Snake melon (Cucumis melo subsp. melo L. var. flexuosus (L.) Naudin) is an ancient and traditional crop in the Mediterranean region. Nevertheless, there has been poor interest in assessing snake melon germplasm where its genetic resources have not been surveyed before despite their potential in adaptation to environmental changes. In this study, we assess the genetic diversity of snake melon landraces collected from different Lebanese regions at both morphological and molecular levels. Morphological characterization using a set of 18 descriptors revealed an important phenotypic variability among the landraces studied. Principle component analysis indicated that fruit hair and its consistency, fruit size, and skin color pattern were good criteria for discriminating among landraces. Based on the scatter plot diagram, landraces of snake melon formed five different groups with one being defined as typical var. flexuosus. Ten simple sequence repeat (SSR) markers were used for the molecular characterization. Fifty-six different alleles were detected, with an average of 5.6 alleles per locus. Polymorphism information content of SSR markers ranged from 0.06 to 0.84 (average 0.38). Cluster analysis based on molecular markers showed high genetic diversity and divided the landraces into five distinct genetic groups, confirming thereby the morphological variability. Findings of this study indicate a significant diversity for the Lebanese snake melon germplasm that must be further conserved and considered in improvement programs of this ancient crop.

Environmental changes, both natural and anthropogenic, mainly related to rising temperatures and water scarcity, are clearly visible around the world. Climate change is important for crop production and is a major issue for the growth and productivity of cucumbers. Processes such as sex determination, flower morphogenesis and fruit development in cucumbers are highly sensitive to various forms of stress induced by climatic changes. It is noteworthy that many factors, including genetic factors, transcription factors, phytohormones and miRNAs, are crucial in regulating these processes and are themselves affected by climate change. Changes in the expression and activity of these factors have been observed as a consequence of climatic conditions. This review focuses primarily on exploring the effects of climate change and abiotic stresses, such as increasing temperature and drought, on the processes of sex determination, reproduction, and fruit development in cucumbers at the molecular level. In addition, it highlights the existing research gaps that need to be addressed in order to improve our understanding of the complex interactions between climate change and cucumber physiology. This, in turn, may lead to strategies to mitigate the adverse effects and enhance cucumber productivity in a changing climate.

The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA’s target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analyses for possible interactions at the level of target proteins, differentially expressed genes (DEGs) and genes affected by genomic polymorphisms. We assume that miRNAs can indirectly influence molecular networks and play a role in many different regulatory pathways, leading to somaclonal variation. This regulation is supposed to occur through the process of the target gene cleavage or translation inhibition, which in turn affects the proteome, as we have shown in the example of molecular networks. This is a new approach combining levels from DNA-seq through mRNA-seq, sRNA-seq and in silico PPI in the area of plants’ somaclonal variation.

The availability of a well-organized and annotated reference genome is essential for genome research and the analysis of re-sequencing approaches. The B10v3 cucumber (Cucumis sativus L.) reference genome has been sequenced and assembled into 8035 contigs, a small fraction of which have been mapped to individual chromosomes. Currently, bioinformatics methods based on comparative homology have made it possible to re-order the sequenced contigs by mapping them to the reference genomes. The B10v3 genome (North-European, Borszczagowski line) was rearranged against the genomes of cucumber 9930 (‘Chinese Long’ line) and Gy14 (North American line). Furthermore, a better insight into the organization of the B10v3 genome was obtained by integrating the data available in the literature on the assignment of contigs to chromosomes in the B10v3 genome with the results of the bioinformatic analysis. The combination of information on the markers used in the assembly of the B10v3 genome and the results of FISH and DArT-seq experiments confirmed the reliability of the in silico assignment. Approximately 98% of the protein-coding genes within the chromosomes were assigned and a significant proportion of the repetitive fragments in the sequenced B10v3 genome were identified using the RagTag programme. In addition, BLAST analyses provided comparative information between the B10v3 genome and the 9930 and Gy14 data sets. This revealed both similarities and differences in the functional proteins found between the coding sequences region in the genomes. This study contributes to better knowledge and understanding of cucumber genome line B10v3.

Plant reproduction is a fundamental process on Earth from the perspective of biodiversity, biomass gain, and crop productivity. It is therefore important to understand the sex determination process, and many researchers are investigating the molecular basis of this phenomenon. However, information on the influence of transcription factors (TFs), genes that encode DNA-binding proteins, on this process is limited, although cucumber is a model plant in this regard. In the present study, based on RNA-seq data for differentially expressed genes (DEGs), we aimed to investigate the regulatory TFs that may influence the metabolic processes in the shoot apex containing the forming flower buds. Therefore, the annotation of the genome of the B10 cucumber line was supplemented with the assigned families of transcription factors. By performing ontology analyses of the DEGs, the processes they participate in were identified, and TFs were located among the results. In addition, TFs that have significantly overrepresented targets among DEGs were detected, and sex-specific interactome network maps were generated, indicating the regulatory TFs based on their effects on DEGs and furthermore, on the processes leading to the formation of different-sex flowers. Among the most overrepresented TF families in the sex comparisons were the NAC, bHLH, MYB, and bZIP families. An interaction network analysis indicated the most abundant families among DEGs’ regulatory TFs were MYB, AP2/ERF, NAC, and bZIP, and those with the most significant impact on developmental processes were identified, namely the AP/ERF family, followed by DOF, MYB, MADS, and others. Thus, the networks’ central nodes and key regulators were identified with respect to male, female, and hermaphrodite forms. Here, we proposed the first model of the regulatory network of TFs that influences the metabolism of sex development in cucumber. These findings may help us to understand the molecular genetics and functional mechanisms underlying sex determination processes.

Plant reproduction is a very important process on Earth from the perspective of biodiversity, biomass gain and crop productivity. It is therefore important to understand sex determination process and many researchers are investigating the molecular basis of this phenomenon. However, information on the influence of transcription factors (TFs) on this process is limited, although cucumber is a model plant in this regard. In the present study, based on RNA-seq data for differential gene expression (DEG) analyses, we aimed to investigate the regulatory TFs that may influence the metabolomic processes in the shoot apex containing the forming flower buds. Therefore, a robust TF database was established for the B10v3 cucumber genome. Sex-specific interactome network maps were generated, indicating the regulatory TFs by their effects on DEGs and further on processes leading to the formation of different sex flowers. The network analysis identified major families of regulatory TFs. The most abundant families were: MYB, AP2/ERF, NAC and bZIP, and those with the greatest impact on developmental processes were identified, namely the AP/ERF family, followed by DOF, MYB, MADS and others. Thus, the central nodes and key regulators in the networks were identified with respect to male, female and hermaphrodite. Here, we proposed the first model of the regulatory network of TFs that influences the metabolism of sex development in cucumber. These findings may help to understand the molecular genetics and functional mechanisms underlying sex determination processes.