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Molecular evolution of the clustered MIC-3 multigene family of Gossypium species

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Abstract

The Gossypium MIC-3 (Meloidogyne Induced Cotton-3) gene family is of great interest for molecular evolutionary studies because of its uniqueness to Gossypium species, multi-gene content, clustered localization, and root-knot nematode resistance-associated features. Molecular evolution of the MIC-3 gene family was studied in 15 tetraploid and diploid Gossypium genotypes that collectively represent seven phylogenetically distinct genomes. Synonymous (dS) and non-synonymous (dN) nucleotide substitution rates suggest that the second of the two exons of the MIC-3 genes has been under strong positive selection pressure, while the first exon has been under strong purifying selection to preserve function. Based on nucleotide substitution rates, we conclude that MIC-3 genes are evolving by a birth-and-death process and that a ‘gene amplification’ mechanism has helped to retain all duplicate copies, which best fits with the “bait and switch” model of R-gene evolution. The data indicate MIC-3 gene duplication events occurred at various rates, once per 1 million years (MY) in the allotetraploids, once per ~2 MY in the A/F genome clade, and once per ~8 MY in the D-genome clade. Variations in the MIC-3 gene family seem to reflect evolutionary selection for increased functional stability, while also expanding the capacity to develop novel “switch” pockets for responding to diverse pests and pathogens. Such evolutionary roles are congruent with the hypothesis that members of this unique resistance gene family provide fitness advantages in Gossypium.

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Acknowledgments

The authors thank Brian E. Scheffler and his lab members for their help in sequencing. We thank Eric J. Devor, Iowa State University, for his critical review and thorough editing of the manuscript. The authors thank the Office of International Research Programs, U.S. Department of Agriculture (USDA) for funding this study under research grant of UZB2-31017-TA-09 and U.S. Civilian Research & Development Foundation (CRDF) for project coordination. The authors thank anonymous reviewer(s) and editor of the manuscript for valuable suggestions.

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Correspondence to Ibrokhim Y. Abdurakhmonov.

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Communicated by D. Lightfoot.

Z. T. Buriev, S. Saha and I. Y. Abdurakhmonov contributed equally to the work.

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Buriev, Z.T., Saha, S., Shermatov, S.E. et al. Molecular evolution of the clustered MIC-3 multigene family of Gossypium species. Theor Appl Genet 123, 1359–1373 (2011). https://doi.org/10.1007/s00122-011-1672-y

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