title: Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla.
abstract: The high chromosome numbers, polyploid genomes, and long juvenile phases of most ornamental orchid species render functional genomics difficult and limit the discovery of genes influencing horticultural traits. The orchid Erycina pusilla has a low chromosome number (2n = 12) and flowers in vitro within 1 year, making it a standout candidate for use as a model orchid. However, transcriptomic and genomic information from E. pusilla remains limited. In this study, next-generation sequencing (NGS) technology was used to identify 90,668 unigenes by de novo assembly. These unigenes were annotated functionally and analyzed with regard to their gene ontology (GO), clusters of orthologous groups (COG), and KEGG pathways. To validate the discovery methods, a homolog of CONSTANS (CO), one of the key genes in the flowering pathway, was further analyzed. The Arabidopsis CO-Like (COL) amino acid sequences were used to screen for homologs in the E. pusilla transcriptome database. Specific primers to the homologous unigenes were then used to isolate BAC clones, which were sequenced to identify 12 E. pusilla CO-like (EpCOL) full-length genes. Based on sequence homology, domain structure, and phylogenetic analysis, these EpCOL genes were divided into four groups. Four EpCOLs fused with GFP were localized in the nucleus. Some EpCOL genes were regulated by light. These results demonstrate that nascent E. pusilla resources (transcriptome and BAC library) can be used to investigate the E. pusilla photoperiod-dependent flowering genes. In future, this strategy can be applied to other biological processes, marketable traits, and molecular breeding in this model orchid.
authors: Department of Life Sciences, Tzu Chi University, Hualien, Taiwan.
authors: Ming-Lun
authors: ML
authors: Chou
authors: Ming-Che
authors: MC
authors: Shih
authors: Ming-Tsair
authors: MT
authors: Chan
authors: Shih-Yi
authors: SY
authors: Liao
authors: Chen-Tran
authors: CT
authors: Hsu
authors: Yao-Ting
authors: YT
authors: Haung
authors: Jeremy J W
authors: JJ
authors: Chen
authors: Der-Chih
authors: DC
authors: Liao
authors: Fu-Hui
authors: FH
authors: Wu
authors: Choun-Sea
authors: CS
authors: Lin
mesh_terms: D029681:Arabidopsis Proteins / Q000235:genetics*; D002940:Circadian Rhythm / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D017343:Genes, Plant / Q000235:genetics*; D049452:Green Fluorescent Proteins / Q000378:metabolism; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D059372:Nucleotide Motifs / Q000235:genetics; D029595:Orchidaceae / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D021381:Protein Transport; D017422:Sequence Analysis, DNA; D013347:Subcellular Fractions / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics
chemical_list: D029681:Arabidopsis Proteins; C092776:CONSTANS protein, Arabidopsis; D004268:DNA-Binding Proteins; D010940:Plant Proteins; D014157:Transcription Factors; D049452:Green Fluorescent Proteins