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Genome-wide identification, characterization, and evolutionary analysis of NBS-encoding resistance genes in barley

3 Biotech volume 8, Article number: 453 (2018) Cite this article

Abstract

In this study, a systematic analysis of Nucleotide-Binding Site (NBS) disease resistance (R) gene family in the barley, Hordeum vulgare L. cv. Bowman, genome was performed. Using multiple computational analyses, we could identify 96 regular NBS-encoding genes and characterize them on the bases of structural diversity, conserved protein signatures, genomic distribution, gene duplications, differential expression, selection pressure, codon usage, regulation by microRNAs and phylogenetic relationships. Depending on the presence or absence of CC and LRR domains; the identified NBS genes were assigned to four distinct groups; NBS–LRR (53.1%), CC-NBS–LRR (14.6%), NBS (26%), and CC-NBS (6.3%). NBS-associated domain analysis revealed the presence of signal peptides, zinc fingers, diverse kinases, and other structural features. Eighty-five of the identified NBS-encoding genes were mapped onto the seven barley chromosomes, revealing that 50% of them were located on chromosomes 7H, 2H, and 3H, with a tendency of NBS genes to be clustered in the distal telomeric regions of the barley chromosomes. Nine gene clusters, representing 22.35% of total mapped barley NBS-encoding genes, were found, suggesting that tandem duplication stands for an important mechanism in the expansion of this gene family in barley. Phylogenetic analysis determined 31 HvNBS orthologs from rice and Brachypodium. 87 out of 96 HvNBSs were supported by expression evidence, exhibiting various and quantitatively uneven expression patterns across distinct tissues, organs, and development stages. Fourteen potential miRNA-R gene target pairs were further identified, providing insight into the regulation of NBS genes expression. These findings offer candidate target genes to engineer disease-resistant barley genotypes, and promote our understanding of the evolution of NBS-encoding genes in Poaceae crops.

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Abbreviations

CC:

Coiled-coil (domain)

IBSC:

The International Barley Genome Sequencing Consortium

LRR:

Leucine-rich repeat (domain)

NBS:

Nucleotide-binding site (domain)

NLR:

NOD-like receptors

miRNA:

MicroRNAs

TIR:

Toll-interleukin-1 receptor (domain)

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Acknowledgements

We gratefully acknowledge Abdennour Sébéi (Centre Régional de Recherches sur les Grandes Cultures, CRRGC, Béja, Tunisia), for his permanent logistic help. This study was financially supported by the Tunisian Ministry of Higher Education and Scientific Research.

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Affiliations

  1. Université de Tunis El Manar, Faculté des Sciences de Tunis, Unité de Recherche Génomique des Insectes Ravageurs des Cultures d’intérêt agronomique (GIRC, UR11ES10), El Manar, 2092, Tunis, Tunisia

    Yosra Habachi-Houimli, Yosra Khalfallah, Maha Mezghani-Khemakhem, Hanem Makni, Mohamed Makni & Dhia Bouktila

  2. Université de Tunis, Institut Supérieur de l’Animation pour la Jeunesse et la Culture (ISAJC), Bir El Bey, Tunisia

    Hanem Makni

  3. Université de Jendouba, Institut Supérieur de Biotechnologie de Béja (ISBB), 9000, Béja, Tunisia

    Dhia Bouktila

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  2. Yosra Khalfallah
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  3. Maha Mezghani-Khemakhem
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  4. Hanem Makni
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  5. Mohamed Makni
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  6. Dhia Bouktila
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Contributions

YHH analyzed data using bioinformatics tools, discussed the results and co-wrote the manuscript, under the guidance of DB. YK helped in performing bioinformatics analyses. MMK, HM, and MM helped to perform this study and contributed to discussions. DB designed this study, guided YHH in all analyses and discussions, and co-wrote the manuscript. All authors have read and approved the final manuscript.

Corresponding author

Correspondence to Dhia Bouktila.

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On behalf of all authors, the corresponding author states that there is no conflict of interest.

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Habachi-Houimli, Y., Khalfallah, Y., Mezghani-Khemakhem, M. et al. Genome-wide identification, characterization, and evolutionary analysis of NBS-encoding resistance genes in barley. 3 Biotech 8, 453 (2018). https://doi.org/10.1007/s13205-018-1478-6

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  • DOI: https://doi.org/10.1007/s13205-018-1478-6

Keywords

  • Hordeum vulgare
  • Nucleotide-binding site
  • Disease-resistance genes
  • Genome analysis