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Having different number if genome copies affect transcription and metabolite production of plants. This may be due to different gene transcription and protein expression, but the reasons for this remains poorly known. Here we measured flavonoid content in leaves of three haploid and diploid grafted plants of Ginkgo biloba , a model gymnosperm important economically for its flavonoid content. We reported the first combined transcriptomic and proteomic analysis of the difference in flavonoid content in three haploid ginkgos to investigate the effect of haploidy. Haploids had always smaller leaves and flavonoid content than the diploids. The selected haploid had also generally lower gene dosage than the selected diploid, with 1149 up-regulated (46.8 %) and 1309 down-regulated (53.2 %) among 2452 differentially expressed genes (DEGs). Of 686 differentially expressed proteins (DEPs) detected, 289 proteins (42.1 %) were upregulated, and 397 proteins (57.9 %) were downregulated in haploids. A particular attention deserves the downregulation of PAL , PAM , FLS , OMT1 hub genes involved in flavonoid biosynthesis regulation. Our study confirms the trend of haploids to have lower metabolic contents and points that lower flavonoid content in ginkgo monoploids could be due to reduced dosage of the corresponding regulatory genes and downregulation of genes involved in flavonoid synthesis. • The first multi-omics combined analysis of haploid Ginkgo biloba. • SPT and MYC2 were speculated to be transcription factors broadly involved in the regulation of haploid ginkgo flavonoids. • PAL , PAM , FLS and OTM1 most likely act as hub genes in ginkgo flavonoid regulation. [ABSTRACT FROM AUTHOR]

As a representative of gymnosperms, the discovery of natural haploids of Ginkgo biloba L. has opened a new door for its research. Haploid germplasm has always been a research material of interest to researchers because of its special characteristics. However, we do not yet know the special features and mechanisms of haploid ginkgo following this significant discovery. In this study, we conducted a homogenous garden experiment on haploid and diploid ginkgo to explore the differences in growth, physiology and biochemistry between the two. Additionally, a high-depth transcriptome database of both was established to reveal their transcriptional differences. The results showed that haploid ginkgo exhibited weaker growth potential, lower photosynthesis and flavonoid accumulation capacity. Although the up-regulated expression of DEGs in haploid ginkgo reached 46.7% of the total DEGs in the whole transcriptome data, the gene sets of photosynthesis metabolic, glycolysis/gluconeogenesis and flavonoid biosynthesis pathways, which were significantly related to these differences, were found to show a significant down-regulated expression trend by gene set enrichment analysis (GSEA). We further found that the major metabolic pathways in the haploid ginkgo transcriptional database were down-regulated in expression compared to the diploid. This study reveals for the first time the phenotypic, growth and physiological differences in haploid ginkgos, and demonstrates their transcriptional patterns based on high-depth transcriptomic data, laying the foundation for subsequent in-depth studies of haploid ginkgos. [ABSTRACT FROM AUTHOR]