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The NCKU OrchidBase

Development and Goals

As one of the largest and most diverse of the angiosperm families [1], thefamily Orchidaceae the 25,000–35,000 species are of ecological and evolutionaryimportance. Like all other living organisms, present-day orchids have evolvedfrom ancestral forms as a result of selection pressure and adaptation. They showa wide diversity of epiphytic and terrestrial growth forms and have successfullycolonized almost every habitat on Earth. Specific interaction between orchidflowers and pollinators [2], sequential and rapid interplay between drift andnatural selection [3], the role of obligate orchid–mycorrhizal interactions [4],and epiphytism may all contribute to the species richness within theOrchidaceae.

The radiation of the orchid family probably took place in a comparatively short period in comparison to that of most flowering plant families, which had already started to diversify in the Mid-Cretaceous [5]. The time of origin of orchids is in dispute, although Dressler suggested that they originated 80 to 40 million years ago (late Cretaceous to late Eocene). Perhaps the only general statement that can be made about the origin of orchids is that most extant groups are probably very young. Recently, the origin of the Orchidaceae was dated using a fossil orchid and its pollinator; the authors [6] showed that the most recent common ancestor of extant orchids lived in the late Cretaceous (76-84 Mya).

 According to molecular phylogenetic studies, Orchidaceae comprise five subfamilies, including Apostasioideae, Cypripedioideae, Vanilloideae, Orchidoideae and Epidendroideae. They are known for their diversity of specialized reproductive and ecological strategies. For successful reproduction, the production of labellum and gynostemium (a fused structure of androecium and gynoecium) to facilitate pollination is well documented and the co-evolution of orchid flowers and pollinators is well known [7-8]. In addition, mature pollen grains packaged as pollinia, pollination-regulated ovary/ovule development, synchronized timing of micro- and mega-gametogenesis for effective fertilization, and the release of thousands or millions of immature embryos (seeds without endosperm) in a mature capsule may also account for the especially successful evolutionary progress of orchids [9]. However, despite their unique developmental reproductive biology, as well as specialized pollination and ecological strategies, orchids remain under-represented in molecular studies relative to other species-rich plant families [10].

 Orchids are one of the most ecological and evolutionary significant plants, and the Orchidacea is one of the most abundant families in angiosperm. The genetic databases will be useful not only for gene discovery but future genomic annotation. For this purpose, OrchidBase was established from 84,617 unigenes collected from ten in-house Phalaenopsis orchid cDNA libraries and 1,562,071 floral non-redundant transcribed sequences collected comprehensively from ten orchid species across five subfamilies of Orchidaceae. The analysis pipeline of database is an automated system written in Perl and C#, and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, and storage of the analyzed information into SQL databases. A web application was implemented with HTML and Microsoft .NET Framework C# program for browsing and querying the database, creation of dynamic web pages on the client side, analyzing Gene Ontology (GO), and for mapping annotated enzymes to KEGG pathways. The online resources for putative annotation can be searched either by text or by using BLAST, and the result can be explored on the website and downloaded. Consequently, the establishment of OrchidBase will provide researchers a high-quality genetic resource for data-mining and facilitate efficient experimental studies on orchid biology and biotechnology.

Reference:

1.Atwood JT:The size of Orchidaceae and the systematic distribution of epiphytic orchids.Selbyana 1986,9:171-186.

2.Cozzolino S, Widmer A: Orchid diversity: an evolutionary consequence of deception? Trends in Ecology &
         Evolution 2005, 20:487-494.

3.Tremblay RL, Ackerman JD, Zimmerman JK, Calvo RN: Variation in sexual reproduction in orchids and its
         evolutionary consequence: a spasmodic journey to diversification. Biological Journal of the Linnean Society
         2005, 84:1-54.

4.Otero JT, Flanagan NS: Orchid diversity – beyond deception. Trends in Ecology & Evolution 2006, 21:64-65.

5.Crane PR, Friis EM, Pedersen KR: The origin and early diversification of angiosperms. Nature 1995, 374:27-33.

6.Ramirez SR, Gravendeel B, Singer RB, Marshall CR, Pierce NE: Dating the origin of the Orchidaceae from a
         fossil orchid with its pollinator.Nature 2007, 448:1042-1045.

7.Yu H, Goh CJ: Molecular genetics of reproductive biology in orchids. Plant Physiol 2001, 127:1390-1393.

8.Schiestl FP, Peakall R, Mant JG, Ibarra F, Schulz C, Franke S, Francke W: The chemistry of sexual
         deception in an orchid-wasp pollination system.Science 2003, 302:437-438.

9.Tsai WC, Hsiao YY, Pan ZJ, Kuoh CS, Chen WH, Chen HH: The role of ethylene in orchid ovule
         development. Plant Sci 2008, 175:98-105.

10.Peakall R: Speciation in the Orchidaceae: confronting the challenges. Molecular Ecology 2007, 16:2834-2837.



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