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

Molecular Genetics and Genomics volume 284, pages 455–475 (2010)Cite this article

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.

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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

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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.

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Author notes

  1. Manoj K. Sharma & Rita Sharma

    Present address: Department of Plant Pathology, University of California, Davis, CA, 95616, USA

Affiliations

  1. Department of Plant Molecular Biology, University of Delhi (South Campus), New Delhi, 110021, India

    Manoj K. Sharma, Rahul Kumar, Amolkumar U. Solanke, Rita Sharma, Akhilesh K. Tyagi & Arun K. Sharma

  2. National Research Centre on Plant Biotechnology, IARI, New Delhi, 110012, India

    Amolkumar U. Solanke

  3. National Institute of Plant Genome Research, New Delhi, 110067, India

    Akhilesh K. Tyagi

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  1. Manoj K. Sharma
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  2. Rahul Kumar
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  3. Amolkumar U. Solanke
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  4. Rita Sharma
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  5. Akhilesh K. Tyagi
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  6. Arun K. Sharma
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Correspondence to Arun K. Sharma.

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Communicated by S. Hohmann.

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438_2010_580_MOESM6_ESM.xlsx

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

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)

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Sharma, M.K., Kumar, R., Solanke, A.U. et al. Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato. Mol Genet Genomics 284, 455–475 (2010). https://doi.org/10.1007/s00438-010-0580-1

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  • DOI: https://doi.org/10.1007/s00438-010-0580-1

Keywords

  • Development
  • Ethylene
  • Ethylene response factor
  • Expression
  • Ripening
  • Stress