A high-quality cucumber genome assembly enhances computational comparative genomics

Abstract

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.

Molecular insight into somaclonal variation phenomena from transcriptome profiling of cucumber (Cucumis sativus L.) lines

“…The upor down-regulated DEGs were specific to individual groups of samples representing a single line (S1, S2, or S3), but the remainder of the genes were similar to the control B10 line. Nonlinear PCA for all genes (21661) detected in the cucumber reference genome B10v3 (Osipowski et al 2020) revealed structure in the data, with obvious subgroups of the somaclonal lines, especially with regard to DEGs (Fig. 3e, f).…”

“…To analyze gene expression and identify DEGs in somaclonal lines and B10 control plants, we performed transcriptome assembly with additional data from PCC Genomics (Osipowski et al 2020). As a reference genome we used the cucumber genomic sequence B10v3 (Gen-Bank: LKUO00000000).…”

“…The DEGs were mapped to individual chromosomes based on previously published data regarding contig positions on chromosomes (Osipowski et al 2020;Skarzyńska et al 2020). Of the total DEGs, 92.11% (385), 90.66% (330), and 76.56% (209) were assigned to chromosomes for the S1, S2, and S3 lines, respectively.…”

Effect of Transgenesis on mRNA and miRNA Profiles in Cucumber Fruits Expressing Thaumatin II

“…The C. sativus genome sequence B10v3 (GenBank: LKUO00000000) and annotated genes were retrieved from PCC Genomics (Polish Consortium of Cucumber Genome Sequencing) [26]). The RNA-seq reads from this project, together with transcriptomic data from previous PCC Genomics research, were used to generate the de novo transcriptome assembly [26]. Gene expression was analyzed by comparing the transcriptome data between the transgenic and wild-type plants.…”

Gynoecy instability in cucumber (Cucumis sativus L.) is due to unequal crossover at the copy number variation-dependent Femaleness (F) locus

“…For example, in Arabidopsis, CNVs could be observed among individuals separated by only one generation; numerous CNVs affecting hundreds of genes had already originated after only five generations [59][60][61] . In cucumber, Osipowski et al 62 reported 626 CNVs among three individual plants derived from a common ancestor after 21 or 22 generations of continuous self-pollination. CNVs could be generated through different genetic mechanisms including nonallelic homologous recombination (NAHR) or unequal crossing over (UCO), which results from aberrant homology recognition during homology-based DNA repair or meiosis 61,63 .…”