title: Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids.
abstract: BACKGROUND
  Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. In addition to the ecological significance, Phalaenopsis has been considered as an economically important floriculture industry worldwide. We aimed to use massively parallel 454 pyrosequencing for a global characterization of the Phalaenopsis transcriptome.
  
  
  RESULTS
  To maximize sequence diversity, we pooled RNA from 10 samples of different tissues, various developmental stages, and biotic- or abiotic-stressed plants. We obtained 206,960 expressed sequence tags (ESTs) with an average read length of 228 bp. These reads were assembled into 8,233 contigs and 34,630 singletons. The unigenes were searched against the NCBI non-redundant (NR) protein database. Based on sequence similarity with known proteins, these analyses identified 22,234 different genes (E-value cutoff, e-7). Assembled sequences were annotated with Gene Ontology, Gene Family and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among these annotations, over 780 unigenes encoding putative transcription factors were identified.
  
  
  CONCLUSIONS
  Pyrosequencing was effective in identifying a large set of unigenes from Phalaenopsis. The informative EST dataset we developed constitutes a much-needed resource for discovery of genes involved in various biological processes in Phalaenopsis and other orchid species. These transcribed sequences will narrow the gap between study of model organisms with many genomic resources and species that are important for ecological and evolutionary studies.
authors.affiliation: Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.
authors.forename: Yu-Yun
authors.initials: YY
authors.lastname: Hsiao
authors.forename: Yun-Wen
authors.initials: YW
authors.lastname: Chen
authors.forename: Shi-Ching
authors.initials: SC
authors.lastname: Huang
authors.forename: Zhao-Jun
authors.initials: ZJ
authors.lastname: Pan
authors.forename: Chih-Hsiung
authors.initials: CH
authors.lastname: Fu
authors.forename: Wen-Huei
authors.initials: WH
authors.lastname: Chen
authors.forename: Wen-Chieh
authors.initials: WC
authors.lastname: Tsai
authors.forename: Hong-Hwa
authors.initials: HH
authors.lastname: Chen
mesh_terms: D020451:Contig Mapping; D030562:Databases, Protein; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D056726:Genetic Association Studies; D029595:Orchidaceae / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors