Transcriptome Analyses of Mosaic (MSC) Mitochondrial Mutants of Cucumber in a Highly Inbred Nuclear Background

Abstract

Cucumber (Cucumis sativus L.) has a large, paternally transmitted mitochondrial genome. Cucumber plants regenerated from cell cultures occasionally show paternally transmitted mosaic (MSC) phenotypes, characterized by slower growth, chlorotic patterns on the leaves and fruit, lower fertility, and rearrangements in their mitochondrial DNAs (mtDNAs). MSC lines 3, 12, and 16 originated from different cell cultures all established using the highly inbred, wild-type line B. These MSC lines possess different rearrangements and under-represented regions in their mtDNAs. We completed RNA-seq on normalized and non-normalized cDNA libraries from MSC3, MSC12, and MSC16 to study their nuclear gene-expression profiles relative to inbred B. Results from both libraries indicated that gene expression in MSC12 and MSC16 were more similar to each other than MSC3. Forty-one differentially expressed genes (DEGs) were upregulated and one downregulated in the MSC lines relative to B. Gene functional classifications revealed that more than half of these DEGs are associated with stress-response pathways. Consistent with this observation, we detected elevated levels of hydrogen peroxide throughout leaf tissue in all MSC lines compared to wild-type line B. These results demonstrate that independently produced MSC lines with different mitochondrial polymorphisms show unique and shared nuclear responses. This study revealed genes associated with stress response that could become selection targets to develop cucumber cultivars with increased stress tolerance, and further support of cucumber as a model plant to study nuclear-mitochondrial interactions.

The Impact of cDNA Normalization on Long-Read Sequencing of a Complex Transcriptome

“…This probably could be achieved by sequencing at a sufficiently deep coverage of a non-normalized library; however, this would result in the highly abundant transcripts being overrepresented in the pre-processed data. In general, our results are in line with several reports based on earlier short-read sequencing platforms (454 and Illumina), in which a higher rate of gene discovery was found in the normalized library (Ewen-Campen et al, 2011; Ekblom et al, 2012; Mroz et al, 2018). It is noteworthy that the sequencing of a merged library of non-normalized and normalized cDNA was employed in many studies to include more genes (Karako-Lampert et al, 2014; Meireles et al, 2018).…”

Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

“…Osteoglycin ( OGN ) is involved in matrix assembly, cellular growth, and migration. Previous study showed that OGN was associated with fat acids composition traits to some extent [ 82 ] and regulated lipid differentiation through the Wnt/β-catenin signaling pathway [ 83 ]. TEAD3 which participates in the fatty acid, triacylglycerol, and ketone body metabolism pathway from the Reactome Pathways database [ 84 ], is a member of the transcriptional enhancer factor (TEF) family of transcription factors.…”

The Impact of Molecular Genetics in Plant Breeding: Realities and Perspectives

“…Besides, cucumber plants regenerated from cell cultures occasionally originate paternally transmitted mosaic (MSC) phenotypes, characterized by slower growth, chlorotic patterns on the leaves and fruit, lower fertility, and rearrangements in their mitochondrial DNAs (Malepszy et al, 1996;Lilly et al, 2001;Bartoszewski et al, 2004;2007;Del Valle-Echeverria et al, 2015). Analysis of nuclear gene expression in MSC mutants will help to understand mitochondrial retrograde signaling and will allow to identify genes associated with stress responses and use them as potential selection targets for breeding (Pawełkowicz et al, 2016;Mróz et al, 2018).…”