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Genome-wide identification of CAMTA gene family members in Phaseolus vulgaris L. and their expression profiling during salt stress

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Abstract

The calmodulin-binding transcriptional activator (CAMTA) family was first observed in tobacco (NtER1) during a screening for the CaM-binding proteins, which are known to be one of the fast response stress proteins. Due to the increased importance of plant transcription factors in recent years; genome-wide identification of CAMTA genes has been performed in several plant species, except for Phaseolus vulgaris. Therefore, our aim was to identify and characterize CAMTA genes in P. vulgaris via in silico genome-wide analysis approach. Our results showed a total of eight CAMTA genes that were identified and observed on five out of 11 chromosomes of P. vulgaris. Four gene couples were found to be segmentally-duplicated and these segmental duplication events were shown to occur from 29.97 to 92.06 MYA. The phylogenetic tree of CAMTA homologs from P. vulgaris, A. thaliana, and G. max. revealed three groups based on their homology and the intron numbers of Pvul-CAMTA genes, ranged from 11 to 12. According to the syteny analysis; CAMTA genes of P. vulgaris and G. max revealed higher similarity, because they have highly similar genomes compared to A. thaliana. All Pvul-CAMTA genes were targeted by miRNAs, which play a role in response mechanism of salt stress. To detect expression levels in different plant tissues, mRNA analysis of Pvul-CAMTA genes were performed using publicly available expression data in Phytozome v12.1. In addition, responses of Pvul-CAMTA genes to salt stress, were also examined via both RNAseq and qRT-PCR analysis. To identify and to obtain insight into biological functions of CAMTA genes in the genome of P. vulgaris, several analyses were conducted using many online and offline bioinformatic tools, genome databases and qRT-PCR analyses. Due to this study being the first in the identification of CAMTA genes in P. vulgaris, this study could be considered as an useful source for future CAMTA genes studies in either P. vulgaris or comparative different plant species.

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All data generated or analysed during this study are included in this published article [and its supplementary information files]

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Authors’ contributions

All authors contributed equally to this manuscript.

Funding

This research has been partly supported by Ankara University Scientific Research Projects Coordination Unit. Project Number: 16H0430010, 2016

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Authors and Affiliations

  1. Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey

    İlker Büyük, Dilara Şener, Ata Umut Özsoy & Sümer Aras

  2. Faculty of Science, Department of Molecular Biology and Genetics, Erzurum Technical University, Erzurum, Turkey

    Emre İlhan

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Büyük, İ., İlhan, E., Şener, D. et al. Genome-wide identification of CAMTA gene family members in Phaseolus vulgaris L. and their expression profiling during salt stress. Mol Biol Rep 46, 2721–2732 (2019). https://doi.org/10.1007/s11033-019-04716-8

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