De novo Sequencing and Comparative Analysis of Two Phalaenopsis Orchid Tissue-Specific Transcriptomes
L. W. Gaoa, , D. H. Jianga, 2, Y. X. Yanga, Y. X. Lia, G. S. Sunb, Z. H. Mab, and C. W. Zhanga
a College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
b Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, Jurong, Jiangsu, China
e-mail: changweizh@njau.edu.cn
1The article is published in the original.
2 These authors contributed equally to the work.
2Abbreviations: bHLH—basic helix-loop-helix; CHI—chalcone-flavanone isomerase; CHS—chalcone synthase; COG—clusters of orthologous groups; DEG—differentially expressed gene; DFR—dihydroflavonol 4-reductase; F3′5′H—flavonoid 3′, 5′‑hydroxylase; FLS—flavonol synthase; GO—gene ontology; GST—glutathione S-transferase; KEGG—Kyoto encyclopedia of genes and genomes; MATE—multidrug and toxic compound extrusion; MRP—multidrug resistance-associated protein; NR—non-redundant databases; NT—nucleotide; PSY—phytoene synthase; qRT-PCR—quantitative real-time PCR; TF—transcription factor; UF3GT—UDP Glc-flavonoid 3-O-glucosyl transferase.
Electronic supplementary material: The online version of this article contains supplementary material, which is available to authorized users.
Received 7 April, 2015
Abstract—In recent years, Phalaenopsis has become a very popular potted flower for the international flower market. The aim of this work was to build a tissue-specific transcriptome to obtain genomic data about the biosynthesis of anthocyanins in Phalaenopsis, compare gene expression levels in different colored Phalaenopsis plants, and to ultimately analyze the anthocyanin biosynthetic pathway in Phalaenopsis. Illumina sequencing technology obtained 888 749 and 1 057 077 sequencing contigs in red and yellow Phalaenopsis buds, respectively. De novo assemblies yielded 51 771 unigenes, and 801 differentially expressed genes were obtained using the reads. These included 358 up-regulated and 443 down-regulated genes in the yellow bud compared with the red bud. Many of the identified differentially expressed genes were related to the biosynthesis of anthocyanins. Quantitative real-time PCR confirmed expression levels of key genes and transcription factors involved in anthocyanin biosynthesis in Phalaenopsis were the same as in our dataset. Our findings allowed the deduction of the anthocyanin biosynthetic pathway in Phalaenopsis.
Keywords: Phalaenopsis, anthocyanins, illumina sequencing, transcriptome
DOI: 10.1134/S1021443716020072