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.
Highlights
The scope of this study was to sequence and assemble the nuclear genome of the highly inbred cucumber (Cucumis sativus L.) B10 Borszczagowski line, annotate the gene structure, assign functions to the genes, and characterize the genetic variations among three individual plants of the B10 line
There is no clear terminology that is accepted by the research community, small nucleotide variants (SNVs) are considered to include single nucleotide polymorphisms (SNPs), multiple nucleotide polymorphisms (MNPs) that are variants in a nucleotide sequence, and insertions/deletions (InDels) of up to 50 nucleotides
On the basis of the Li 2014 study (Li 2014), we applied the following filters to the results of FreeBayes to increase the accuracy of this pipeline: low-complexity region exclusion, maximum read depth, unbiased double strand coverage, quality filter of minimum variant quality 30 (Phred), and minimum read depth > 30
Summary
The scope of this study was to sequence and assemble the nuclear genome of the highly inbred cucumber (Cucumis sativus L.) B10 Borszczagowski line, annotate the gene structure, assign functions to the genes, and characterize the genetic variations among three individual plants of the B10 line. It is extremely important to have a very good genome reference sequence because resequencing the lines and aligning them to the reference sequence enables the study of natural evolutionary changes. Molecular Genetics and Genomics (2020) 295:177–193 as well as changes caused by breeding processes. Our aim was to estimate the nature of genomic variation in the realtime evolutionary process. Comparative genomics can reveal detailed genetic variations in the form of small nucleotide variants (SNVs), larger structural rearrangements as structural variants (SVs), and copy number variations (CNVs). There is no clear terminology that is accepted by the research community, SNVs are considered to include single nucleotide polymorphisms (SNPs), multiple nucleotide polymorphisms (MNPs) that are variants in a nucleotide sequence, and insertions/deletions (InDels) of up to 50 nucleotides
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