonia-lyase (PAL) route as the predominant salicylic acid pathway across Rosaceae. It also shows that whole-genome duplication and smaller-scale gene duplications created different evolutionary patterns in major rose-family lineages, while tissue-specific regulation divided pathway activity among branches, leaves, and flowers. The findings connect genome evolution with metabolic innovation in economically important fruit crops and ornamentals.
Salicylic acid (SA) helps plants coordinate disease resistance, stress acclimation, growth, and development. Higher plants can produce SA through the isochorismate synthase (ICS) route or the phenylalanine ammonia-lyase (PAL) route. However, research has concentrated largely on the ICS system of Arabidopsis thaliana, leaving the evolutionary history of PAL-dependent production poorly resolved. Spiraea is especially informative because it was among the earliest botanical sources associated with natural salicylates and helped inspire the name aspirin. Yet the genus lacked a high-quality chromosome-level reference genome, and SA-pathway genes remained inconsistently annotated across Rosaceae. Because of these challenges, deeper investigation is needed into how PAL-mediated SA biosynthesis evolved, diversified, and became regulated across rose-family lineages and tissues.
Researchers from Hangzhou Xixi National Wetland Park Service Center, Zhejiang Xixi Wetland Ecosystem Observation and Research Station, the South China Botanical Garden of the Chinese Academy of Sciences, the South China National Botanical Garden, and Guangzhou Dublin International College of Life Sciences and Technology at South China Agricultural University published (DOI: 10.1093/hr/uhag108) the study in Horticulture Research on April 2, 2026. The team assembled the first chromosome-level genome of Spiraea chinensis and compared it with representative Rosaceae and outgroup genomes, integrating evolutionary analysis with tissue transcriptomes and direct measurements of salicylic acid accumulation.
The researchers assembled a 228.11-megabase reference representing one haploid chromosome set across nine pseudochromosomes and annotated 29,265 protein-coding genes. Phylogenomic analysis placed Spiraea chinensis near the base of the Amygdaloideae subfamily, with its lineage diverging from other genera about 57.8 million years ago. Comparative analyses showed that chromosome fission, chromosome fusion, whole-genome duplication (WGD), and small-scale duplication (SSD) helped reshape Rosaceae genomes and salicylic acid biosynthesis. The phenylalanine ammonia-lyase pathway remained broadly conserved, but its gene copies had different evolutionary origins. In Amygdaloideae, WGD was the main source of pathway expansion, whereas Rosoideae displayed a more mixed pattern involving WGD and SSD. Of 36 identified PAL gene copies, 31 were WGD-derived. All seven core pathway enzymes showed tissue-dependent expression, and duplicated copies differed sharply in activity, indicating that gene duplication was followed by regulatory specialization rather than simple redundancy. WGD-derived copies generally retained conserved genomic positions and stable expression, while lineage-specific SSD-derived paralogs showed more variable expression. Ultra-performance liquid chromatography–tandem mass spectrometry (UPLC–MS/MS) measured the highest SA levels in branches, at 606–1,038 nanograms per gram of fresh weight, followed by leaves at 183–432 and flowers at 42–56.
The authors said the results show that evolution did not expand every part of the pathway in the same way. Central genes were often retained after whole-genome duplication, helping preserve reliable metabolic output, while smaller duplications gave other gene copies greater freedom to specialize across lineages and tissues. They said this balance between stability and flexibility may help Rosaceae plants maintain a dependable supply of a key defense hormone while adjusting its production to different organs and ecological conditions. The authors added that the new Spiraea chinensis genome provides an important baseline for future experiments involving pathogens and environmental stress.
The study provides a genomic framework for investigating stress resilience in Rosaceae crops and ornamentals, including apple, pear, peach, strawberry, rose, and spiraea. Conserved pathway genes may become candidates for breeding or biotechnology strategies designed to strengthen baseline defense, while tissue-specialized copies could offer more precise targets for modifying stress responses without broadly disrupting growth. The genome may also support research on related phenylpropanoid products, including lignin, flavonoids, pigments, and floral volatiles, because these compounds share upstream metabolic resources with salicylic acid. However, the study did not include targeted stress treatments, so future work should combine stress experiments, spatially resolved transcriptomics, functional validation, and metabolic-flux analysis to determine how individual duplicated genes respond to specific threats.
###
References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhag108
Funding information
This work was supported by the Guangdong Flagship Project of Basic and Applied Basic Research (2023B0303050001), the National Natural Science Foundation of China (32500199), and the Guangzhou Youth Doctor ‘Sailing’ Project (2025A04J0277).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.