Journal Article

OrchidBase: A Collection of Sequences of the Transcriptome Derived from Orchids

Chih-Hsiung Fu, Yun-Wen Chen, Yu-Yun Hsiao, Zhao-Jun Pan, Zhong-Jian Liu, Yueh-Min Huang, Wen-Chieh Tsai and Hong-Hwa Chen

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 52, issue 2, pages 238-243
Published in print February 2011 | ISSN: 0032-0781
Published online January 2011 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcq201
OrchidBase: A Collection of Sequences of the Transcriptome Derived from Orchids

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry

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Orchids are one of the most ecological and evolutionarily significant plants, and the Orchidaceae is one of the most abundant families of the angiosperms. Genetic databases will be useful not only for gene discovery but also for future genomic annotation. For this purpose, OrchidBase was established from 37,979,342 sequence reads collected from 11 in-house Phalaenopsis orchid cDNA libraries. Among them, 41,310 expressed sequence tags (ESTs) were obtained by using Sanger sequencing, whereas 37,908,032 reads were obtained by using next-generation sequencing (NGS) including both Roche 454 and Solexa Illumina sequencers. These reads were assembled into 8,501 contigs and 76,116 singletons, resulting in 84,617 non-redundant transcribed sequences with an average length of 459 bp. The analysis pipeline of the database is an automated system written in Perl and C#, and consists of the following components: automatic pre-processing of EST reads, assembly of raw sequences, annotation of the assembled sequences and storage of the analyzed information in SQL databases. A web application was implemented with HTML and a Microsoft .NET Framework C# program for browsing and querying the database, creating dynamic web pages on the client side, analyzing gene ontology (GO) and mapping annotated enzymes to KEGG pathways. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. Consequently, the establishment of OrchidBase will provide researchers with a high-quality genetic resource for data mining and facilitate efficient experimental studies on orchid biology and biotechnology. The OrchidBase database is freely available at http://lab.fhes.tn.edu.tw/est.

Keywords: Expressed sequence tags; KEGG pathways; OrchidBase; Phalaenopsis orchids

Journal Article.  2267 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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