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Genome-wide and molecular evolution analyses of the KT/HAK/KUP family in tomato (Solanum lycopersicum L.)

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Abstract

Potassium transporters belonging to the KT/HAK/KUP family play an important role in plant growth, development, mineral nutrition, and stress adaptation. In this study, we identified 19 KT/HAK/KUP family genes in tomato, distributed on 10 chromosomes, by using bioinformatics methods. A complete overview of the KT/HAK/KUP (SlHAK) genes in tomato is presented, including chromosome location, phylogeny, gene structure, and evolution pattern. Phylogenetic analysis of 19 SlHAK proteins suggested that group IV of the KT/HAK/KUP family is absent in the tomato genome. In addition, five pairs of segmental duplicated paralogs and two pairs of tandem duplicated paralogs were identified in the tomato KT/HAK/KUP family. This suggests that segmental duplication is predominant for the expansion of the SlHAK genes. Calculation of the approximate dates of duplication events using the synonymous substitution rate indicated that the segmental duplication of the KT/HAK/KUP genes in tomato originated 35.89–62.77 million years ago. Adaptive evolution analysis showed that purifying selection contributed to the evolution of segmental duplicated pairs. Furthermore, Tajima’s relative rate test indicated that all segmental duplicated pairs evolved at similar rates. As a first step toward a genome-wide analysis of the KT/HAK/KUP gene family in tomato, our results provide valuable information for understanding the function and evolution of the KT/HAK/KUP gene family in tomato and other species.

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Acknowledgments

This work was supported by Science and Technology and a grant from the Next-Generation BioGreen 21 Program (SSAC grant PJ009495), Rural Development Administration, Republic of Korea.

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The authors declare no conflict of interest in the content of this work.

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Authors and Affiliations

  1. Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea

    Tae Kyung Hyun & Yeonggil Rim

  2. College of Pharmacy, Catholic University of Daegu, Gyeongsan, 712-702, Republic of Korea

    Ekyune Kim

  3. Majors in Plant Resource and Environment, College of Agriculture & Life Sciences, SARI, Jeju National University, Jeju, 690-756, Republic of Korea

    Ju-Sung Kim

  4. The Research Institute for Subtropical Agriculture and Biotechnology, Jeju National University, Jeju, Republic of Korea

    Ju-Sung Kim

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  1. Tae Kyung Hyun
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  2. Yeonggil Rim
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Correspondence to Ju-Sung Kim.

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13258_2014_174_MOESM1_ESM.tif

Protein domain of the KT/HAK/KUP gene family in tomato. K+ transporter domain (k_trans; PF02705) is shown as boxes based on identification by Pfam

13258_2014_174_MOESM2_ESM.tif

Phylogenetic analysis of the KT/HAK/KUP gene family in tomato (Sl), Arabidopsis thaliana (At) and rice (Os, Oryza sativa L)

Regulatory sequences and cis-elements in the SlHAK promoter regions

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Hyun, T.K., Rim, Y., Kim, E. et al. Genome-wide and molecular evolution analyses of the KT/HAK/KUP family in tomato (Solanum lycopersicum L.). Genes Genom 36, 365–374 (2014). https://doi.org/10.1007/s13258-014-0174-0

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  • DOI: https://doi.org/10.1007/s13258-014-0174-0

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