Research Article

PhalDB:A comprehensive database for molecular mining of the Phalaenopsis genome, transcriptome and miRNome

Published: October 05, 2018
Genet. Mol. Res. 17(4): GMR18051 DOI:
Cite this Article:
C.Y. Lee, K.K. Viswanath, J.Z. Huang, C.P. Lee, C.P. Lin, T.C. Cheng, B.C. Chang, S.W. Chin, F.C. Chen (2018). PhalDB:A comprehensive database for molecular mining of the Phalaenopsis genome, transcriptome and miRNome. Genet. Mol. Res. 17(4): GMR18051.


The orchid family Orchidaceae is one of the largest families of angiosperms; it includes approximately 35,000 species, displays a wide range of unique flower shapes and is a valued ornamental crop. Among the various species of orchids, the Phalaenopsis genus is the most widely commercialized among blooming potted plants. Our aim was to provide in-depth sequence information for the various parts of flowers, different time treatments of the protocorm-like bodies and temperature treated shortened stems for flowering pathway regulation, in addition to adding to the available data on normal and peloric mutants. We also obtained transcriptome data from shortened stems under cool temperature for spike induction. The deep sequenced, assembled and annotated information was integrated and built into a database that we named PhalDB. Existing databases, such as OrchidBase, OrchidBase 2.0, Orchidstra, and Orchidstra 2.0 mainly contain information on expressed sequence tags, unigenes, and microRNA only from floral organs of orchid species. These databases do not include information about somaclonal variations and cool temperature treatment, which are important for commercial variety development. PhalDB provides sequence information from 24 samples and covers the above-mentioned tissues or conditions so that comprehensive gene data related to flower development, somaclonal variation and some horticulture traits are available for searching. A user can access DNA level information and miRNA structure, etc. It also provides an opportunity to explore mRNA level information and interactions between genes and miRNA. PhalDB is equipped with a BLAST tool to perform similarity searches among the various gene sequences.