Convergent evolutionary patterns of heterostyly across angiosperms support the pollination-precision hypothesis.

Since the insights by Charles Darwin, heterostyly, a floral polymorphism with morphs bearing stigmas and anthers at reciprocal heights, has become a model system for the study of natural selection. Based on his archetypal heterostylous flower, including regular symmetry, few stamens and a tube, Darwin hypothesised that heterostyly evolved to promote outcrossing through efficient pollen transfer between morphs involving different areas of a pollinator's body, thus proposing his seminal pollination-precision hypothesis. Here we update the number of heterostylous and other style-length polymorphic taxa to 247 genera belonging to 34 families, notably expanding known cases by 20%. Using phylogenetic and comparative analyses across the angiosperms, we show numerous independent origins of style-length polymorphism associated with actinomorphic, tubular flowers with a low number of sex organs, stamens fused to the corolla, and pollination by long-tongued insects. These associations provide support for the Darwinian pollination-precision hypothesis as a basis for convergent evolution of heterostyly across angiosperms.

Molecular and evolutionary mechanisms of self-incompatibility in angiosperms.

As an intraspecific outcrossing mechanism, self-incompatibility (SI) widely adopted by hermaphroditic plants is usually controlled by a polymorphic multi-allelic S locus. Typically, six molecular types of SI have been found, including type-I controlled by the pistil S S-RNase and pollen S SLFs commonly spread in Plantaginaceae, Solanaceae, Rosaceae and Rutaceae, type-II by SRK and SCR in Brassicaceae, type-III by PrsS and PrpS in Papaveraceae, type-IV by CYP-GLO2-KFB-CCM-PUM in Primulaceae, type-V by TsSPH1-TsYUC6-TsBAHD in Turneraceae and type-VI by HPS10-S and DUF247I-S in Poaceae, with type-I characterized as a non-self recognition system but types-II, -III and -VI self ones. Furthermore, remarkable progresses have been made in their origin and evolutionary mechanisms recently. Among them, type-I SI possessed a single origin in the most recent common ancestor of eudicots and types II-V dynamically evolved following its losses, while type-VI SI exclusively existed in monocot Poaceae may be regained after the loss of the ancient type-I. Here, we mainly review the molecular and evolutionary mechanisms of angiosperm SI systems, thus providing a helpful reference for their theoretical research and breeding application.

Community-wide patterns in pollen and ovule production, their ratio (P/O), and other floral traits along an elevation gradient in southwestern China.

BACKGROUND: As the male and female gametophytes of flowering plants, pollen and ovules largely determine the upper and lower boundaries of plant reproductive success. It is commonly predicted that pollen and ovule number per flower should increase, and pollen-ovule ratio (P/O) per flower should decrease with increasing elevation in response to a more stochastic pollination environment. Here, we aimed to determine the response of pollen number, ovule number, and P/O to other floral traits and elevation gradients for 84 insect-pollinated herbaceous flowering plant species in five sub-alpine and alpine communities (2709 to 3896 m a.s.l.) on Yulong Snow Mountain, southwestern China. RESULTS: Six floral traits, including P/O, floral display area, flower number, tube depth, flower shape, and pollen presentation, were highly correlated with pollen and ovule number per flower. With increasing elevation, pollen number and P/O per flower increased marginally and significantly, respectively; ovule number per individual, flower number per individual, stigma stamen separation, and inflorescence height decreased significantly. However, ovule number per flower and other floral traits (i.e., floral display area, tube depth, stigma height, stamen height, and pollen and P/O per individual) did not change with elevation. We detected significant phylogenetic signals for pollen number, ovule number, and P/O, suggesting that these traits may be highly conserved and with limited response to changing environmental conditions. CONCLUSIONS: Results revealed patterns of plant reproductive character evolution along elevation gradients and the potential factors governing their spatial variation in high-elevation environments. Plant species at high elevations are more likely adapted to cross-pollination, indicated by increased P/O per flower at high elevations on Yulong Mountain. Combined effects of phylogenetic history and plant-pollinator interactions should determine plant trait evolution.

An analysis of codon utilization patterns in the chloroplast genomes of three species of Coffea.

BACKGROUND: The chloroplast genome of plants is known for its small size and low mutation and recombination rates, making it a valuable tool in plant phylogeny, molecular evolution, and population genetics studies. Codon usage bias, an important evolutionary feature, provides insights into species evolution, gene function, and the expression of exogenous genes. Coffee, a key crop in the global tropical agricultural economy, trade, and daily life, warrants investigation into its codon usage bias to guide future research, including the selection of efficient heterologous expression systems for coffee genetic transformation. RESULTS: Analysis of the codon utilization patterns in the chloroplast genomes of three Coffea species revealed a high degree of similarity among them. All three species exhibited similar base compositions, with high A/T content and low G/C content and a preference for A/T-ending codons. Among the 30 high-frequency codons identified, 96.67% had A/T endings. Fourteen codons were identified as ideal. Multiple mechanisms, including natural selection, were found to influence the codon usage patterns in the three coffee species, as indicated by ENc-GC3s mapping, PR2 analysis, and neutral analysis. Nicotiana tabacum and Saccharomyces cerevisiae have potential value as the heterologous expression host for three species of coffee genes. CONCLUSION: This study highlights the remarkable similarity in codon usage patterns among the three coffee genomes, primarily driven by natural selection. Understanding the gene expression characteristics of coffee and elucidating the laws governing its genetic evolution are facilitated by investigating the codon preferences in these species. The findings can enhance the efficacy of exogenous gene expression and serve as a basis for future studies on coffee evolution.

Pollen production per flower increases with floral display size across animal-pollinated flowering plants.

PREMISE: The number of open flowers on a plant (i.e., floral display size) can influence plant fitness by increasing pollinator attraction. However, diminishing marginal fitness returns with increasing floral display are expected as pollinators tend to visit more flowers per plant consecutively. An extended flower visitation sequence increases the fraction of ovules disabled by self-pollination (ovule discounting) and reduces the fraction of a plant's own pollen that is exported to sire seeds in other plants (pollen discounting). Hermaphroditic species with a genetic system that prevents self-fertilization (self-incompatibility) would avoid ovule discounting and its fitness cost, whereas species without such a genetically based barrier would not. Contrarily, pollen discounting would be an unavoidable consequence of a large floral display irrespective of selfing barriers. Nevertheless, the increasing fitness costs of ovule and pollen discounting could be offset by respectively increasing ovule and pollen production per flower. METHODS: We compiled data on floral display size and pollen and ovule production per flower for 1241 animal-pollinated, hermaphroditic angiosperm species, including data on the compatibility system for 779 species. We used phylogenetic general linear mixed models to assess the relations of pollen and ovule production to floral display size. RESULTS: Our findings provide evidence of increasing pollen production, but not of ovule production, with increasing display size irrespective of compatibility system and even after accounting for potentially confounding effects like flower size and growth form. CONCLUSIONS: Our comparative study supports the pollen-discount expectation of an adaptive link between per-flower pollen production and floral display across animal-pollinated angiosperms.

Biosynthesis and transport of pollen coat precursors in angiosperms.

The pollen coat is a hydrophobic mixture on the pollen grain surface, which plays an important role in protecting male gametes from various environmental stresses and microorganism attacks, and in pollen-stigma interactions during pollination in angiosperms. An abnormal pollen coat can result in humidity-sensitive genic male sterility (HGMS), which can be used in two-line hybrid crop breeding. Despite the crucial functions of the pollen coat and the application prospect of its mutants, few studies have focused on pollen coat formation. In this Review, the morphology, composition and function of different types of pollen coat are assessed. On the basis of the ultrastructure and development process of the anther wall and exine found in rice and Arabidopsis, the genes and proteins involved in the biosynthesis of pollen coat precursors and the possible transport and regulation process are sorted. Additionally, current challenges and future perspectives, including potential strategies utilizing HGMS genes in heterosis and plant molecular breeding, are highlighted.

Pollen-stigma incompatibility within and between species: Tread lightly, sedate the dogs, and don't wake the guards!

In a recent issue of Nature, Huang et al. identify and show how to overcome the barriers to successful pollen germination after interspecific crosses.1 Their findings answer a long-standing question about reproductive barriers in flowering plants and open the door to harnessing genetic diversity of distant relatives for crop improvement.

The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae.

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae.

Complete chloroplast genome of the medicinal plant Cleome paradoxa R.Br. Ex DC: Comparative analysis, and phylogenetic relationships among the members of Cleomaceae.

The cleome species of the Cleomaceae family have several medical uses, including applications such as antioxidants and insecticides. In the present study, we sequenced the complete chloroplast genome (cp genome) of Cleome paradoxa. The chloroplast genome is 159,393 bp long, with a typical four-region structure: a large single copy (LSC) region of 88,191 bp, a small single copy (SSC) region of 18,620 bp, and inverted repeat regions (IRa and IRb) of 26,291 bp each. The proportion of GC content was 35.79 %. The chloroplast genome of C. paradoxa contains 133 genes, 81 of which encode proteins, 29 encode tRNA, and 4 encode rRNA. We noticed a divergence in the location and number of certain genes at the IR-LSC and IR-SSC boundaries. The phylogenetic tree constructed from the complete chloroplast genome data broadly supported the taxonomic situation of Cleome paradoxa as belonging to the Cleomaceae family and Cleome species. The cp genome of C. paradoxa was rich in single sequence repeats (SSRs), with a total of 314 SSRs. Additionally, several genes were under positive selection. These results could be useful for determining the genetic variations and resolving conflicting relationships among Cleomaceae species.

Why does pollen morphology vary? Evolutionary dynamics and morphospace occupation in the largest angiosperm order (Asterales).

Morphological diversity (disparity) is a key component of biodiversity and increasingly a focus of botanical research. Despite the wide range of morphologies represented by pollen grains, to date there are few studies focused on the controls on pollen disparity and morphospace occupation, and fewer still considering these parameters in a phylogenetic framework. Here, we analyse morphospace occupation, disparity and rates of morphological evolution in Asterales pollen, in a phylogenetic context. We use a dataset comprising 113 taxa from across the Asterales phylogeny, with pollen morphology described using 28 discrete characters. The Asterales pollen morphospace is phylogenetically structured around groups of related taxa, consistent with punctuated bursts of morphological evolution at key points in the Asterales phylogeny. There is no substantial difference in disparity among these groups of taxa, despite large differences in species richness and biogeographic range. There is also mixed evidence for whole-genome duplication as a driver of Asterales pollen morphological evolution. Our results highlight the importance of evolutionary history for structuring pollen morphospace. Our study is consistent with others that have shown a decoupling of biodiversity parameters, and reinforces the need to focus on disparity as a key botanical metric in its own right.

De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.).

This study reported the first-ever de novo transcriptome analysis of Operculina turpethum, a high valued endangered medicinal plant, using the Illumina HiSeq 2500 platform. The de novo assembly generated a total of 64,259 unigenes and 20,870 CDS (coding sequence) with a mean length of 449 bp and 571 bp respectively. Further, 20,218 and 16,458 unigenes showed significant similarity with identified proteins of NR (non-redundant) and UniProt database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. A total of 17,444 DEGs were identified among which majority of the DEGs (Differentially Expressed Gene) involved in secondary metabolite biosynthesis were found to be significantly upregulated in stem as compared to root tissues. The qRT-PCR validation of 9 unigenes involved in phenylpropanoid and terpenoid biosynthesis also showed a similar expression pattern. This finding suggests that stem tissues, rather than root tissues, could be used to prevent uprooting of O. turpethum in the wild, paving the way for the plant's effective conservation. Moreover, the study formed a valuable repository of genetic information which will provide a baseline for further molecular research.

From birth to function: Male gametophyte development in flowering plants.

Male germline development in flowering plants involves two distinct and successive phases, microsporogenesis and microgametogenesis, which involve one meiosis followed by two rounds of mitosis. Many aspects of distinctions after mitosis between the vegetative cell and the male germ cells are seen, from morphology to structure, and the differential functions of the two cell types in the male gametophyte are differentially needed and required for double fertilization. The two sperm cells, carriers of the hereditary substances, depend on the vegetative cell/pollen tube to be delivered to the female gametophyte for double fertilization. Thus, the intercellular communication and coordinated activity within the male gametophyte probably represent the most subtle regulation in flowering plants to guarantee the success of reproduction. This review will focus on what we have known about the differentiation process and the functional diversification of the vegetative cell and the male germ cell, the most crucial cell types for plant fertility and crop production.

Insights into angiosperm evolution, floral development and chemical biosynthesis from the Aristolochia fimbriata genome.

Aristolochia, a genus in the magnoliid order Piperales, has been famous for centuries for its highly specialized flowers and wide medicinal applications. Here, we present a new, high-quality genome sequence of Aristolochia fimbriata, a species that, similar to Amborella trichopoda, lacks further whole-genome duplications since the origin of extant angiosperms. As such, the A. fimbriata genome is an excellent reference for inferences of angiosperm genome evolution, enabling detection of two novel whole-genome duplications in Piperales and dating of previously reported whole-genome duplications in other magnoliids. Genomic comparisons between A. fimbriata and other angiosperms facilitated the identification of ancient genomic rearrangements suggesting the placement of magnoliids as sister to monocots, whereas phylogenetic inferences based on sequence data we compiled yielded ambiguous relationships. By identifying associated homologues and investigating their evolutionary histories and expression patterns, we revealed highly conserved floral developmental genes and their distinct downstream regulatory network that may contribute to the complex flower morphology in A. fimbriata. Finally, we elucidated the genetic basis underlying the biosynthesis of terpenoids and aristolochic acids in A. fimbriata.

Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps).

Monitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.

Exploring environmental selection on genome size in angiosperms.

Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO2-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.

Transcriptome Characterization and Identification of Molecular Markers (SNP, SSR, and Indels) in the Medicinal Plant Sarcandra glabra spp.

Sarcandra glabra has significant metabolically active bioingredients of pharmaceutical importance. The deficiency of molecular markers for S. glabra is a hindrance in molecular breeding for genetic improvement. In this study, 57.756 million pair-end reads were generated by transcriptome sequencing in S. glabra (Thunb.) Nakai and its subspecies S. glabra ssp. brachystachys. A total of 141,954 unigenes with 646.63 bp average length were assembled. A total of 25,620 simple sequence repeats, 726,476 single nucleotide polymorphisms, and 42,939 insertions and deletions were identified, and the associated unigenes and differentially expressed genes were characterized. This work enhanced the molecular marker resources and will facilitate molecular breeding and gene mining in S. glabra spp.

Pollen transport: Illuminating a key mechanism of disassortative pollination.

Floral sexual polymorphisms have evolved repeatedly in angiosperms and are thought to reduce self-pollination and increase pollen export. Using a powerful pollen-labeling technique, quantum dots, a new study shows that pollen placement on pollinator bodies plays a critical role in disassortative pollination.

Consequences of whole genome duplication for 2n pollen performance.

The vegetative cell of the angiosperm male gametophyte (pollen) functions as a free-living, single-celled organism that both produces and transports sperm to egg. Whole-genome duplication (WGD) should have strong effects on pollen because of the haploid to diploid transition and because of both genetic and epigenetic effects on cell-level phenotypes. To disentangle historical effects of WGD on pollen performance, studies can compare 1n pollen from diploids to neo-2n pollen from diploids and synthetic autotetraploids to older 2n pollen from established neo-autotetraploids. WGD doubles both gene number and bulk nuclear DNA mass, and a substantial proportion of diploid and autotetraploid heterozygosity can be transmitted to 2n pollen. Relative to 1n pollen, 2n pollen can exhibit heterosis due to higher gene dosage, higher heterozygosity and new allelic interactions. Doubled genome size also has consequences for gene regulation and expression as well as epigenetic effects on cell architecture. Pollen volume doubling is a universal effect of WGD, whereas an increase in aperture number is common among taxa with simultaneous microsporogenesis and pored apertures, mostly eudicots. WGD instantly affects numerous evolved compromises among mature pollen functional traits and these are rapidly shaped by highly diverse tissue interactions and pollen competitive environments in the early post-WGD generations. 2n pollen phenotypes generally incur higher performance costs, and the degree to which these are met or evolve by scaling up provisioning and metabolic vigor needs further study.

Evolution and diversity of the angiosperm anther: trends in function and development.

KEY MESSAGE: Anther development and dehiscence is considered from an evolutionary perspective to identify drivers for differentiation, functional conservation and to identify key questions for future male reproduction research. Development of viable pollen and its timely release from the anther are essential for fertilisation of angiosperm flowers. The formation and subsequent dehiscence of the anther are under tight regulatory control, and these processes are remarkably conserved throughout the diverse families of the angiosperm clade. Anther development is a complex process, which requires timely formation and communication between the multiple somatic anther cell layers (the epidermis, endothecium, middle layer and tapetum) and the developing pollen. These layers go through regulated development and selective degeneration to facilitate the formation and ultimate release of the pollen grains. Insight into the evolution and divergence of anther development and dehiscence, especially between monocots and dicots, is driving greater understanding of the male reproductive process and increased, resilient crop yields. This review focuses on anther structure from an evolutionary perspective by highlighting their diversity across plant species. We summarise new findings that illustrate the complexities of anther development and evaluate how they challenge established models of anther form and function, and how they may help to deliver future sustainable crop yields.