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Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in cucumber (Cucumis sativus)

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Abstract

YTH domain-containing RNA-binding proteins are involved in post-transcriptional regulation and play important roles in the growth and development as well as abiotic stress responses of plants. However, YTH genes have not been previously studied in cucumber (Cucumis sativus). In this study, a total of five YTH genes (CsYTH1–CsYTH5) were identified in cucumber, which could be mapped on three out of the seven cucumber chromosomes. All CsYTH proteins had highly conserved C-terminal YTH domains, and two of them (CsYTH1 and CsYTH4) harbored extra CCCH and P/Q/N-rich domains. The phylogenesis, conserved motifs and exon–intron structure of YTH genes from cucumber, Arabidopsis and rice were also analyzed. The phylogenetically closely clustered YTHs shared similar gene structures and conserved motifs. An analysis of the cis-acting regulatory elements in the upstream region of these genes resulted in the identification of many cis-elements related to stress, hormone and development. Expression analysis based on the transcriptome data showed that some CsYTHs had development- or tissue-specific expression. In addition, their expression levels were altered under various stresses such as salt, drought, cold, and abscisic acid (ABA) treatments. These findings lay the foundation for the functional analysis of CsYTHs in the future.

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Acknowledgements

This work was funded by the Key Project of Youth Science Foundation of Jiangxi Province (20171ACB21025), the National Natural Science Foundation of China (31460522 and 31660578).

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    Authors and Affiliations

    1. Department of Biochemistry and Molecular Biology, College of Science, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China

      Yong Zhou, Lunwei Jiang & Shiqiang Liu

    2. Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, China

      Lifang Hu

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    Correspondence to Shiqiang Liu.

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    Yong Zhou and Lifang Hu contributed equally to this work.

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    Zhou, Y., Hu, L., Jiang, L. et al. Genome-wide identification and expression analysis of YTH domain-containing RNA-binding protein family in cucumber (Cucumis sativus). Genes Genom 40, 579–589 (2018). https://doi.org/10.1007/s13258-018-0659-3

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