Global transcriptome analysis and identification of a CONSTANS -like gene family in the orchid Erycina pusilla
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ORIGINAL ARTICLE
Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla Ming-Lun Chou • Ming-Che Shih • Ming-Tsair Chan • Shih-Yi Liao Chen-Tran Hsu • Yao-Ting Haung • Jeremy J. W. Chen • Der-Chih Liao • Fu-Hui Wu • Choun-Sea Lin
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Received: 15 November 2012 / Accepted: 17 January 2013 Ó Springer-Verlag Berlin Heidelberg 2013
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 M.-L. Chou and M.-C. Shih contributed equally to this work.
Electronic supplementary material The online version of this article (doi:10.1007/s00425-013-1850-z) contains supplementary material, which is available to authorized users. M.-L. Chou S.-Y. Liao Department of Life Sciences, Tzu Chi University, Hualien, Taiwan M.-C. Shih M.-T. Chan C.-T. Hsu D.-C. Liao F.-H. Wu C.-S. Lin (&) Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan e-mail: [email protected] M.-T. Chan Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, Taiwan Y.-T. Haung Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-yi, Taiwan J. J. W. Chen Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
(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. Keywords Expression profiling Flower induction Next-generation sequencing Orchidaceae Photoperiod RNA-Seq Abbreviations CO CO, CO-like, TOC1 FT Hd1 COL NGS ESTs RNA-Seq RACE GO
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