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Molecular Genetics and Genomics

, Volume 284, Issue 6, pp 455–475 | Cite as

Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato

  • Manoj K. Sharma
  • Rahul Kumar
  • Amolkumar U. Solanke
  • Rita Sharma
  • Akhilesh K. Tyagi
  • Arun K. Sharma
Original Paper

Abstract

Ethylene responsive transcription factors have been shown to be intimately connected to plant development, defense responses and stress signaling pathways and in order to use them for plant improvement, we need to have better understanding of these proteins. In this study, 85 ERF genes have been identified from tomato using raw EST data in various public repositories. Phylogenetic analysis with tomato ERF domains revealed their distribution in all the groups, previously identified in model systems. MEME motif analysis resulted in identification of conserved domains, characteristic to member of each clade, in addition to ERF domain. Expression analysis during vegetative and reproductive stages of development using QPCR and tomato GeneChip® arrays, revealed their tissue-specific/preferential accumulation. In total, 57 genes were found to be differentially expressed during temporal stages of tomato fruit development. The expression analysis of 23 ERF family genes representing each clade in response to seven abiotic stress treatments revealed their differential expression in response to more than one abiotic stress treatments. Results suggest that ERF genes play diverse roles in plant’s life and comprehensive data generated will be helpful in conducting functional genomics studies to understand their precise role during plant development and stress response.

Keywords

Development Ethylene Ethylene response factor Expression Ripening Stress 

Abbreviations

CAP3

Contig assembly program

ERF

Ethylene responsive factor

EST

Expressed sequence tag

GEO

Gene Expression Omnibus

HMM

Hidden Markov Model

IMG

Immature green

MEME

Multiple EM (Expectation Maximization) for Motif Elicitation

NCBI

National Center for Biotechnology Information

NJ

Neighbor-joining

PTFD

Plant Transcription Factor Database

SGN

SOL Genomics Network

SMART

Simple Modular Architecture Research Tool

TFGD

Tomato Functional Genomics Database

TGI

Tomato Gene Indices

Notes

Acknowledgments

This work has been funded by Department of Biotechnology, Government of India. RK and AUS acknowledge Council for Scientific and Industrial Research (CSIR) for senior research fellowships.

Supplementary material

438_2010_580_MOESM1_ESM.xlsx (14 kb)
(XLSX 15 KB)
438_2010_580_MOESM2_ESM.txt (90 kb)
(TXT 90 KB)
438_2010_580_MOESM3_ESM.txt (21 kb)
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438_2010_580_MOESM4_ESM.pdf (290 kb)
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438_2010_580_MOESM5_ESM.jpg (1.4 mb)
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438_2010_580_MOESM6_ESM.xlsx (74 kb)
MEME Suite version 4.0.0 (Optimum width 6-200 AA; Any number of repetitions; Maximum number of motifs 25) was used to identify conserved motifs in tomato ERFs (XLSX 75 KB)
438_2010_580_MOESM7_ESM.xlsx (77 kb)
Conserved motif sequences were blast searched in NCBI to find homologous sequences from other plants and non-plant organisms to study taxonomic hierarchy of these motifs (XLSX 78 KB)
438_2010_580_MOESM8_ESM.xlsx (16 kb)
(XLSX 16 KB)

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Manoj K. Sharma
    • 1
    • 2
  • Rahul Kumar
    • 1
  • Amolkumar U. Solanke
    • 1
    • 3
  • Rita Sharma
    • 1
    • 2
  • Akhilesh K. Tyagi
    • 1
    • 4
  • Arun K. Sharma
    • 1
  1. 1.Department of Plant Molecular BiologyUniversity of Delhi (South Campus)New DelhiIndia
  2. 2.Department of Plant PathologyUniversity of CaliforniaDavisUSA
  3. 3.National Research Centre on Plant Biotechnology, IARINew DelhiIndia
  4. 4.National Institute of Plant Genome ResearchNew DelhiIndia

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