Insight into the Organization of the B10v3 Cucumber Genome by Integration of Biological and Bioinformatic Data

Abstract

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.

From Sequencing to Genome Editing in Cucurbitaceae: Application of Modern Genomic Techniques to Enhance Plant Traits

“…Cucumis sativus, commonly known as cucumber, is characterised by well-established reference lines, such as 9930 (a Chinese line) and Gy14 (a North American line) and the longest B10v3 (North European) [49][50][51]. Recently, a system for integrating experimental data with high-throughput genomic data was used by Turek et al [52], where a model of genome comparison and a merging of experimental data were proposed [52]. As more and more genomes are sequenced and assembled, comparative genomics methods and adaptive genome drafts are increasingly needed to standardise gene location and annotation information.…”

Understanding Transcription Factors and How They Affect Processes in Cucumber Sex Determination

“…Recently, genomes were compared using structural data presented in databases as well as previously reported experimental data. It was shown that the B10v3 genome was the longest due to its 342.5 Mbp assembled length [ 4 ]. Among others, in order to obtain the most complete picture of the relevant elements, in this study, we focused on this version of the genome for further analyses.…”

Genetics and marker-assisted breeding for sex expression in cucumber

“…About 94% of the cucumber genome is covered by B10 and is considered the most comprehensive draft version to date ( Osipowski et al, 2020 ). Recently, Turek et al (2023) gave more insight into the genome of B10v3 accession by comparing it with the genome of cucumber lines Gy-14 and 9930. Recent advances in genome sequencing have provided stimulating opportunities to accelerate research in cucumber breeding.…”