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In plants, heteromorphic self-incompatibility (HetSI) is a strategy for avoiding self-pollination and promoting outcrossing, and during this process, numerous protein-protein interaction events occur between the pistil and pollen. Previous studies in Primula and Fagopyrum that focused on HetSI systems have provided interesting insights; however, the molecular mechanism underlying HetSI remains largely unknown. In this study, we profiled the proteome of Plumbago auriculata stigmas before and after self-incompatible (SI) and self-compatible (SC) pollination. Comparative analyses were conducted by 4D-DIA (Four-dimensional data independent acquisition), a promising technology that increases the sensitivity and reduces the spectral complexity of proteomic analysis by adding a fourth dimension, ion mobility. The results revealed 33387 peptides and 5311 proteins in all samples. The pathways in which the differentially expressed proteins (DEPs) identified in the P × P (Pin style self-pollinated with pin pollen) vs. PS (Pin style) and T × T (Thrum style self-pollinated with thrum pollen) vs. TS (Thrum style) comparisons were significantly enriched were biosynthesis of secondary metabolites and pentose and glucuronate interconversions. In the P × T (Pin style cross-pollinated with thrum pollen) vs. PS and T × P (Thrum style cross-pollinated with pin pollen) vs. TS comparison, the top three pathways were biosynthesis of secondary metabolites, pentose and glucuronate interconversions, and phenylpropanoid biosynthesis. The phenylpropanoid biosynthesis, cutin, suberine and wax biosynthesis, and flavonoid biosynthesis pathways were enriched in the P × T vs. P × P comparison, and starch and sucrose metabolism, glycerophospholipid metabolism, and alpha-linolenic acid metabolism were abundant in the T × T vs. T × P comparison. The enriched pathways between PS and TS were the biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and pentose and glucuronate interconversion. Self-incompatibility protein S1 (SI S1), Mitogen-activated protein kinase 3/4 (MPK3/4), Mitogen-activated protein kinase kinase 2/3 (M2K2/3), Exocyst complex component EXO70A1 (E70A1) and Thioredoxin H1/2 (TRXH1/2) were found to be HetSI-related candidates, and O-fucosyltransferase 23 (OFT23), 3- ketoacyl-CoA synthase 6 (KCS6), Receptor-like protein kinase FERONIA (FERON), Fimbrin-5 (FIMB5), Pollen-specific leucine-rich repeat extensin-like protein 4 (PLRX4), Transcription initiation factor IIB-2 (TF2B2) and Pectinesterase 1 (AL11A), etc., were identified as other regulatory transducers. These findings combined with our morphological and reactive oxygen species (ROS) intensity analyses indicate that P. auriculata has typical dry-stigmas and that the HetSI mechanism might differ between the pin and thrum. SI S1 might be the key factor in HetSI, and ROS are overexpressed during SC pollination to rapidly activate the mitogen-activated protein kinase (MAPK)-mediated phosphorylation of E70A1 to maintain stigma receptivity in plants with HetSI. [ABSTRACT FROM AUTHOR]

Cytonuclear coordination between biparental-nuclear genomes and uniparental-cytoplasmic organellar genomes in plants is often resolved by genetic and transcriptional cytonuclear responses. Whether this mechanism also acts in allopolyploid members of other kingdoms is not clear. Additionally, cytonuclear coordination of interleaved allopolyploid cells/individuals within the same population is underexplored. The yeast Saccharomyces pastorianus provides the opportunity to explore cytonuclear coevolution during different growth stages and from novel dimensions. Using S. pastorianus cells from multiple growth stages in the same environment, we show that nuclear mitochondria-targeted genes have undergone both asymmetric gene conversion and growth stage-specific biased expression favoring genes from the mitochondrial genome donor (Saccharomyces eubayanus). Our results suggest that cytonuclear coordination in allopolyploid lager yeast species entails an orchestrated and compensatory genetic and transcriptional evolutionary regulatory shift. The common as well as unique properties of cytonuclear coordination underlying allopolyploidy between unicellular yeasts and higher plants offers novel insights into mechanisms of cytonuclear evolution associated with allopolyploid speciation. [ABSTRACT FROM AUTHOR]

Summary: This study explores how allopolyploidization reshapes the biased expression and asymmetric epigenetic modification of homoeologous gene pairs, and examines the regulation types and epigenetic basis of expression bias.We analyzed the gene expression and four epigenetic modifications (DNA methylation, H3K4me3, H3K27me3 and H3K27ac) of 29 976 homoeologous gene pairs in resynthesized, natural allopolyploid Brassica napus and an in silico 'hybrid'.We comprehensively elucidated the biased gene expression, asymmetric epigenetic modifications and the generational transmission characteristics of these homoeologous gene pairs in B. napus. We analyzed cis/trans effects and the epigenetic basis of homoeolog expression bias. There was a significant positive correlation between two active histone modifications and biased gene expression.We revealed that parental legacy was the dominant principle in the remodeling of homoeolog expression bias and asymmetric epigenetic modifications in B. napus, and further clarified that this depends on whether there were differences in the expression/epigenetic modifications of gene pairs in parents/progenitors. The maternal genome was dominant in the homoeolog expression bias of resynthesized B. napus, and this phenomenon was attenuated in natural B. napus. Furthermore, cis rather than trans effects were dominant when epigenetic modifications potentially affected biased expression of gene pairs in B. napus. [ABSTRACT FROM AUTHOR]