A De Novo Floral Transcriptome Reveals Clues into Phalaenopsis Orchid Flower Development

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2015 May 14

PMID 25970572

Citations 12

Authors

Jian-Zhi Huang

Chih-Peng Lin

Ting-Chi Cheng

Bill Chia-Han Chang

Shu-Yu Cheng

Yi-Wen Chen

Chen-Yu Lee

Shih-Wen Chin

Fure-Chyi Chen

Affiliations

Soon will be listed here.

Abstract

Phalaenopsis has a zygomorphic floral structure, including three outer tepals, two lateral inner tepals and a highly modified inner median tepal called labellum or lip; however, the regulation of its organ development remains unelucidated. We generated RNA-seq reads with the Illumina platform for floral organs of the Phalaenopsis wild-type and peloric mutant with a lip-like petal. A total of 43,552 contigs were obtained after de novo assembly. We used differentially expressed gene profiling to compare the transcriptional changes in floral organs for both the wild-type and peloric mutant. Pair-wise comparison of sepals, petals and labellum between peloric mutant and its wild-type revealed 1,838, 758 and 1,147 contigs, respectively, with significant differential expression. PhAGL6a (CUFF.17763), PhAGL6b (CUFF.17763.1), PhMADS1 (CUFF.36625.1), PhMADS4 (CUFF.25909) and PhMADS5 (CUFF.39479.1) were significantly upregulated in the lip-like petal of the peloric mutant. We used real-time PCR analysis of lip-like petals, lip-like sepals and the big lip of peloric mutants to confirm the five genes' expression patterns. PhAGL6a, PhAGL6b and PhMADS4 were strongly expressed in the labellum and significantly upregulated in lip-like petals and lip-like sepals of peloric-mutant flowers. In addition, PhAGL6b was significantly downregulated in the labellum of the big lip mutant, with no change in expression of PhAGL6a. We provide a comprehensive transcript profile and functional analysis of Phalaenopsis floral organs. PhAGL6a PhAGL6b, and PhMADS4 might play crucial roles in the development of the labellum in Phalaenopsis. Our study provides new insights into how the orchid labellum differs and why the petal or sepal converts to a labellum in Phalaenopsis floral mutants.

Citing Articles

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References

Chang Y, Kao N, Li J, Hsu W, Liang Y, Wu J . Characterization of the possible roles for B class MADS box genes in regulation of perianth formation in orchid. Plant Physiol. 2009; 152(2):837-53. PMC: 2815905. DOI: 10.1104/pp.109.147116. View

Matas A, Yeats T, Buda G, Zheng Y, Chatterjee S, Tohge T . Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. Plant Cell. 2011; 23(11):3893-910. PMC: 3246317. DOI: 10.1105/tpc.111.091173. View

Wang Z, Gerstein M, Snyder M . RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2008; 10(1):57-63. PMC: 2949280. DOI: 10.1038/nrg2484. View

Bowman J, Smyth D, Meyerowitz E . Genetic interactions among floral homeotic genes of Arabidopsis. Development. 1991; 112(1):1-20. DOI: 10.1242/dev.112.1.1. View

Zhang J . Overexpression analysis of plant transcription factors. Curr Opin Plant Biol. 2003; 6(5):430-40. DOI: 10.1016/s1369-5266(03)00081-5. View

Uddenberg D, Reimegard J, Clapham D, Almqvist C, VON Arnold S, Emanuelsson O . Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor. Plant Physiol. 2012; 161(2):813-23. PMC: 3561021. DOI: 10.1104/pp.112.207746. View

Kanehisa M, Goto S . KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 1999; 28(1):27-30. PMC: 102409. DOI: 10.1093/nar/28.1.27. View

Rijpkema A, Zethof J, Gerats T, Vandenbussche M . The petunia AGL6 gene has a SEPALLATA-like function in floral patterning. Plant J. 2009; 60(1):1-9. DOI: 10.1111/j.1365-313X.2009.03917.x. View

Roberts A, Pachter L . Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods. 2012; 10(1):71-3. PMC: 3880119. DOI: 10.1038/nmeth.2251. View

10.

Aceto S, Sica M, De Paolo S, DArgenio V, Cantiello P, Salvatore F . The analysis of the inflorescence miRNome of the orchid Orchis italica reveals a DEF-like MADS-box gene as a new miRNA target. PLoS One. 2014; 9(5):e97839. PMC: 4022656. DOI: 10.1371/journal.pone.0097839. View

11.

Chang Y, Chiu Y, Wu J, Yang C . 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. 2009; 50(8):1425-38. DOI: 10.1093/pcp/pcp087. View

12.

Corley S, Carpenter R, Copsey L, Coen E . Floral asymmetry involves an interplay between TCP and MYB transcription factors in Antirrhinum. Proc Natl Acad Sci U S A. 2005; 102(14):5068-73. PMC: 555980. DOI: 10.1073/pnas.0501340102. View

13.

Theissen G . Development of floral organ identity: stories from the MADS house. Curr Opin Plant Biol. 2001; 4(1):75-85. DOI: 10.1016/s1369-5266(00)00139-4. View

14.

Duan Y, Xing Z, Diao Z, Xu W, Li S, Du X . Characterization of Osmads6-5, a null allele, reveals that OsMADS6 is a critical regulator for early flower development in rice (Oryza sativa L.). Plant Mol Biol. 2012; 80(4-5):429-42. DOI: 10.1007/s11103-012-9958-2. View

15.

Sedeek K, Qi W, Schauer M, Gupta A, Poveda L, Xu S . Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids. PLoS One. 2013; 8(5):e64621. PMC: 3667177. DOI: 10.1371/journal.pone.0064621. View

16.

Schulz M, Zerbino D, Vingron M, Birney E . Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics. 2012; 28(8):1086-92. PMC: 3324515. DOI: 10.1093/bioinformatics/bts094. View

17.

Lohmann J, Weigel D . Building beauty: the genetic control of floral patterning. Dev Cell. 2002; 2(2):135-42. DOI: 10.1016/s1534-5807(02)00122-3. View

18.

Raju N, Gnanesh B, Lekha P, Jayashree B, Pande S, Hiremath P . The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC Plant Biol. 2010; 10:45. PMC: 2923520. DOI: 10.1186/1471-2229-10-45. View

19.

Wellmer F, Alves-Ferreira M, Dubois A, Riechmann J, Meyerowitz E . Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet. 2006; 2(7):e117. PMC: 1523247. DOI: 10.1371/journal.pgen.0020117.eor. View

20.

Goto K, Meyerowitz E . Function and regulation of the Arabidopsis floral homeotic gene PISTILLATA. Genes Dev. 1994; 8(13):1548-60. DOI: 10.1101/gad.8.13.1548. View