ABSTRACT. Paphiopedilum orchids (Orchidaceae) have attracted much attention from botanists and horticulturists because of their peculiar leaves and beautiful flowers. Furthermore, the dry roots of Paphiopedilum plants have well-known medicinal uses. However, it is unknown how sensitive and plastic the root genes are to environmental changes or how these environmental changes regulate the biosynthesis of active ingredients. In this study, we chose Paphiopedilum concolor for root sequencing, as it is widely used as a parent in breeding experiments. A total of 3.77 Gb of sequence data were generated by Illumina paired-end sequencing. De novo assemblies yielded 72,952 contigs, 67,434 scaffolds, 64,304 unigenes with average lengths of 937, 1022, and 1047 bp, respectively. Based on Basic Local Alignment Search Tool with known protein sequences, 40,815 (63.5%) unigenes were annotated with an E-value cutoff of 1.0E-5. Among the unigenes, 24,605 were classified in the Gene Ontology database, 17,361 were assigned to Cluster of Orthologous Groups, and 14,170 were annotated in Kyoto Encyclopedia of Genes and Genomes. Among these annotations, over 1195 unigenes related to secondary metabolic pathways, as well as 609 unigenes involved in plant hormone synthesis and signal transduction, were identified. In addition, 5322 potential simple sequence repeats (SSRs) were identified, and 4989 primer pairs for 3975 sequences containing SSRs were obtained. This study provides valuable insights into the mechanisms of genes that regulate root growth and development and provides a comprehensive resource for genes related to secondary metabolism in roots and for marker-assisted studies in Paphiopedilum.

ABSTRACT. The influence of warm day and cool night conditions on induction of spikes in Phalaenopsis orchids has been studied with respect to photosynthetic efficiency, metabolic cycles and physiology. However, molecular events involved in spike emergence induced by warm day and cool night conditions are not clearly understood. We examined gene expression induced by warm day and cool night conditions in the Phalaenopsis hybrid Fortune Saltzman through suppression subtractive hybridization, which allowed identification of flowering-related genes in warm day and cool night conditions in spikes and leaves at vegetative phase grown under warm daily temperatures. In total, 450 presumably regulated expressed sequence tags (ESTs) were identified and classified into functional categories, including metabolism, development, transcription factor, signal transduction, transportation, cell defense, and stress. Furthermore, database comparisons revealed a notable number of Phalaenopsis hybrid Fortune Saltzman ESTs that matched genes with unknown function. The expression profiles of 24 genes (from different functional categories) have been confirmed by quantitative real-time PCR in induced spikes and juvenile apical leaves. The results of the real-time PCR showed that, compared to the vegetative apical leaves, the transcripts of genes encoding flowering locus T, AP1, AP2, KNOX1, knotted1-like homeobox protein, R2R3-like MYB, adenosine kinase 2, S-adenosylmethionine synthetase, dihydroflavonol 4-reductase, and naringenin 3-dioxygenase accumulated significantly higher levels, and genes encoding FCA, retrotransposon protein Ty3 and C3HC4-type RING finger protein accumulated remarkably lower levels in spikes of early developmental stages. These results suggested that the genes of two expression changing trends may play positive and negative roles in the early floral transition of Phalaenopsis orchids. In conclusion, spikes induced by warm day and cool night conditions were complex in Phalaenopsis orchids; nevertheless, several molecular flowering pathway-related genes were found. The acquired data form the basis for a molecular understanding of spike induction by warm day and cool night conditions in Phalaenopsis orchids.