Orchidstra: An Integrated Orchid Functional Genomics Database Special Focus Issue Chun-lin Su1,3, Ya-Ting Chao1,3, Shao-Hua Yen1, Chun-Yi Chen1, Wan-Chieh Chen1, Yao-Chien Alex Chang2 and Ming-Che Shih1,* 1Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan 2Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 10617, Taiwan. 3These authors contributed equally to this work. *Corresponding author: E-mail:
[email protected]; Fax, +886-2-26515693. (Received November 9, 2012; Accepted January 5, 2013) A specialized orchid database, named Orchidstra (URL: Abbreviations: BLAST, basic local alignment search tool; – Databases http://orchidstra.abrc.sinica.edu.tw), has been constructed CAM, crassulacean acid metabolism; EIF5A, eukaryotic trans- to collect, annotate and share genomic information for lation initiation factor 5A; EST, expressed sequence tag; GO, orchid functional genomics studies. The Orchidaceae is a Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and large family of Angiosperms that exhibits extraordinary bio- Genomes; miRNA, microRNA; NGS, next-generation sequen- diversity in terms of both the number of species and their cing; SRA, sequence read archive; TSA, transcriptome distribution worldwide. Orchids exhibit many unique biolo- shotgun assembly. gical features; however, investigation of these traits is cur- rently constrained due to the limited availability of genomic information. Transcriptome information for five orchid spe- Introduction cies and one commercial hybrid has been included in the Orchidaceae, the orchid family, diverged from the Liliaceae Orchidstra database. Altogether, these comprise >380,000 and Amaryllidaceae, is the largest family of Angiosperms, with non-redundant orchid transcript sequences, of which >800 genera and >25,000 species.