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Planta

, Volume 237, Issue 6, pp 1425–1441 | Cite as

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
Original Article

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.

Keywords

Expression profiling Flower induction Next-generation sequencing Orchidaceae Photoperiod RNA-Seq 

Abbreviations

CO

CONSTANS

CO, CO-like, TOC1

CCT

FT

FLOWERING LOCUS T

Hd1

HEADING DATE 1

COL

CO-like

NGS

Next-generation sequencing

ESTs

Expressed sequence tags

RNA-Seq

RNA sequencing

RACE

Rapid amplification of cDNA ends

GO

Gene ontology

COG

Clusters of orthologous groups

BBX

B-box zinc finger protein family

PPFD

Photosynthetic photon flux density

TAIR

The Arabidopsis information resource

OOGB

Oncidium orchid genome base

Notes

Acknowledgments

We would like to thank Ms. Anita K. Snyder and Ms. Miranda Loney for giving comments on the manuscript. This research was supported by Academia Sinica and Development Program of Industrialization for Agricultural Biotechnology, Taiwan (MCS and CSL) and National Science Council, Taiwan (grant No. NSC97-2311-B-320-002-MY3 to MLC).

Supplementary material

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Ming-Lun Chou
    • 1
  • Ming-Che Shih
    • 2
  • Ming-Tsair Chan
    • 2
    • 3
  • Shih-Yi Liao
    • 1
  • Chen-Tran Hsu
    • 2
  • Yao-Ting Haung
    • 4
  • Jeremy J. W. Chen
    • 5
  • Der-Chih Liao
    • 2
  • Fu-Hui Wu
    • 2
  • Choun-Sea Lin
    • 2
  1. 1.Department of Life SciencesTzu Chi UniversityHualienTaiwan
  2. 2.Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan
  3. 3.Academia Sinica Biotechnology Center in Southern TaiwanTainanTaiwan
  4. 4.Department of Computer Science and Information EngineeringNational Chung Cheng UniversityChia-yiTaiwan
  5. 5.Institute of Biomedical SciencesNational Chung-Hsing UniversityTaichungTaiwan

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