IntroductionJasminum sambac (L.) Aiton is a major ornamental species in the family Oleaceae and genus Jasminum. It carries ornamental, medicinal, and economic value: a renowned raw material for scented tea and fragrances, with broad applications in horticulture and wellness, hence the epithet “the first fragrance under heaven”1. China has a long history of jasmine cultivation, with major production areas in Guangxi, Fujian, Sichuan, and Yunnan; among them, Heng County (Guangxi) and Qianwei County (Sichuan) are typical concentrated production regions2. However, as the industry has expanded, jasmine production has come under serious threat from diseases, especially southern blight caused by Sclerotium rolfsii Sacc.3 Southern blight is a destructive, soil-borne fungal disease with a very broad host range, infecting more than 500 plant species including jasmine, peanut, tomato, and sunflower3. In the main jasmine-growing regions of southern China, its incidence has risen year by year and has become a key constraint on yield and quality4. The disease typically initiates at the stem base, where white, web-like mycelia develop and brown sclerotia form; it causes basal/root rot and can lead to whole-plant death2. Because sclerotia can persist for long periods in soil or crop residues and epidemics readily occur under hot, humid conditions, control is challenging5. Field surveys reveal substantial variation in cultivar resistance, offering opportunities for the exploitation of resistant germplasm and resistance breeding6,7. At present, no chemical agents provide highly effective and durable control of southern blight8, and biological control is becoming an important alternative. Trichoderma harzianum shows significant efficacy against jasmine southern blight9, and Trichoderma-based biocontrol formulations not only suppress disease but also improve soil microbial community structure and enhance rhizosphere stability10. In parallel, agronomic measures (e.g., crop rotation and soil management) and integrated management strategies have been proposed to curb epidemics8. Pathogen-secreted virulence factors—such as oxalic acid and polygalacturonases—also play crucial roles in pathogenesis, deepening our understanding of disease mechanisms11,12.Beyond external control, intrinsic plant defenses are critical for resisting infection. Multiple hormone signaling pathways are involved, among which jasmonic acid (JA) and salicylic acid (SA) play central roles in induced resistance. For example, during infection of konjac, JA and SA levels rise markedly alongside increased expression of related genes, highlighting the importance of both pathways13. Similar findings in other crops point to a general role for JA/SA signaling in resistance to soil-borne diseases14.With advances in genomics and transcriptomics, attention has increasingly focused on transcription factors in plant stress responses. The LBD (Lateral Organ Boundaries Domain) gene family comprises plant-specific transcription factors that harbor a highly conserved LOB domain and specifically recognize the “GCGGCG” motif to regulate downstream gene expression15. LBD members participate broadly in the development of lateral organs (lateral roots, branches, leaves, floral organs) and also function in stress responses, secondary growth, regeneration, and metabolic regulation16,17,18,19. Notably, one of the first functional studies of LBD genes in plant–fungus interactions demonstrated that AtLBD20 from Arabidopsis acts as a negative regulator of jasmonate-mediated defense responses and increases susceptibility to the necrotrophic root-infecting fungus Fusarium oxysporum20. In the broader context of necrotrophic pathogens, transcriptional reprogramming controlled by transcription factors has been recognized as a key layer of defense because classical R-gene-mediated resistance is often ineffective against necrotrophs21,22. Together these findings underscore the value of targeting transcription factors such as LBDs for improving resistance to necrotrophic pathogens. Based on our systematic analysis of the jasmine LBD family, we hypothesize that certain members act early during southern blight infection by modulating signal transduction and defense-related metabolic pathways.In summary, southern blight is now a major constraint on the sustainable development of the jasmine industry. Although conventional agronomic and chemical control measures can mitigate losses to some extent, durable solutions will rely on breeding for resistance and deeper elucidation of the underlying molecular mechanisms. Focusing on the early defense response of jasmine to southern blight, this study integrates transcriptomic and metabolomic analyses with a systematic characterization of the LBD gene family to delineate regulatory patterns and provide a theoretical basis and potential targets for resistance breeding in jasmine.Results and analysisIdentification and basic propertiesWe identified 38, 39, and 36 LBD genes in ‘Hutou’ (Ht), single-petal (Sj), and double-petal (Dj) jasmine, respectively, by combining genome annotation, chromosomal mapping, and BLAST validation. Their general characteristics are summarized in Table 1. Protein lengths spanned ~ 142–452 aa, with theoretical pI values centered around ~ 6.5 and most members showing an instability index > 40, suggesting weakly acidic and largely unstable proteins (full statistics in Table S1). Gene names were assigned in chromosomal order within each genome.Table 1 Summary of physicochemical properties and predicted subcellular localization of LBD family proteins in jasmine.Full size tableChromosomal distribution of jasmine LBD genesLBD loci were unevenly distributed across 12 chromosomes in each genome: Ht peaked on chr1 (6 genes), Sj on chr3 (8), and Dj on chr1 (5), with at least one chromosome in each genome harboring a single locus. Because the spatial patterns do not affect downstream conclusions, detailed karyoplots are relegated to Fig. S1.Phylogenetic analysis of the LBD gene family in jasmineA maximum-likelihood tree built from jasmine and Arabidopsis LBD proteins resolved two major classes (Class I, Class II) and seven subfamilies (Fig. 1). Class I dominated (118/156; 75.6%), while subfamilies ranged from 13 (II-a) to 35 (I-c) members. All subfamilies contained representatives from Ht/Sj/Dj and Arabidopsis, but lineage representation was uneven, consistent with differential expansion.Fig. 1The alternative text for this image may have been generated using AI.Full size imagePhylogeny of LBD proteins from three jasmine types and Arabidopsis.A maximum-likelihood phylogenetic tree was constructed using full-length LBD protein sequences from single-petal jasmine, double-petal jasmine, ‘Hutou’ jasmine, and Arabidopsis thaliana. Different color branches denote distinct LBD subfamilies (Class I and Class II). The tree reveals conserved clustering patterns among jasmine species and their evolutionary relationship with Arabidopsis homologs, indicating a high degree of sequence conservation and diversification within the LBD family.Gene structure and conserved domain analysis of jasmine LBD genesExon–intron architectures were simple (mostly 1–2 exons; a minority with ≥ 3 in Sj), indicating compact gene models (Fig. 2). All proteins harbored the canonical LBD domain, whereas a few contained additional domains (e.g., COG6, PRK11815), hinting at functional diversification. MEME analysis showed motifs 1 and 2 to be universally present, with diagnostic motifs restricted to specific classes or subfamilies (e.g., Class II–specific motifs; I-c–specific motifs), and most motifs concentrated toward the C terminus, suggesting higher C-terminal conservation and N-terminal divergence. This N-terminal divergence likely reflects relaxed evolutionary constraint on regulatory or interaction regions outside the conserved LOB domain, allowing sequence diversification that may underlie functional specificity among LBD members.Fig. 2The alternative text for this image may have been generated using AI.Full size imageExon–intron maps, domain architecture, and motif composition of jasmine LBDs. (A) Hutou jasmine, (B) single-petal jasmine, and (C) double-petal jasmine.Cis-acting element and transcription factor binding site (TFBS) analysis of jasmine LBD promotersAcross the 2-kb promoter regions of Jasminum sambac LBD genes, we detected 22 representative cis-elements associated with light, hormone, stress, and developmental responses, as well as diverse transcription factor binding sites (TFBSs). Light-responsive motifs were nearly ubiquitous, while approximately 72–77% of genes carried ABA-responsive elements, 71–72% contained defense or stress-related motifs, and about half included drought-responsive MYB sites in each genome. Moreover, 18 TF families were identified in promoter regions, with BBR-BPC, Dof, and MIKC_MADS showing the highest binding frequencies. Although Ht, Sj, and Dj shared most TF families, several lineage-specific patterns were observed—for instance, WRKY binding sites appeared uniquely in Dj. The wide variation in TFBS number per gene suggests member-specific transcriptional regulation. Detailed element-by-gene matrices and TFBS heatmaps are provided in Figs. S2 and S3, respectively.Collinearity (synteny) analysis of the jasmine LBD gene familyIntra-genome analyses detected 12 duplicated pairs in Ht, 9 in Sj, and 7 in Dj, indicating modest family expansion mainly via segmental/tandem duplication. Inter-genome synteny yielded 55 (Ht–Sj), 52 (Ht–Dj), and 48 (Sj–Dj) orthologous pairs (Fig. 3), supporting conserved relationships among cultivars(Full intra-/cross-species panels in Fig. S4). Cross-species macrosynteny with Arabidopsis and rice further corroborated conservation (summary edges shown below; full panels in supplement).Fig. 3The alternative text for this image may have been generated using AI.Full size imageSynteny summary among the three jasmine genomes (single consolidated chord/links panel). Genome-wide collinearity analysis was performed using TBtools based on MCScanX results. Colored links represent homologous LBD gene pairs among single-petal jasmine, double-petal jasmine, and ‘Hutou’ jasmine. The outer circle indicates chromosomal positions, while the inner chords illustrate intergenomic syntenic relationships. Extensive cross-links reflect strong collinearity among the three genomes, supporting conserved genomic organization and shared evolutionary origins of the LBD family.Ka/Ks analysis of syntenic LBD gene pairs revealed that all calculable ratios were