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Theoretical and Applied Genetics

, Volume 111, Issue 6, pp 1118–1126 | Cite as

SuperSAGE combined with PCR walking allows global gene expression profiling of banana (Musa acuminata), a non-model organism

  • Bert CoemansEmail author
  • Hideo Matsumura
  • Ryohei Terauchi
  • Serge Remy
  • Rony Swennen
  • László Sági
Original Paper

Abstract

Super-serial analysis of gene expression (SuperSAGE) was used to characterize, for the first time, the global gene expression pattern in banana (Musa acuminata). A total of 10,196 tags were generated from leaf tissue, representing 5,292 expressed genes. Forty-nine tags of the top 100 most abundantly expressed transcripts were annotated by homology to cDNA or EST sequences. Typically for leaf tissue, analysis of the transcript profiles showed that the majority of the abundant transcripts are involved in energy production, mainly photosynthesis. However, the most abundant tag was derived from a type 3 metallothionein transcript, which accounted for nearly 3% of total transcripts analysed. Furthermore, the 26-bp long SuperSAGE tags were applied in 3′-rapid amplification of cDNA ends (3′RACE) for the identification of unknown tags. In combination with thermal asymmetric interlaced PCR (TAIL-PCR), this allowed the recovery of a full gene sequence of a novel NADPH:protochlorophyllide oxidoreductase, the key enzyme in chlorophyll biosynthesis. SuperSAGE in conjunction with 3′RACE and TAIL-PCR will be a powerful tool for transcriptomics of non-model, but otherwise important organisms.

Keywords

Musa Acuminata Race Product Protochlorophyllide Oxidoreductase SuperSAGE Library Global Musa Genomic Consortium 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

MT

metallothionein

RACE

rapid amplification of cDNA ends

SAGE

serial analysis of gene expression

TAIL-PCR

thermal asymmetric interlaced PCR

Notes

Acknowledgements

The authors are indebted to Dr. S. Reich and Dr. D. Krüger (Humboldt University, Berlin, Germany) for providing the EcoP15I endonuclease and Dr. K.W. Kinzler (Johns Hopkins University, Baltimore, USA) for making the SAGE2000 software available. We are also grateful to Ms. I. Van den houwe (INIBAP Transit Center, Katholieke Universiteit Leuven, Belgium) for providing the plant material. Many thanks are due to Mr. I. Op De Beeck, Mr. C.O. Dimkpa and Ms. E. Thiry for technical assistance. Access to the Syngenta Musa 3′ EST database, donated by Syngenta to the International Network for the Improvement of Banana and Plantain (INIBAP) for use within the framework of the Global Musa Genomics Consortium is acknowledged. The research conducted at the Katholieke Universiteit Leuven was supported via an agreement with INIBAP by a grant of the Belgian Directorate-General for Development Cooperation (DGDC).

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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Bert Coemans
    • 1
    Email author
  • Hideo Matsumura
    • 2
  • Ryohei Terauchi
    • 2
  • Serge Remy
    • 1
  • Rony Swennen
    • 1
  • László Sági
    • 1
  1. 1.Laboratory of Tropical Crop ImprovementKatholieke Universiteit LeuvenLeuvenBelgium
  2. 2.Iwate Biotechnology Research CenterKitakamiJapan

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