Skip to main content
SpringerLink
Log in

Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla

  • Original Article
  • Published:
Planta Aims and scope Submit manuscript

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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

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

References

  • Albani MC, Coupland G (2010) Comparative analysis of flowering in annual and perennial plants. Curr Top Dev Biol 91:323–348

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Amasino R (2010) Seasonal and developmental timing of flowering. Plant J 61:1001–1013

    Article  PubMed  CAS  Google Scholar 

  • Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208

    Article  PubMed  CAS  Google Scholar 

  • Ballerini ES, Kramer EM (2011) In the light of evolution: a reevaluation of conservation in the CO-FT regulon and its role in photoperiodic regulation of flowering time. Front Plant Sci 2:18

    Article  Google Scholar 

  • Ben-Naim O, Eshed R, Parnis A, Teper-Bamnolker P, Shalit A, Coupland G, Samach A, Lifschitz E (2006) The CCAAT binding factor can mediate interactions between CONSTANS-like proteins and DNA. Plant J 46:462–476

    Article  PubMed  CAS  Google Scholar 

  • Borden KLB (1998) RING fingers and B-boxes: zinc-binding protein–protein interaction domains. Biochem Cell Biol 76:351–358

    Article  PubMed  CAS  Google Scholar 

  • Bouzidi MF, Franchel J, Tao Q, Stormo K, Mraz A, Nicolas P, Mouzeyar S (2006) A sunflower BAC library suitable for PCR screening and physical mapping of targeted genomic regions. Theor Appl Genet 113:81–89

    Article  PubMed  CAS  Google Scholar 

  • Campoli C, Drosse B, Searle I, Coupland G, von Korff M (2012) Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS. Plant J 69:868–880

    Article  PubMed  CAS  Google Scholar 

  • Cenci A, Somma S, Chantret N, Dubcovsky J, Blanco A (2004) PCR identification of durum wheat BAC clones containing genes coding for carotenoid biosynthesis enzymes and their chromosome localization. Genome 47:911–917

    Article  PubMed  CAS  Google Scholar 

  • Chang YY, Chiu YF, Wu JW, Yang CH (2009) Four orchid (Oncidium Gower Ramsey) AP1/AGL9-like MADS box genes show novel expression patterns and cause different effects on floral transition and formation in Arabidopsis thaliana. Plant Cell Physiol 50:1425–1438

    Article  PubMed  CAS  Google Scholar 

  • Chang YY, Kao NH, Li JY, Hsu WH, Liang YL, Wu JW, Yang CH (2010) Characterization of the possible roles for B Class MADS box genes in regulation of perianth formation in Orchid (Oncidium Gower Ramsey). Plant Physiol 152:837–853

    Article  PubMed  CAS  Google Scholar 

  • Chang YY, Chu YW, Chen CW, Leu WM, Hsu HF, Yang CH (2011) Characterization of Oncidium ‘Gower Ramsey’ transcriptomes using 454 GS-FLX pyrosequencing and their application to the identification of genes associated with flowering time. Plant Cell Physiol 52:1532–1545

    Article  PubMed  CAS  Google Scholar 

  • Chen J, Chen JY, Wang JN, Kuang JF, Shan W, Lu WJ (2012) Molecular characterization and expression profiles of MaCOL1, a CONSTANS-like gene in banana fruit. Gene 496:110–117

    Article  PubMed  CAS  Google Scholar 

  • Cheng XF, Wang ZY (2005) Overexpression of COL9, a CONSTANS-LIKE gene, delays flowering by reducing expression of CO and FT in Arabidopsis thaliana. Plant J 43:758–768

    Article  PubMed  CAS  Google Scholar 

  • Chia TY, Müller A, Jung C, Mutasa-Göttgens ES (2008) Sugar beet contains a large CONSTANS-LIKE gene family including a CO homologue that is independent of the early-bolting (B) gene locus. J Exp Bot 59:2735–2748

    Article  PubMed  CAS  Google Scholar 

  • Chiou CY, Yeh KW (2008) Differential expression of MYB gene (OgMYB1) determines color patterning in floral tissue of Oncidium Gower Ramsey. Plant Mol Biol 66:379–388

    Article  PubMed  CAS  Google Scholar 

  • Chiu YT, Lin CS, Chang C (2011) In vitro fruting and seed production in Erycina pusilla (L.) N. H. Willams and M. W. Chase. Propag Ornam Plants 11:131–136

    Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  PubMed  CAS  Google Scholar 

  • Datta S, Hettiarachchi GH, Deng XW, Holm M (2006) Arabidopsis CONSTANS-LIKE3 is a positive regulator of red light signaling and root growth. Plant Cell 18:70–84

    Article  PubMed  CAS  Google Scholar 

  • Delseny M, Han B, Hsing YI (2010) High throughput DNA sequencing: the new sequencing revolution. Plant Sci 179:407–422

    Article  PubMed  CAS  Google Scholar 

  • Febrer M, Wilhelm E, Al-Kaff N, Wright J, Powell W, Bevan MW, Boulton MI (2009) Rapid identification of the three homoeologues of the wheat dwarfing gene Rht using a novel PCR-based screen of three-dimensional BAC pools. Genome 52:993–1000

    Article  PubMed  CAS  Google Scholar 

  • Fu CH, Chen YW, Hsiao YY, Pan ZJ, Liu ZJ, Huang YM, Tsai WC, Chen HH (2011) OrchidBase: a collection of sequences of the transcriptome derived from orchids. Plant Cell Physiol 52:238–243

    Article  PubMed  CAS  Google Scholar 

  • Garber M, Grabherr MG, Guttman M, Trapnell C (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8:469–477

    Article  PubMed  CAS  Google Scholar 

  • Garner W, Allard HA (1920) Effect of the relative length of day and night and other factors of the environment on growth and reproduction in plants. J Agricultural Res 18:553–606

    Google Scholar 

  • González-Schain ND, Díaz-Mendoza M, Zurczak M, Suárez-López P (2012) Potato CONSTANS is involved in photoperiodic tuberization in a graft-transmissible manner. Plant J 70:678–690

    Article  PubMed  Google Scholar 

  • Griffiths S, Dunford RP, Coupland G, Laurie DA (2003) The evolution of CONSTANS-like gene families in barley, rice, and Arabidopsis. Plant Physiol 131:1855–1867

    Article  PubMed  CAS  Google Scholar 

  • Hao D, Ma P, Mu J, Chen S, Xiao P, Peng Y, Huo L, Xu L, Sun C (2012) De novo characterization of the root transcriptome of a traditional Chinese medicinal plant Polygonum cuspidatum. Sci China Life Sci 55:452–466

    Article  PubMed  CAS  Google Scholar 

  • Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R; Gene Ontology Consortium (2004) The gene ontology (GO) database and informatics resource. Nucleic Acids Res 32:D258–D261

    Article  Google Scholar 

  • Hayama R, Coupland G (2003) Shedding light on the circadian clock and the photoperiodic control of flowering. Curr Opin Plant Biol 6:13–19

    Article  PubMed  CAS  Google Scholar 

  • Hayama R, Coupland G (2004) The molecular basis of diversity in the photoperiodic flowering responses of Arabidopsis and rice. Plant Physiol 135:677–684

    Article  PubMed  CAS  Google Scholar 

  • Hayama R, Izawa T, Shimamoto K (2002) Isolation of rice genes possibly involved in the photoperiodic control of flowering by a fluorescent differential display method. Plant Cell Physiol 43:494–504

    Article  PubMed  CAS  Google Scholar 

  • Hepworth SR, Valverde F, Ravenscroft D, Mouradov A, Coupland G (2002) Antagonistic regulation of flowering-time gene SOC1 by CONSTANS and FLC via separate promoter motifs. EMBO J 21:4327–4337

    Article  PubMed  CAS  Google Scholar 

  • Holefors A, Opseth L, Ree Rosnes AK, Ripel L, Snipen L, Fossdal CG, Olsen JE (2009) Identification of PaCOL1 and PaCOL2, two CONSTANS-like genes showing decreased transcript levels preceding short day induced growth cessation in Norway spruce. Plant Physiol Biochem 47:105–115

    Article  PubMed  CAS  Google Scholar 

  • Hou CJ, Yang CH (2009) Functional analysis of FT and TFL1 orthologs from orchid (Oncidium Gower Ramsey) that regulate the vegetative to reproductive transition. Plant Cell Physiol 50:1544–1557

    Article  PubMed  CAS  Google Scholar 

  • Hsiao YY, Pan ZJ, Hsu CC, Yang YP, Hsu YC, Chuang YC, Shih HH, Chen WH, Tsai WC, Chen HH (2011) Research on orchid biology and biotechnology. Plant Cell Physiol 52:1467–1486

    Article  PubMed  CAS  Google Scholar 

  • Hsu HF, Yang CH (2002) An orchid (Oncidium Gower Ramsey) AP3-like MADS gene regulates floral formation and initiation. Plant Cell Physiol 43:1198

    Article  PubMed  CAS  Google Scholar 

  • Hsu HF, Huang CH, Chou LT, Yang CH (2003) Ectopic expression of an orchid (Oncidium Gower Ramsey) AGL6 -like gene promotes flowering by activating flowering time genes in Arabidopsis thaliana. Plant Cell Physiol 44:783–794

    Article  PubMed  CAS  Google Scholar 

  • Hsu HF, Hsieh WP, Chen MK, Chang YY, Yang CH (2010) C/D class MADS box genes from two monocots, orchid (Oncidium Gower Ramsey) and lily (Lilium longiflorum), exhibit different effects on floral transition and formation in Arabidopsis thaliana. Plant Cell Physiol 51:1029–1045

    Article  PubMed  CAS  Google Scholar 

  • Hsu CT, Liao DC, Wu FH, Liu NT, Shen SC, Chou SJ, Tung SY, Yang CH, Chan MT, Lin CS (2011) Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey. BMC Plant Biol 11:60–74

    Article  PubMed  CAS  Google Scholar 

  • Imaizumi T, Kay SA (2006) Photoperiodic control of flowering: not only by coincidence. Trends Plant Sci 11:550–558

    Article  PubMed  CAS  Google Scholar 

  • Iseli C, Jongeneel CV, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1:138–148

    Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280

    Article  PubMed  CAS  Google Scholar 

  • Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484

    Article  PubMed  CAS  Google Scholar 

  • Khanna R, Kronmiller B, Maszle DR, Coupland G, Holm M, Mizuno T, Wu SH (2009) The Arabidopsis B-box zinc finger family. Plant Cell 21:3416–3420

    Article  PubMed  CAS  Google Scholar 

  • Kikuchi R, Kawahigashi H, Oshima M, Ando T, Handa H (2012) The differential expression of HvCO9, a member of the CONSTANS-like gene family, contributes to the control of flowering under short-day conditions in barley. J Exp Bot 63:773–784

    Article  PubMed  CAS  Google Scholar 

  • Koornneef M, Hanhart CJ, van der Veen JH (1991) A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet 229:57–66

    Article  PubMed  CAS  Google Scholar 

  • Kurup S, Jones HD, Holdsworth MJ (2000) Interactions of the developmental regulator ABI3 with proteins identified from developing Arabidopsis seeds. Plant J 21:143–155

    Article  PubMed  CAS  Google Scholar 

  • Ledger S, Strayer C, Ashton F, Kay SA, Putterill J (2001) Analysis of the function of two circadian-regulated CONSTANS-LIKE genes. Plant J 26:15–22

    Article  PubMed  CAS  Google Scholar 

  • Levy YY, Dean C (1998) The transition to flowering. Plant Cell 10:1973–1990

    PubMed  CAS  Google Scholar 

  • Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272

    Article  PubMed  CAS  Google Scholar 

  • Li D, Deng Z, Qin B, Liu X, Men Z (2012) De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13:192

    Article  PubMed  CAS  Google Scholar 

  • Mardis ER (2008) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402

    Article  PubMed  CAS  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    PubMed  CAS  Google Scholar 

  • Metzker ML (2010) Sequencing technologies—the next generation. Nat Rev Genet 11:31–46

    Article  PubMed  CAS  Google Scholar 

  • Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264

    Article  PubMed  CAS  Google Scholar 

  • Mouradov A, Cremer F, Coupland G (2002) Control of flowering time: interacting pathways as a basis for diversity. Plant Cell 14(Suppl):S111–S130

    PubMed  CAS  Google Scholar 

  • Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco cultures. Physiol Plant 15:473–497

    Article  CAS  Google Scholar 

  • Nemoto Y, Kisaka M, Fuse T, Yano M, Ogihara Y (2003) Characterization and functional analysis of three wheat genes with homology to the CONSTANS flowering time gene in transgenic rice. Plant J 36:82–93

    Article  PubMed  CAS  Google Scholar 

  • Ness RW, Siol M, Barrett SC (2011) De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants. BMC Genomics 12:298

    Article  PubMed  CAS  Google Scholar 

  • Pan IC, Liao DC, Wu FH, Daniell H, Singh ND, Chang C, Shih MC, Chan MT, Lin CS (2012) Complete chloroplast genome sequence of an orchid model plant candidate: Erycina pusilla apply in tropical Oncidium breeding. PLoS One 7:e34738

    Article  PubMed  CAS  Google Scholar 

  • Patel RK, Jain M (2012) NGS QC Toolkit: a toolkit for quality control of next generation sequencing data. PLoS One 7:e30619

    Article  PubMed  CAS  Google Scholar 

  • Pellegrino G, Bellusci F, Musacchio A (2009) Genetic integrity of sympatrichybridising plant species: the case of Orchis italica and O. anthropophora. Plant Biol 11:434–441

    Article  PubMed  CAS  Google Scholar 

  • Pinheiro F, De Barros F, Palma-Silva C, Meyer D, Fay MF, Suzuki RM, Lexer C, Cozzolino S (2010) Hybridization and introgression across different ploidy levels in the neotropical orchids Epidendrum fulgens and E. puniceoluteum (Orchidaceae). Mol Ecol 19:3981–3994

    Article  PubMed  Google Scholar 

  • Putterill J, Robson F, Lee K, Simon R, Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80:847–857

    Article  PubMed  CAS  Google Scholar 

  • Robson F, Costa MM, Hepworth SR, Vizir I, Piñeiro M, Reeves PH, Putterill J, Coupland G (2001) Functional importance of conserved domains in the flowering-time gene CONSTANS demonstrated by analysis of mutant alleles and transgenic plants. Plant J 28:619–631

    Article  PubMed  CAS  Google Scholar 

  • Russell A, Samuel R, Klejna V, Barfuss MH, Rupp B, Chase MW (2010) Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes. Ann Bot 106:37–56

    Article  PubMed  CAS  Google Scholar 

  • Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF, Coupland G (2000) Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288:1613–1616

    Article  PubMed  CAS  Google Scholar 

  • Shi CY, Yang H, Wei CL, Yu O, Zhang ZZ, Jiang CJ, Sun J, Li YY, Chen Q, Xia T, Wan XC (2011) Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12:131

    Article  PubMed  CAS  Google Scholar 

  • Simpson GG, Dean C (2002) Arabidopsis, the Rosetta stone of flowering time? Science 296:285–289

    Article  PubMed  CAS  Google Scholar 

  • Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, Más P, Panda S, Kreps JA, Kay SA (2000) Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homolog. Science 289:768–771

    Article  PubMed  CAS  Google Scholar 

  • Su CL, Chao YT, Alex Chang YC, Chen WC, Chen CY, Lee AY, Hwa KT, Shih MC (2011) De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome. Plant Cell Physiol 52:1501–1514

    Article  PubMed  CAS  Google Scholar 

  • Suárez-López P, Wheatley K, Robson F, Onouchi H, Valverde F, Coupland G (2001) CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature 410:1116–1120

    Article  PubMed  Google Scholar 

  • Sun X, Zhou S, Meng F, Liu S (2012) De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing. Plant Cell Rep 31:1823–1828

    Article  PubMed  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  PubMed  CAS  Google Scholar 

  • Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV (2001) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 29:22–28

    Article  PubMed  CAS  Google Scholar 

  • Thiruvengadam M, Yang CH (2009) Ectopic expression of two MADS box genes from orchid (Oncidium Gower Ramsey) and lily (Lilium longiflorum) alters flower transition and formation in Eustoma grandiflorum. Plant Cell Rep 28:1463–1473

    Article  PubMed  CAS  Google Scholar 

  • Thomas B (2006) Light signals and flowering. J Exp Bot 57:3387–3393

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Torok M, Elkin LD (2000) Two B or not two B? Overview of the rapidly expanding B-box family of proteins. Differentiation 67:63–71

    Article  Google Scholar 

  • Turck F, Fornara F, Coupland G (2008) Regulation and identity of florigen: FLOWERING LOCUS T moves center stage. Annu Rev Plant Biol 59:573–594

    Article  PubMed  CAS  Google Scholar 

  • Valcerde F (2011) CONSTANS and the evolutionary origin of photoperiodic timing of flowering. J Exp Bot 62:2453–2463

    Article  Google Scholar 

  • Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang H, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, dePamphilis CW (2009) Comparison of next generation sequencing technologies for transcriptome characterization. BMC Genomics 10:347

    Article  PubMed  Google Scholar 

  • Wang Z, Fang B, Chen J, Zhang X, Luo Z, Huang L, Chen X, Li Y (2010) De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). BMC Genomics 11:726

    Article  PubMed  CAS  Google Scholar 

  • Yamashino T, Matsushika A, Fujimori T, Sato S, Kato T, Tabata S, Mizuno T (2003) A link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant Cell Physiol 44:619–629

    Article  PubMed  CAS  Google Scholar 

  • Yang SS, Tu ZJ, Cheung F, Xu WW, Lamb JF, Jung HJ, Vance CP, Gronwald JW (2011) Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems. BMC Genomics 12:199

    Article  PubMed  CAS  Google Scholar 

  • Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2484

    PubMed  CAS  Google Scholar 

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297

    Article  PubMed  CAS  Google Scholar 

  • Yim YS, Moak P, Sanchez-Villeda H, Musket TA, Close P, Klein PE, Mullet JE, McMullen MD, Fang Z, Schaeffer ML, Gardiner JM, Coe EH Jr, Davis GL (2007) A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps. BMC Genomics 8:47

    Article  PubMed  Google Scholar 

  • Zhang JX, Wu KL, Tian LN, Zeng SJ, Duan J (2011) Cloning and characterization of a novel CONSTANS-like gene from Phalaenopsis hybrid. Acta Physiol Plant 33:409–417

    Article  CAS  Google Scholar 

Download references

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).

Author information

Authors and Affiliations

  1. Department of Life Sciences, Tzu Chi University, Hualien, Taiwan

    Ming-Lun Chou & Shih-Yi Liao

  2. Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan

    Ming-Che Shih, Ming-Tsair Chan, Chen-Tran Hsu, Der-Chih Liao, Fu-Hui Wu & Choun-Sea Lin

  3. Academia Sinica Biotechnology Center in Southern Taiwan, Tainan, Taiwan

    Ming-Tsair Chan

  4. Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-yi, Taiwan

    Yao-Ting Haung

  5. Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan

    Jeremy J. W. Chen

Authors
  1. Ming-Lun Chou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ming-Che Shih
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ming-Tsair Chan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shih-Yi Liao
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chen-Tran Hsu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yao-Ting Haung
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Jeremy J. W. Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Der-Chih Liao
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Fu-Hui Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Choun-Sea Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Choun-Sea Lin.

Additional information

M.-L. Chou and M.-C. Shih contributed equally to this work.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Chou, ML., Shih, MC., Chan, MT. et al. Global transcriptome analysis and identification of a CONSTANS-like gene family in the orchid Erycina pusilla . Planta 237, 1425–1441 (2013). https://doi.org/10.1007/s00425-013-1850-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00425-013-1850-z

Keywords

Search

Navigation