Journal Article

OrchidBase 2.0: Comprehensive Collection of Orchidaceae Floral Transcriptomes

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

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 54, issue 2, pages e7-e7
Published in print February 2013 | ISSN: 0032-0781
Published online January 2013 | e-ISSN: 1471-9053 | DOI: http://dx.doi.org/10.1093/pcp/pcs187
OrchidBase 2.0: Comprehensive Collection of Orchidaceae Floral Transcriptomes

More Like This

Show all results sharing these subjects:

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

GO

Show Summary Details

Preview

Both floral development and evolutionary trends of orchid flowers have long attracted the interest of biologists. However, expressed sequences derived from the flowers of other orchid subfamilies are still scarce except for a few species in Epidendroideae. In order to broadly increase our scope of Orchidaceae genetic information, we updated the OrchidBase to version 2.0 which has 1,562,071 newly added floral non-redundant transcribed sequences (unigenes) collected comprehensively from 10 orchid species across five subfamilies of Orchidaceae. A total of 662,671,362 reads were obtained by using next-generation sequencing (NGS) Solexa Illumina sequencers. After assembly, on average 156,207 unigenes were generated for each species. The average length of a unigene is 347 bp. We made a detailed annotation including general information, relative expression level, gene ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway mapping and gene network prediction. 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. We have re-designed the user interface in the new version. Users can enter the Phalaenopsis transcriptome or Orchidaceae floral transcriptome to browse or search the unigenes. OrchidBase 2.0 is freely available at http://orchidbase.itps.ncku.edu.tw/.

Keywords: Floral transcriptome; Gene network; KEGG pathways; Orchidaceae, OrchidBase; Orchid flowers

Journal Article.  2743 words.  Illustrated.

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

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.