Transcriptomics and Metabolomics Analysis Reveal the Mechanism of Petal Number Variation in Gardenia jasminoides

<b>Background/Objectives</b>: This study was based on the joint analysis of transcriptome and metabolome to explore the key genes and metabolic pathways of gardenia single flower petal number variation and to explore the possible mechanism of floral organ variation. <b>Methods</b>: Five, six, and seven petals of single-flower gardenia were selected as test materials for transcriptome and metabolome determination to excavate the key genes in regulating petal number in gardenia. <b>Results</b>: Metabolomic analysis identified triethylamine, succinic acid, succinylaldehyde, 2-phenylethanol, and o-xylene as the top five differentially expressed metabolites affecting petal number variation in gardenia. In the KEGG enrichment analysis, gardenia five, six, and seven DEGs were mainly enriched in amphetamine biosynthesis, the biosynthesis of plant secondary metabolites; transcriptome results showed that the identified differential transcription factors mainly come from NAC, ERF, C2H2, MYB, and MADS-box gene families; the expression of <i>GjMADS50</i>, <i>GjMADS59</i>, and <i>GjERF28</i> changed with the increase in petal number. The commonality between gardenia five, six, and seven flowers exceeded the difference, and the expression pattern of MADS-box and ERF gene family members was the upregulation of <i>GjERF28</i>, <i>GjERF39</i>, and <i>GjMADS67</i> and downregulation of <i>GjMADS50</i>, <i>GjMADS59</i>, and <i>GjMADS60</i>. <b>Conclusions</b>: We propose that ERF transcription factors may determine the initial number of petal primordia by mediating gibberellin biosynthesis or signaling, thereby coordinately regulating floral meristem activity and specific metabolic states.