Variation in plastid genomes in the gynodioecious species Silene vulgaris

Abstract

BackgroundGynodioecious species exist in two sexes – male-sterile females and hermaphrodites. Male sterility in higher plants often results from mitonuclear interaction between the CMS (cytoplasmic male sterility) gene(s) encoded by mitochondrial genome and by nuclear-encoded restorer genes. Mitochondrial and nuclear-encoded transcriptomes in females and hermaphrodites are intensively studied, but little is known about sex-specific gene expression in plastids. We have compared plastid transcriptomes between females and hermaphrodites in two haplotypes of a gynodioecious species Silene vulgaris with known CMS candidate genes.ResultsWe generated complete plastid genome sequences from five haplotypes S. vulgaris including the haplotypes KRA and KOV, for which complete mitochondrial genome sequences were already published. We constructed a phylogenetic tree based on plastid sequences of S. vulgaris. Whereas lowland S. vulgaris haplotypes including KRA and KOV clustered together, the accessions from high European mountains diverged early in the phylogram. S. vulgaris belongs among Silene species with slowly evolving plastid genomes, but we still detected 212 substitutions and 112 indels between two accessions of this species. We estimated elevated Ka/Ks in the ndhF gene, which may reflect the adaptation of S. vulgaris to high altitudes, or relaxed selection. We compared depth of coverage and editing rates between female and hermaphrodite plastid transcriptomes and found no significant differences between the two sexes. We identified 51 unique C to U editing sites in the plastid genomes of S. vulgaris, 38 of them in protein coding regions, 2 in introns, and 11 in intergenic regions. The editing site in the psbZ gene was edited only in one of two plastid genomes under study.ConclusionsWe revealed no significant differences between the sexes in plastid transcriptomes of two haplotypes of S. vulgaris. It suggests that gene expression of plastid genes is not affected by CMS in flower buds of S. vulgaris, although both sexes may still differ in plastid gene expression in specific tissues. We revealed the difference between the plastid transcriptomes of two S. vulgaris haplotypes in editing rate and in the coverage of several antisense transcripts. Our results document the variation in plastid genomes and transcriptomes in S. vulgaris.

Differentially Expressed Genes Shared by Two Distinct Cytoplasmic Male Sterility (CMS) Types of Silene vulgaris Suggest the Importance of Oxidative Stress in Pollen Abortion

“…We might have therefore directly compared the transcriptomes from three compartments-mitochondrial, plastid, and cytoplasmic-constructed from the same RNA samples. The mitochondrial transcriptomes exhibited only very few differences in coverage or editing between F and H [12,24], the plastid transcriptomes were completely identical between F and H [25]. Our observations contradict some studies, e.g., [19], which described numerous mitochondrial DE genes between male sterile and male fertile individuals.…”

“…The KRA and KOV haplotypes of S. vulgaris therefore carry different CMS determinants. Besides CMS-associated genes or regions, mitochondrial [ 12 , 24 ] and plastid [ 25 ] transcriptomes showed no significant differences between F and H plants.…”

“…We utilized RNA-seq data sets previously adopted for comparative mitochondrial and plastid transcriptomic studies in two S. vulgaris haplotypes [ 12 , 24 , 25 ] and compared nuclear gene expression between F and H flower buds. We found general similarity of differentially expressed (DE) genes between crops and S. vulgaris .…”

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

“…Plastome structure and synteny in the three newly sequenced Rhus accessions are somewhat typical for angiosperms (Wicke et al, 2011;. The degree of overall plastome sequence variation among the three Rhus accessions is similar to what is observed in other intraspecific studies of plastid genomic variation among photosynthetic angiosperms, for example, in: Silene vulgaris (Moench) Garcke (Krüger et al, 2019), Macadamia integrifolia Maiden & Betche (Nock et al, 2019), Quercus acutissima Carruth. (Zhang et al, 2020), Utricularia amethystina Salzm.…”

Characterization of Rheum palmatum mitochondrial genome and comparative analysis among Caryophyllales species

“…In the order Caryophyllales, the sizes of mitogenomes varied from 253 kb [46] to 11.3 Mb [47] . Among the 25 reported mitogenome assemblies for 20 species in Caryophyllales, 23 genome assemblies were circular molecules, one (Chenopodium album) was linear, and one (Silene vulgaris KRA) [48][49] consisted of a combination of circles, relaxed circles, linear molecules, and supercoiled DNA. Out of the total mitogenome assemblies, 11 were single-chromosome organization, whereas the remaining 14 were multi-chromosomal organizations.…”