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Genome-wide characterization and expression pattern of auxin response factor (ARF) gene family in soybean and common bean

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Abstract

Auxin response factors (ARFs) encode one of the most abundant groups of auxin-mediated response transcription factors in higher plants and play a major role in various biological processes. The success of whole genome sequencing allows for comprehensive phylogenetic analysis of ARF genes in plants. Here, we identified 80 ARF genes belonging to five different groups in legume species, soybean (Glycine max, 55) and common bean (Phaseolus vulgaris, 25), based on phylogenetic analysis and supported by motif analysis. There is no member ARF of common bean in group V which contained two members from soybean, GmARF12 and GmARF55. The duplication events among two species were also observed by using Ks values. A majority of the ARF genes (96.1 %; 38 GmARFs and 56.0 %, 14 PvARFs) were segmentally duplicated while only two and one of ARF G. max and P. vulgaris genes were tandemly duplicated, respectively. In addition, expression profiling indicated that ARF genes in soybean and common bean perform various functions in plant growth and development, excluding flowering development. Furthermore, diversity of cis-elements in promoter regions also revealed differential expression of ARF proteins.

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Acknowledgments

This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2015R1D1A1A09060925).

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Authors and Affiliations

  1. Department of Biotechnology, Chonnam National University, Chonnam, Yeosu, 59626, Republic of Korea

    Bao Le, Muhammad Amjad Nawaz, Hafiz Mamoon Rehman & Gyuhwa Chung

  2. Department of Molecular Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea

    Thu Le

  3. Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, 17058, Republic of Korea

    Seung Hwan Yang

  4. Educational Scientific Center of Nanotechnology, Engineering School, Far Eastern Federal University, 37 Pushkinskaya Street, Vladivostok, Russian Federation, 690950

    Kirill S. Golokhvast

  5. National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, Jeonju, 54874, Republic of Korea

    Eunho Son

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Bao Le, Muhammad Amjad Nawaz, Hafiz Mamoon Rehman, Thu Le, Seung Hwan Yang, Kirill S. Golokhvast, Eunho Son and Gyuhwa Chung declares that they have no conflict of interest.

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Le, B., Nawaz, M.A., Rehman, H.M. et al. Genome-wide characterization and expression pattern of auxin response factor (ARF) gene family in soybean and common bean. Genes Genom 38, 1165–1178 (2016). https://doi.org/10.1007/s13258-016-0462-y

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