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Nanopore sequencing data and structural variants identified in Prunus avium seedlings derived through mutagenesis.

ABSTRACT: DNA from four sweet cherry seedlings derived from gamma-irradiated female parents was sequenced via nanopore technology (Oxford Nanopore MinION). Total data yield was 8.07 Gb, ranging from 0.92 to 3.36 Gb per sample, with the average length of mapped reads ranging from 22 Kbp-24 Kbp. Sequence data was then analysed to identify and characterize variants using a published sweet cherry reference genome. Small and medium-sized indels (55-135 bp), as well as structural variants, including several large indels and complex variants were detected. Of these, 20 variants were localized within protein-coding gene sequences, including those encoding a putative F-box protein, an ADP-ribose glyxohydrolase protein, a predicted 26S protease regulatory subunit, an E3 ubiquitin protein ligase, a UDP-galactose/UDP-blucose transporter, an alpha/beta hydrolase domain-containing protein, a rhodanese-like domain-containing protein, a cytochrome p450 protein, phosphoinositide phosphatase, cysteine synthase-like, phosphoenolpyruvate carboxylase 4, and several uncharacterized proteins. These variations could have functional and phenotypic consequences that are useful in basic research and breeding.

SUBMITTER: McCord P

PROVIDER: S-EPMC9253453 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundThe nuclear DNA is conventionally used to assess the diversity and relatedness among different species, but variations at the DNA genome level has also been used to study the relationship among different organisms. In most species, mitochondrial and chloroplast genomes are inherited maternally; therefore it is anticipated that organelle DNA remains completely associated. Many research studies were conducted simultaneously on organelle genome. The objectives of this study was to analyze the genetic relationship between chloroplast and mitochondrial DNA in three Chinese Prunus genotypes viz., Prunus persica, Prunus domestica, and Prunus avium.ResultsWe investigated the genetic diversity of Prunus genotypes using simple sequence repeat (SSR) markers relevant to the chloroplast and mitochondria. Most of the genotypes were genetically similar as revealed by phylogenetic analysis. The Y2 Wu Xing (Cherry) and L2 Hong Xin Li (Plum) genotypes have a high similarity index (0.89), followed by Zi Ye Li (0.85), whereas; L1 Tai Yang Li (plum) has the lowest genetic similarity (0.35). In case of cpSSR, Hong Tao (Peach) and L1 Tai Yang Li (Plum) genotypes demonstrated similarity index of 0.85 and Huang Tao has the lowest similarity index of 0.50. The mtSSR nucleotide sequence analysis revealed that each genotype has similar amplicon length (509 bp) except M5Y1 i.e., 505 bp with CCB256 primer; while in case of NAD6 primer, all genotypes showed different sizes. The MEHO (Peach), MEY1 (Cherry), MEL2 (Plum) and MEL1 (Plum) have 586 bps; while MEY2 (Cherry), MEZI (Plum) and MEHU (Peach) have 585, 584 and 566 bp, respectively. The CCB256 primer showed highly conserved sequences and minute single polymorphic nucleotides with no deletion or mutation. The cpSSR (ARCP511) microsatellites showed the harmonious amplicon length. The CZI (Plum), CHO (Peach) and CL1 (Plum) showed 182 bp; whileCHU (Peach), CY2 (Cherry), CL2 (Plum) and CY1 (Cherry) showed 181 bp amplicon lengths.ConclusionsThese results demonstrated high conservation in chloroplast and mitochondrial genome among Prunus species during the evolutionary process. These findings are valuable to study the organelle DNA diversity in different species and genotypes of Prunus to provide in depth insight in to the mitochondrial and chloroplast genomes.

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Nanopore sequencing data and structural variants identified in Prunus avium seedlings derived through mutagenesis.

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