title: Genome-wide transcriptome and expression profile analysis of Phalaenopsis during explant browning.
abstract: BACKGROUND
  Explant browning presents a major problem for in vitro culture, and can lead to the death of the explant and failure of regeneration. Considerable work has examined the physiological mechanisms underlying Phalaenopsis leaf explant browning, but the molecular mechanisms of browning remain elusive. In this study, we used whole genome RNA sequencing to examine Phalaenopsis leaf explant browning at genome-wide level.
  
  
  RESULTS
  We first used Illumina high-throughput technology to sequence the transcriptome of Phalaenopsis and then performed de novo transcriptome assembly. We assembled 79,434,350 clean reads into 31,708 isogenes and generated 26,565 annotated unigenes. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript. Using the transcriptome data as a reference, we next analyzed the differential gene expression of explants cultured for 0, 3, and 6 d, respectively. We then identified differentially expressed genes (DEGs) before and after Phalaenopsis explant browning. We also performed GO, KEGG functional enrichment and Pfam analysis of all DEGs. Finally, we selected 11 genes for quantitative real-time PCR (qPCR) analysis to confirm the expression profile analysis.
  
  
  CONCLUSIONS
  Here, we report the first comprehensive analysis of transcriptome and expression profiles during Phalaenopsis explant browning. Our results suggest that Phalaenopsis explant browning may be due in part to gene expression changes that affect the secondary metabolism, such as: phenylpropanoid pathway and flavonoid biosynthesis. Genes involved in photosynthesis and ATPase activity have been found to be changed at transcription level; these changes may perturb energy metabolism and thus lead to the decay of plant cells and tissues. This study provides comprehensive gene expression data for Phalaenopsis browning. Our data constitute an important resource for further functional studies to prevent explant browning.
authors: Fujian Key Laboratory of Physiology and Biochemistry for Subtropical Plants, Fujian Institute of Subtropical Botany, Xiamen, 361006, P. R. China.
authors: Chuanjun
authors: C
authors: Xu
authors: Fujian Key Laboratory of Physiology and Biochemistry for Subtropical Plants, Fujian Institute of Subtropical Botany, Xiamen, 361006, P. R. China.
authors: Biyu
authors: B
authors: Zeng
authors: Fujian Key Laboratory of Physiology and Biochemistry for Subtropical Plants, Fujian Institute of Subtropical Botany, Xiamen, 361006, P. R. China.
authors: Junmei
authors: J
authors: Huang
authors: Fujian Key Laboratory of Physiology and Biochemistry for Subtropical Plants, Fujian Institute of Subtropical Botany, Xiamen, 361006, P. R. China.
authors: Wen
authors: W
authors: Huang
authors: Fujian Key Laboratory of Physiology and Biochemistry for Subtropical Plants, Fujian Institute of Subtropical Botany, Xiamen, 361006, P. R. China; Xiamen Overseas Chinese Subtropical Plant Introduction Garden, Fujian Institute of Subtropical Botany, Xiamen, 361002, P. R. China.
authors: Yumei
authors: Y
authors: Liu
mesh_terms: D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D029595:Orchidaceae / Q000235:genetics* / Q000378:metabolism; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome