Genetic variation is expressed by the presence of polymorphisms in compared genomes of individuals that can be transferred to next generations. The aim of this work was to reveal genome dynamics by predicting polymorphisms among the genomes of three individuals of the highly inbred B10 cucumber (Cucumis sativus L.) line. In this study, bioinformatic comparative genomics was used to uncover cucumber genome dynamics (also called real-time evolution). We obtained a new genome draft assembly from long single molecule real-time (SMRT) sequencing reads and used short paired-end read data from three individuals to analyse the polymorphisms. Using this approach, we uncovered differentiation aspects in the genomes of the inbred B10 line. The newly assembled genome sequence (B10v3) has the highest contiguity and quality characteristics among the currently available cucumber genome draft sequences. Standard and newly designed approaches were used to predict single nucleotide and structural variants that were unique among the three individual genomes. Some of the variant predictions spanned protein-coding genes and their promoters, and some were in the neighbourhood of annotated interspersed repetitive elements, indicating that the highly inbred homozygous plants remained genetically dynamic. This is the first bioinformatic comparative genomics study of a single highly inbred plant line. For this project, we developed a polymorphism prediction method with optimized precision parameters, which allowed the effective detection of small nucleotide variants (SNVs). This methodology could significantly improve bioinformatic pipelines for comparative genomics and thus has great practical potential in genomic metadata handling.

Sex determination and flower morphogenesis are very broad and complex processes controlled at many levels. Four clones have been isolated from cucumber transcriptomes, mapped onto the cucumber genome and checked if the corresponding genes expression differed between the vegetative and generative tissues (leaf, shoot apex, and 1-to 2-mm flower buds) of monoecious and gynoecious cucumber lines. To determine the role, and characteristics of identified genes in flower morphogenesis, as well as to understand the flower reproduction in cucumber, comprehensive computational studies using upstream regulatory elements and protein motifs were performed. A genome-wide overview of cucumber clones revealed that sequence of only one clone was mapped in the coding site. The gene was described as CsPSTK1 encoding serine/threonine kinase. The results allow us to conclude that cucumber generative organs differ in responsiveness to plant hormones due to the distinct signal transductions that are mediated by protein kinases in male and female organs of the floral buds and shoot apices. Protein kinases may be an alternative way for hormonal signal transduction in flowers of the opposite sex, taking part in the inhibition of unwanted generative organs that cause the development of a unisex flower.

Sex determination and flower morphogenesis are very broad and complex processes controlled at many levels. Four clones have been isolated from cucumber transcriptomes, mapped onto the cucumber genome and checked if the corresponding genes expression differed between the vegetative and generative tissues (leaf, shoot apex, and 1-to 2-mm flower buds) of monoecious and gynoecious cucumber lines. To determine the role, and characteristics of identified genes in flower morphogenesis, as well as to understand the flower reproduction in cucumber, comprehensive computational studies using upstream regulatory elements and protein motifs were performed. A genome-wide overview of cucumber clones revealed that sequence of only one clone was mapped in the coding site. The gene was described as CsPSTK1 encoding serine/threonine kinase. The results allow us to conclude that cucumber generative organs differ in responsiveness to plant hormones due to the distinct signal transductions that are mediated by protein kinases in male and female organs of the floral buds and shoot apices. Protein kinases may be an alternative way for hormonal signal transduction in flowers of the opposite sex, taking part in the inhibition of unwanted generative organs that cause the development of a unisex flower.

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