Transcriptomic Analysis of Paeonia delavayi Wild Population Flowers to Identify Differentially Expressed Genes Involved in Purple-Red and Yellow Petal Pigmentation

• Published in: PloS one Vol. 10; no. 8; p. e0135038
• Main Authors: Shi, Qianqian, Zhou, Lin, Wang, Yan, Li, Kui, Zheng, Baoqiang, Miao, Kun
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 12.08.2015; Public Library of Science (PLoS)
• Subjects: Annotations; Biosynthesis; Breeding; Color; Computational Biology; Cultivars; Data processing; Flavonoids; Flavonoids - biosynthesis; Flowers; Flowers & plants; Flowers - genetics; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene mapping; Gene sequencing; Genes; Genetic engineering; Genomics; High-Throughput Nucleotide Sequencing; Laboratories; Molecular chains; Molecular modelling; Molecular Sequence Annotation; Ornamental plants; Paeonia - genetics; Paeonia - metabolism; Paeonia delavayi; Petals; Pigmentation; Pigmentation - genetics; Pigments; R&D; Research & development; Ribonucleic acid; RNA; Transcription factors; Transcriptome; Trees; Trends; Beijing China; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0135038

Tree peony (Paeonia suffruticosa Andrews) is a very famous traditional ornamental plant in China. P. delavayi is a species endemic to Southwest China that has aroused great interest from researchers as a precious genetic resource for flower color breeding. However, the current understanding of the molecular mechanisms of flower pigmentation in this plant is limited, hindering the genetic engineering of novel flower color in tree peonies. In this study, we conducted a large-scale transcriptome analysis based on Illumina HiSeq sequencing of cDNA libraries generated from yellow and purple-red P. delavayi petals. A total of 90,202 unigenes were obtained by de novo assembly, with an average length of 721 nt. Using Blastx, 44,811 unigenes (49.68%) were found to have significant similarity to accessions in the NR, NT, and Swiss-Prot databases. We also examined COG, GO and KEGG annotations to better understand the functions of these unigenes. Further analysis of the two digital transcriptomes revealed that 6,855 unigenes were differentially expressed between yellow and purple-red flower petals, with 3,430 up-regulated and 3,425 down-regulated. According to the RNA-Seq data and qRT-PCR analysis, we proposed that four up-regulated key structural genes, including F3H, DFR, ANS and 3GT, might play an important role in purple-red petal pigmentation, while high co-expression of THC2'GT, CHI and FNS II ensures the accumulation of pigments contributing to the yellow color. We also found 50 differentially expressed transcription factors that might be involved in flavonoid biosynthesis. This study is the first to report genetic information for P. delavayi. The large number of gene sequences produced by transcriptome sequencing and the candidate genes identified using pathway mapping and expression profiles will provide a valuable resource for future association studies aimed at better understanding the molecular mechanisms underlying flower pigmentation in tree peonies.