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Abstract Background and Aims Large clades of angiosperms are often characterized by diverse interactions with pollinators, but how these pollination systems are structured phylogenetically and biogeographically is still uncertain for most families. Apocynaceae is a clade of >5300 species with a worldwide distribution. A database representing >10 % of species in the family was used to explore the diversity of pollinators and evolutionary shifts in pollination systems across major clades and regions. Methods The database was compiled from published and unpublished reports. Plants were categorized into broad pollination systems and then subdivided to include bimodal systems. These were mapped against the five major divisions of the family, and against the smaller clades. Finally, pollination systems were mapped onto a phylogenetic reconstruction that included those species for which sequence data are available, and transition rates between pollination systems were calculated. Key Results Most Apocynaceae are insect pollinated with few records of bird pollination. Almost three-quarters of species are pollinated by a single higher taxon (e.g. flies or moths); 7 % have bimodal pollination systems, whilst the remaining approx. 20 % are insect generalists. The less phenotypically specialized flowers of the Rauvolfioids are pollinated by a more restricted set of pollinators than are more complex flowers within the Apocynoids + Periplocoideae + Secamonoideae + Asclepiadoideae (APSA) clade. Certain combinations of bimodal pollination systems are more common than others. Some pollination systems are missing from particular regions, whilst others are over-represented. Conclusions Within Apocynaceae, interactions with pollinators are highly structured both phylogenetically and biogeographically. Variation in transition rates between pollination systems suggest constraints on their evolution, whereas regional differences point to environmental effects such as filtering of certain pollinators from habitats. This is the most extensive analysis of its type so far attempted and gives important insights into the diversity and evolution of pollination systems in large clades.

The shift from outcrossing to selfing is common in flowering plants, but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.

Although self-incompatibility in apples (Malus × domestica Borkh.) is regulated by a single S-locus with multiple S-haplotypes that comprise pistil S (S-RNase) and pollen S genes, it is not desirable in commercial orchards because it requires cross-pollination to achieve stable fruit production. Therefore, it is important to identify and characterize self-compatible apple cultivars. However, little is known about self-compatibility (SC) and its underlying molecular mechanisms in apples. In this study, we discovered that ‘Vered’, an early maturing and low chilling-requiring apple cultivar, exhibits stable SC, which was evaluated via self-pollination tests. The S-genotype of ‘Vered’ was designated as S24S39sm. Results of genetic analysis of selfed progeny of ‘Vered’ revealed that SC is associated with the S39sm-haplotype, and molecular analyses indicated that it is caused by alternative splicing and a 205-bp deletion in S39sm-RNase. These events induce frameshifts and ultimately produce the defective S39sm-RNase isoforms that lack their C-terminal half. These results enabled us to develop a 117-bp DNA marker that can be used to assist in the selection of self-compatible apples with the dysfunctional S39sm-RNase. Thus, analysis of ‘Vered’ provided insights into the molecular mechanism of the very rare trait of natural stylar-part SC. Moreover, ‘Vered’ is a valuable genetic resource for breeding cultivars with SC and/or low chilling requirement in apple. Our findings contribute to a better understanding of self-compatible molecular mechanisms in apple and provide for the accelerated breeding of self-compatible apple cultivars.Key messageThis study identifies the apple cultivar, ‘Vered’, as a stylar-part self-compatible genetic resource. We reveal the molecular mechanism underlying self-compatibility and develop an efficient selection marker for the self-compatibility.

Diversified reproductive systems can be observed in the plant kingdom and applied in crop breeding; however, their impacts on crop genomic variation and breeding remain unclear. Grapevine ( Vitis vinifera L.), a widely planted fruit tree, underwent a shift from dioecism to monoecism during domestication and involves crossing, self-pollination, and clonal propagation for its cultivation. In this study, we discover that the reproductive types, namely, crossing, selfing, and cloning, dramatically impact genomic landscapes and grapevine breeding based on comparative genomic and population genetics of wild grapevine and a complex pedigree of Pinot Noir. The impacts are widely divergent, which show interesting patterns of genomic purging and the Hill-Robertson interference. Selfing reduces genomic heterozygosity, while cloning increases it, resulting in a “double U-shaped” site frequency spectrum (SFS). Crossing and cloning conceal while selfing purges most deleterious and structural burdens. Moreover, the close leakage of large-effect deleterious and structural variations in repulsion phases maintains heterozygous genomic regions in 4.3% of the grapevine genome after successive selfing for nine generations. Our study provides new insights into the genetic basis of clonal propagation and genomic breeding of clonal crops by purging deleterious variants while integrating beneficial variants through various reproductive systems. Effects of reproductive systems on crop genomic variation and breeding remain unclear. Here, the authors report that reproductive types impact genomic landscapes and grapevine breeding based on comparative genomic and population genetic analyses of wild grapevine and a complex pedigree of Pinot Noir.

The abrupt origin and rapid diversification of the flowering plants during the Cretaceous has long been considered an \"abominable mystery.\" While the cause of their high diversity has been attributed largely to coevolution with pollinators and herbivores, their ability to outcompete the previously dominant ferns and gymnosperms has been the subject of many hypotheses. Common among these is that the angiosperms alone developed leaves with smaller, more numerous stomata and more highly branching venation networks that enable higher rates of transpiration, photosynthesis, and growth. Yet, how angiosperms pack their leaves with smaller, more abundant stomata and more veins is unknown but linked-we show-to simple biophysical constraints on cell size. Only angiosperm lineages underwent rapid genome downsizing during the early Cretaceous period, which facilitated the reductions in cell size necessary to pack more veins and stomata into their leaves, effectively bringing actual primary productivity closer to its maximum potential. Thus, the angiosperms' heightened competitive abilities are due in no small part to genome downsizing.

Inferences about past processes of adaptation and speciation require a gene-scale and genome-wide understanding of the evolutionary history of diverging taxa. In this study, we use genome-wide capture of nuclear gene sequences, plus skimming of organellar sequences, to investigate the phylogenomics of monkeyflowers in Mimulus section Erythranthe (27 accessions from seven species ) . Taxa within Erythranthe , particularly the parapatric and putatively sister species M . lewisii (bee-pollinated) and M . cardinalis (hummingbird-pollinated), have been a model system for investigating the ecological genetics of speciation and adaptation for over five decades. Across >8000 nuclear loci, multiple methods resolve a predominant species tree in which M . cardinalis groups with other hummingbird-pollinated taxa (37% of gene trees), rather than being sister to M . lewisii (32% of gene trees). We independently corroborate a single evolution of hummingbird pollination syndrome in Erythranthe by demonstrating functional redundancy in genetic complementation tests of floral traits in hybrids; together, these analyses overturn a textbook case of pollination-syndrome convergence. Strong asymmetries in allele sharing (Patterson’s D-statistic and related tests) indicate that gene tree discordance reflects ancient and recent introgression rather than incomplete lineage sorting. Consistent with abundant introgression blurring the history of divergence, low-recombination and adaptation-associated regions support the new species tree, while high-recombination regions generate phylogenetic evidence for sister status for M . lewisii and M . cardinalis . Population-level sampling of core taxa also revealed two instances of chloroplast capture, with Sierran M . lewisii and Southern Californian M . parishii each carrying organelle genomes nested within respective sympatric M . cardinalis clades. A recent organellar transfer from M . cardinalis , an outcrosser where selfish cytonuclear dynamics are more likely, may account for the unexpected cytoplasmic male sterility effects of selfer M . parishii organelles in hybrids with M . lewisii . Overall, our phylogenomic results reveal extensive reticulation throughout the evolutionary history of a classic monkeyflower radiation, suggesting that natural selection (re-)assembles and maintains species-diagnostic traits and barriers in the face of gene flow. Our findings further underline the challenges, even in reproductively isolated species, in distinguishing re-use of adaptive alleles from true convergence and emphasize the value of a phylogenomic framework for reconstructing the evolutionary genetics of adaptation and speciation.

Main conclusion Goji displays characteristics of gametophytic self-incompatibility. The S-RNase gene, expressed in the style, serves as the S determinant in the pistil, playing a key role in regulating goji's self-incompatibility. Goji, a plant commonly found worldwide, has been traditionally used for medicinal and culinary purposes in Chinese culture. However, breeding this species is challenging due to its self-incompatibility (SI). This study utilized ‘Ningqi 1’, ‘Ningqi 6’, and ‘Ningqi 8’, which exhibit significant variations in SI, as the experimental subjects. Detailed observations of floral organs and artificial pollination trials were conducted to elucidate the SI traits among different goji cultivars. Furthermore, the crucial pistil S factor that mediates SI in goji has been successfully cloned and subjected to analysis. The study revealed that goji exhibits gametophytic self-incompatibility (GSI). ‘Ningqi 1’ has a facultative selfing breeding system, while ‘Ningqi 6’ and ‘Ningqi 8’ involve facultative cross-pollination. Four S-RNase genes were successfully cloned from goji plants. Differential expression analysis revealed exclusive expression of S-RNase genes in the style. ‘Ningqi 8’ had significantly higher expression of the S 2 -RNase gene compared to the S 1 -RNase gene, suggesting that the S 2 -RNase gene may play a pivotal role in regulating the SI mechanism of ‘Ningqi 8’. This research provides insights into the cytological mechanisms of SI in goji, informing the planning of pollination tree arrangements and the selection of parental stocks for self-compatible breeding programs. It also lays the groundwork for future molecular studies on SI in goji.

Volatile organic compounds (VOCs) are emitted by plants as a consequence of their interaction with biotic and abiotic factors, and have a very important role in plant evolution. Floral VOCs are often involved in defense and pollinator attraction. These interactions often change rapidly over time, so a quick response to those changes is required. Epigenetic factors, such as DNA methylation and histone modification, which regulate both genes and transcription factors, might trigger adaptive responses to these evolutionary pressures as well as regulating the rhythmic emission of VOCs through circadian clock regulation. In addition, transgenerational epigenetic effects and whole genome polyploidy could modify the generation of VOCs’ profiles of offspring, contributing to long-term evolutionary shifts. In this article, we review the available knowledge about the mechanisms that may act as epigenetic regulators of the main VOC biosynthetic pathways, and their importance in plant evolution.

Pollen grains undergo dramatic changes in cellular water potential as they deliver the male germ line to female gametes, and it has been proposed that mechanosensitive ion channels may sense the resulting mechanical stress. Here, we identify and characterize MscS-like 8 (MSL8), a pollen-specific, membrane tension–gated ion channel required for pollen to survive the hypoosmotic shock of rehydration and for full male fertility. MSL8 negatively regulates pollen germination but is required for cellular integrity during germination and tube growth. MSL8 thus senses and responds to changes in membrane tension associated with pollen hydration and germination. These data further suggest that homologs of bacterial MscS have been repurposed in eukaryotes to function as mechanosensors in multiple developmental and environmental contexts.

Key message This study indicated that the CCHC-type zinc finger protein PbrZFP719 involves into self-incompatibility by affecting the levels of reactive oxygen species and cellulose content at the tips of pollen tubes. S-RNase-based self-incompatibility (SI) facilitates cross-pollination and prevents self-pollination, which in turn increases the costs associated with artificial pollination in fruit crops. Self S-RNase exerts its inhibitory effects on pollen tube growth by altering cell structures and components, including reactive oxygen species (ROS) level and cellulose content. Presently, only a limited number of genes have been implicated in the gametophytic SI. In this study, the CCHC-type z inc finger proteins ( ZFP ), PbrZFP719 , was found to be more highly expressed in pollen grains and pollen tubes than other ZFP s. Experimental over-expression of PbrZFP719 via pollen magnetofection and its knockdown using antisense oligonucleotides demonstrated that PbrZFP719 positively mediates pollen tube growth in pear. Further analyses revealed that variations in PbrZFP719 expression correlate with the changes in ROS levels and cellulose content at the tips of pollen tubes. Notably, PbrZFP719 expression was reduced in pollen tubes treated with self S-RNase. These results suggest that self S-RNase can inhibit pollen tube growth by decreasing ROS levels and cellulose content through the downregulation of PbrZFP719 expression. The information provide insights into a novel mechanism by which self S-RNase inhibits pollen tube growth during SI reaction and offers a refined approach for gene over-expression in pollen tube.