Molecular evolution and genome-wide analysis of the SBP-box family in cucumber ( Cucumis sativas )
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ORIGINAL PAPER
Molecular evolution and genome‑wide analysis of the SBP‑box family in cucumber (Cucumis sativas) Yue You1 · Yuanting Zheng1 · Jian Wang1 · Guang Chen1 · Sujuan Li1 · Jianfeng Shao1 · Guoan Qi2 · Fei Xu1 · Gangjun Wang1 · Zhong‑Hua Chen3,4 · Shengchun Xu1 Received: 22 September 2020 / Accepted: 20 October 2020 © Springer Nature B.V. 2020
Abstract SQUAMOSA promoter binding protein (SBP)-box gene family encodes a group of transcription factors that play essential roles in plant development and stress responses. However, the SBP-box gene family has not been well characterized in cucumber (Cucumis sativas). In the present study, we identified 15 putative SBP-box genes (CuSBPs) distributing on 4 chromosomes of cucumber. Evolutionary analysis showed that the green plant SBP family originated from liverworts. Phylogenic analysis divided CuSBPs into 6 groups similar to those of Arabidopsis and rice. Intron–exon and motif structure within each group shared common features. Expression pattern analysis of transcriptional data for flowering demonstrated conserved CuSBPs function in vegetative-to-reproductive transition. Gene expression of cucumber leaves in response to powdery mildew showed that conserved CuSBPs function in regulatory pathways such as hormone regulation pathways. Moreover, codon bias analysis explained the mutation and selection pressure exerted on SBP-box genes. This study comprehensively characterized cucumber CuSBP gene family, which is likely to provide a foundation to explore the functions of CuSBPs for improving yield, quality and stress tolerance of cucumber in the future. Keywords Codon usage bias · Cucumis sativas · Flowering · Gene family evolution · Powdery mildew
Background Transcription factors (TFs) are proteins binding to DNA sequence in specific manner to regulate transcription of target gene to specifically express in different cell types, Yue You and Yuanting Zheng have contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10725-020-00677-2) contains supplementary material, which is available to authorized users. * Shengchun Xu [email protected] 1
Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
2
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
3
School of Science, Western Sydney University, Penrith, NSW 2751, Australia
4
Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
tissues and developmental stages in response to diverse environmental conditions and regulating plant defense and stress resistance(Singh et al. 2002). SQUAMOSA promoter binding protein (SBP)-box genes are plant-specific TFs that regulate development (Ferreira e Silva et al. 2014; Xu et al. 2016) and stress responses (Singh and Jha 2017; Singh et al. 2017). Typically, SBP-box proteins tend to have a highly conserved SBP domain with 76 amino acids containing two zinc finger-like motifs and
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