Oncidium hybridum

<em>Oncidium</em>, an important tropical orchid, has high ornamental value due to its specific color and occupies an important market position for the worldwide flower. Transcriptome analysis of flower and leaf color formation provides new sources for producing novel <em>Oncidium hybridum </em>cultivars. We sequenced 12 samples of flowers (yellow and white) and leaves (striped and normal) of <em>O. hybridum</em> and assembled 381,136 and 453,566 unigene sequences from RNA-seq data, respectively. Among unigenes, 662 and 1,324 differentially expressed genes were identified in flower and leaf samples, respectively. Gene ontology and pathway enrichment showed that secondary metabolite biosynthetic pathways were responsible for flower and leaf color formation. It was determined that <em>UGT75C1</em>, <em>E2.4.1.115</em>, <em>CCD7</em>, <em>E2.1.1.76</em>, and <em>CCoAOMT</em> are involved in regulating flower color, and <em>UGT75C1</em>, <em>LHCB</em>, <em>UGT</em>, <em>RP-L18Ae</em>, and A<em>BCB1</em> play crucial roles in regulating leaf color. Kyoto Encyclopedia of Genes and Genomes analysis revealed that <em>UGT75C1</em> was significantly enriched in the anthocyanin biosynthetic pathway, showing effects on flower and leaf colors. This study was the first detailed analysis of the molecular mechanisms of <em>O. hybridum </em>flower and leaf colors, and the results advanced the understanding of the genetic basis of flower and leaf colors; they also provided additional support for the improving commercial value and producing novel cultivars of <em>O. hybridum</em>.