Genome-wide identification of CLE gene family and their potential roles in bolting and fruit bearing in cucumber (Cucumis sativus L.)

Abstract

AbstractBackgroundSignal peptides are essential for plant growth and development. In plants, biological processes including cell-cell communication, cellular proliferation and differentiation, cellular determination of self-incompatibility, and defensive responses, all depend heavily on peptide-signaling networks such as CLE (CLAVATA3/Embryo surrounding region-related). The CLEs are indispensable in different periods of plant growth and development, especially in maintaining the balance between proliferation and differentiation of stem cells in various meristematic tissues.The working system ofCLEgenes in cucumber, an important economical vegetable (Cucumis sativusL.), has not been fully studied yet. The distributional patterns of chromosome-level genome assembly in cucumber provide a fundamental basis for a genome-wide comparative analysis ofCLEgenes in such plants.ResultsA total of 26 individualCLEgenes were identified in Chinese long ‘9930’ cucumber, the majority of which belong to unstable short alkaline and hydrophilic peptides. A comparative analysis showed a close relationship in the development of CLE genes amongArabidopsis thaliana, melon, and cucumber. Half of the exon-intron structures of allCsCLEsgenes are single-exon genes, and motif 1, a typical CLE domain near the C-terminal functioning in signal pathways, is found in all cucumber CLE proteins but CsCLE9. The analysis of CREs (Cis-Regulatory Elements) in the upstream region of the 26 cucumberCLEgenes indicates a possible relationship betweenCsCLEgenes and certain functions of hormone response elements. Cucumber resulted closely related toArabidopsisand melon, having seven and 15 orthologousCLEgenes inArabidopsisand melon, respectively. Additionally, the calculative analysis of a pair of orthologous genes in cucumber showed that as a part of the evolutionary process,CLEgenes are undergoing a positive selection process which leads to functional differentiation. The specific expression of these genes was vigorous at the growth and development period and tissues. Cucumber geneCLV3was overexpressed inArabidopsis, more than half of the transformed plants in T1 generation showed the phenomena of obvious weakness of the development of growing point, no bolting, and a decreased ability of plant growth. Only two bolted strains showed that either the pod did not develop or the pod was short, and its development was significantly inferior to that in the wild type.ConclusionsIn this study, 26CLEgenes were identified in Chinese long ‘9930’ cucumber genome. TheCLEgenes were mainly composed of alkaline hydrophilic unstable proteins. The genes of theCLEfamily were divided into seven classes, and shared close relationships with their homologs inArabidopsisand melon. The specific expression of these genes was evaluated in different periods of growth and tissue development, andCLV3, which the representative gene of the family, was overexpressed inArabidopsis, suggesting that it has a role in bolting and fruit bearing in cucumber.