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Characterization of the tubby-like proteins (TLPs) gene family in Cucumis sativus L.: insights into the evolution, structure, and expression patterns under salt stress

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Abstract

Cucumber (Cucumis sativus L.) is a member of the Cucurbitaceae family and can be eaten raw in salads or cooked as a vegetable. The yield of cucumber is limited due to many factors including biotic and abiotic stresses. Tubby-like proteins (TLP) family genes are important regulators of growth and development in plants and are involved in a variety of biotic and abiotic stress responses. The specific function of the TLP family in cucumber has not been thoroughly investigated by a genetic study. Hence, we performed a comparative genomic analysis of cucumber TLP family genes using bioinformatics techniques. Herein, a total of 11 TLP proteins were identified from the cucumber genome and further divided into four different subgroups. Moreover, these CsTLPs were distributed randomly on the five chromosomal positions of cucumber. Motif analysis suggested that motif1 was commonly present in all CsTLPs proteins except CsTLP6. Gene ontology analysis of CsTLPs showed their involvement in the plasma membrane, cellular protein modifications, signal transduction, and stress responses. Similarly, Cis-acting elements showed stress-related elements, validating their role in mitigating various stresses. Expression profiling indicated that CsTLPs expressed dominantly with diverse expression patterns in various organs of the cucumber. The genes CsTLP2, CsTLP5, CsTLP7, and CsTLP10 showed higher expression as compared to the rest of the CsTLPs members under salt stress. The above findings and details can serve as a starting point for further research on TLP function in plants, especially in cucumbers.

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Acknowledgements

The authors extend their appreciation to the Researchers Supporting Project number (RSP-2024R369), King Saud University, Riyadh, Saudi Arabia. We acknowledge the Chinese Government for providing scholarships to I.U. for completing his M.Sc. degree research. We are thankful to National Institute for Genomics and Advanced Biotechnology (NIGAB), Pakistan, and Hongzhi’s Lab, China for providing the research facilities.

Funding

This research was conducted with the funds of the Science and Technology Program of Yunnan Province (Grant No. 202102AE090051) and the Yunnan Provincial Science and Technology Talent and Platform Project (202205AF150017).

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Author notes

  1. Ikram Ullah, Muhammad Uzair and Obaid Ur Rehman have equally contributed to this work.

Authors and Affiliations

  1. College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, 650201, China

    Ikram Ullah & Hongzhi Wu

  2. National Institute for Genomics and Advanced Biotechnology (NIGAB), Islamabad, 45500, Pakistan

    Muhammad Uzair & Obaid Ur Rehman

  3. Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan

    Safira Attacha & Syed Jehangir Shah

  4. Department of Biochemistry, Science College, King Saud University, 2455-11451, Riyadh, Saudi Arabia

    Kotb A. Attia

  5. School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009, China

    Sheraz Ahmad

  6. Department of Horticulture, Ghazi University, Dera Ghazi Khan, Pakistan

    Muhammad Salman

  7. Department of Horticulture, Faculty of Crop Production Sciences, The University of Agriculture Peshawar, Peshawar, Pakistan

    Hamid Ali

  8. Department of Agricultural Sciences, College of Agriculture and Environmental Sciences, Government College University, Faisalabad, 38000, Pakistan

    Muhammad Abdul Rehman Rashid

  9. Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City, Giza, 12588, Egypt

    Asmaa M. Abushady

  10. Department of Genetics, Agriculture College, Ain Shams University, Cairo, Egypt

    Asmaa M. Abushady

  11. Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan

    Sajid Fiaz

  12. Institute of Science and Technology, Niigata University, Ikarashi-2, Nishiku, Niigata, 950-2181, Japan

    Itoh Kimiko

  13. College of Horticulture, Northwest A&F University, Yangling, 712100, China

    Rugang Chen

  14. Institute of Horticultural Research, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China

    Jiaxun Liu

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  1. Ikram Ullah
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Contributions

Conceptualization, IU, MU, JL, and HW; methodology, software, and validation, OR, MS, SA, HA, MARR, SF, and IU; formal analysis and investigation, IU, OR, and MU; writing—original draft preparation, review, and editing, IU, MU, SA, SJS, KAA, AMA, IK, MARR, and HW; visualization, MU; supervision, HW, RC, and JL; funding acquisition, HW. All authors have read and agreed to the published version of the manuscript.

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Correspondence to Jiaxun Liu or Hongzhi Wu.

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Ullah, I., Uzair, M., Rehman, O.U. et al. Characterization of the tubby-like proteins (TLPs) gene family in Cucumis sativus L.: insights into the evolution, structure, and expression patterns under salt stress. Genet Resour Crop Evol 71, 2019–2036 (2024). https://doi.org/10.1007/s10722-023-01722-5

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