Germins and germin-like proteins (GLPs) are glycoproteins closely associated with plant development and stress response in the plant kingdom. Here, we carried out genome-wide identification and expression analysis of the GLP gene family in cucumber to study their possible functions. A total of 38 GLP genes were identified in cucumber, which could be mapped to six out of the seven cucumber chromosomes. A phylogenetic analysis of the GLP members from cucumber, Arabidopsis and rice showed that these GLPs could be divided into six groups, and cucumber GLPs in the same group had highly similar conserved motif distribution and gene structure. Gene duplication analysis revealed that six cucumber GLP genes were located in the segmental duplication regions of cucumber chromosomes, while 14 genes were associated with tandem duplications. Tissue expression profiles of cucumber GLP genes showed that many genes were preferentially expressed in specific tissues. In addition, some cucumber GLP genes were differentially expressed under salt, drought and ABA treatments, as well as under DM inoculation. Our results provide important information for the functional identification of GLP genes in the growth, development and stress response of cucumber.

Heat shock protein 70 (Hsp70) is a class of HSPs involved in plant growth and development, stress response and regulation. The Hsp70 proteins exist widely in the plant world, but the detail information about Hsp70s is still unclear in cucumber. Based on the available cucumber genome, a total of 12 Hsp70 genes (CsHsp70-1 to CsHsp70-12) were identified in this study, and they were distributed among five out of seven chromosomes. The CsHsp70s were divided into four groups based on a phylogenetic analysis by using protein sequences from cucumber and other plants, and their conserved motifs were relatively conserved. Gene duplication analysis showed that segmental duplication is the main driving force of expansion in cucumber CsHsp70 genes. Promoter analysis of CsHsp70 genes showed that they contained many cis-acting elements involved in hormone and stress responses. Expression analysis by RNA-seq and qRT-PCR indicated that the expression of most CsHsp70 genes was associated with multiple biotic and abiotic stresses in cucumber. This study introduces the characteristics of cucumber CsHsp70 genes and the regulation of their expression levels in various abiotic and biotic stresses, which provided a basis for functional exploration and utilization of CsHsp70 genes in the future.

Calcium ions are important second messengers, playing an important role in the signal transduction pathways. Hyperosmolality gated calcium-permeable channels (OSCA) gene family members play critical modulating roles in response to osmotic-related abiotic stress as well as other abiotic and biotic stresses, which has been reported in many plant species such as Arabidopsis, rice, maize, and wheat. However, there has been no report about the identification and expression profile of the OSCA genes in cucumber. In this study, a total of nine OSCA genes were identified, which are unevenly distributed on the six chromosomes of cucumber. Phylogenetic analysis revealed that the OSCAs of cucumber, Arabidopsis, rice and maize were clustered into four clades. The motif arrangement of CsOSCAs was strongly conserved, and the CsOSCA genes in each group had similar genetic structure. A total of 11 and 10 types of cis-elements related to hormone and stress, respectively, were identified in the promoter regions of CsOSCA genes. Gene expression analysis indicated that the CsOSCA genes have different expression patterns in various tissues, and some of them were regulated by three osmotic-related abiotic stresses (salt, drought and ABA) and three biotic stresses (powdery mildew, downy mildew, and root-knot nematode). As the first genome-wide identification and characterization of the OSCA gene family in cucumber, this study lays a foundation for research on the biological function and evolutionary process of this gene family, which is of great significance for exploiting stress resistant cucumber varieties.

As a class of zinc finger transcription factors, B-box (BBX) proteins play diverse roles in numerous biological processes, and they have been identified in a series of plant species in recent years. However, the roles of BBX genes in regulating cucumber growth regulation and stress response have not yet been established. Here, a total of 22 BBX family genes were identified via an analysis of the latest cucumber genome data, which were classified into five groups (I–V) on the basis of their phylogenetic features and number of B-box domains and CCT domains. The CsBBX genes were unevenly distributed across the seven cucumber chromosomes, and segmental duplication was found to play a significant role in the expansion of the cucumber BBX gene family. Gene structure and motif composition analysis suggested that the evolutionarily close CsBBXs have similar conserved motif composition and gene structure. Most CsBBX genes possessed 1–3 introns, and intron gain rather than intron loss could contribute to the different structures of CsBBX genes across different groups during their evolution. Promoter analysis revealed the presence of 13 kinds of hormone-related and nine kinds of stress-related cis-regulatory elements in the promoter regions of these CsBBX genes. Expression analysis via RNA-seq and qRT-PCR suggested that the CsBBX genes exhibit differential expression in different tissues and in response to various abiotic and biotic stresses. This work constitutes a starting point for further revealing the function of the CsBBX genes and sheds light on the potential molecular mechanism of stress resistance in cucumber.

Leaf color mutants are the ideal materials to study the regulation mechanisms of chlorophyll biosynthesis and chloroplast development or as markers for crop breeding. In this study, we identified a virescent true leaf mutant se59 from the ethyl methane sulfonate (EMS)-induced mutant lines of cucumber (Cucumis sativus L.). The se59 mutant showed normal cotyledons, but the true leaf displays light green at early growth stage, which can recover normal green later. The se59 locus was controlled by a single recessive nuclear gene. The grana stacking in the chloroplasts of se59 decreased significantly, and both the photosynthetic ability and the photosynthetic pigment contents of the se59 were significantly lower than those of wild type. The results of BSA-seq and genotyping showed that an Invertase/Pectin Methyl Esterase Inhibitor (INV/PMEI) protein encoded by CsSE59 is a candidate gene for the virescent true leaf mutant. The expression level of CsSE59 in stem, leaf and root is high. Based on the transcriptome analysis of the first true leaf of se59 mutant, the expression levels of 17 leaf color related genes changed significantly, suggesting CsSE59 may regulate virescent true leaf by interacting with some of these genes in cucumber. The identification of CsSE59 is helpful to clarify the role of INV/PMEI in chloroplast development and to understand the mechanisms of leaf color variation in cucumber.

SIMILAR TO RCD-ONE (SRO) is a plant-specific small protein family that controls many biological processes including physiological development and stress responses. The SRO gene family has been studied in several plant species, but no detailed characterization and expression profiles of this important gene family were performed in cucumber. In this study, we characterize the SRO genes in cucumber, and determined their transcript levels in various tissues and under exposure to diverse biotic and abiotic stressors. Four SRO genes (named as CsSRO1–CsSRO4) were identified and isolated, which were distributed on three different chromosomes. Gene duplication analysis showed that only one pair of segmental duplication event was identified, but no tandem duplication events were detected. All CsSROs consist of the PARP domain and a C-terminal RST domain, while the N-terminal WWE domain was only present in CsSRO2 and CsSRO4. SROs from 15 plant species are divided into two groups (I and II), and group I can be further divided into four subgroups (Ia to Id) according to the phylogenetic tree. The conserved motif and gene structure analyses showed that SROs within the same branch of the phylogenetic tree have analogous conserved motifs configuration and gene structures. However, SRO genes possessed variable numbers of introns in different subgroups, which may affect the evolution of new family members. RNA-Seq data and qRT-PCR results showed that the four CsSRO genes have distinct expression pattern in various tissues and under diverse stresses, suggesting their multiple functions in plant growth and stress responses. The findings provide a basis for further research aiming at functional characterization of the regulatory mechanism to reveal the roles of CsSRO genes in developmental and stress-related processes of cucumber.