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Transcriptome-wide identification of R2R3-MYB transcription factors in barley with their boron responsive expression analysis

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Abstract

MYB family of transcription factors (TF) comprises one of the largest transcription factors in plants and is represented in all eukaryotes. They include highly conserved MYB repeats (1R, R2R3, 3R, and 4R) in the N-terminus. In addition to this, they have diverse C-terminal sequences which help the protein gain wide distinct functions, such as controlling development, secondary metabolism, hormonal regulation and response to biotic and abiotic stress. Stress-responsive roles of the MYB TFs were reported for drought, salt, wounding, cold, freezing, dehydration and osmotic stresses. This study describes the identification of barley R2R3-MYB TFs including their expression analysis in tissues under control and Boron (B) toxic conditions. Conserved motifs for MYB proteins were searched into barley full-transcriptome RNA-seq data and a total of 320 protein sequences were filtered as MYB TFs in which 51 of them corresponded to R2R3 MYB TFs. Using various bioinformatics tools, their conserved domain structures, chromosomal distributions, gene duplications, comparative functional analysis, as well as phylogenetic relations with Arabidopsis thaliana, were conducted. Beside the RNA-seq data-based expression pattern analysis of 51 R2R3 MYB TFs, quantitative analysis of selected R2R3 MYB TF genes was assessed in control and B-stressed root and leaf tissues. Critical B-induced R2R3 MYB TFs were identified. It was concluded that the results would be useful for functional characterizations of R2R3-type MYB transcription factors that are possibly involved in both B stress and divergent regulation mechanisms in plants.

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Abbreviations

AMV:

Myeloblastosis virus

DBD:

DNA-binding domain

Gb:

Gigabase

IBSC:

International Barley Genome Sequencing Consortium

RPKM:

Reads per kilobase per million mapped reads

RT-qPCR:

Reverse transcriptase quantitative PCR

TAD:

Trans-acting domain

TF:

Transcription factors

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Acknowledgments

This study is supported by TUBITAK (Scientific and Technological Research Council of Turkey) (grant no.: 111T015) and the Scientific Research Fund of Fatih University under the project number of P50031105_G(1941). Also, we would like to thank Miss. Berçem Yeman for the manuscript proofreading.

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Authors and Affiliations

  1. Department of Biology, Faculty of Arts and Science, Fatih University, Buyukcekmece, Istanbul, Turkey

    Huseyin Tombuloglu & Guzin Kekec

  2. Department of Biology, Faculty of Science, Çankırı Karatekin University, Ballıca, Çankırı, Turkey

    Turgay Unver

  3. Department of Genetics and Bioengineering, International Burch, Sarajevo, Bosnia and Herzegovina

    Mehmet Serdal Sakcali

Authors
  1. Huseyin Tombuloglu
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  2. Guzin Kekec
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  3. Mehmet Serdal Sakcali
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  4. Turgay Unver
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Correspondence to Huseyin Tombuloglu.

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Communicated by S. Hohmann.

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Tombuloglu, H., Kekec, G., Sakcali, M.S. et al. Transcriptome-wide identification of R2R3-MYB transcription factors in barley with their boron responsive expression analysis. Mol Genet Genomics 288, 141–155 (2013). https://doi.org/10.1007/s00438-013-0740-1

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