Origin of the Taxaceae aril: evolutionary implications of seed-cone teratologies in Pseudotaxus chienii

An integrative view on the systematic position of the cupressophyte Cephalotaxus

We made an in-depth review of historical studies of the cupressophyte conifer genus Cephalotaxus Siebold & Zucc. with an emphasis on its systematic position. We suggest that the systematic position of the genus is better understood using an integrative approach, so the evolution of phenetic characters is discussed within the context of recent phylogenomics. We propose that the genus should be classified as a separate family Cephalotaxaceae belonging to the clade consisting of Cupressaceae, Cephalotaxaceae, and Taxaceae; the family Cephalotaxaceae is sister to the Taxaceae but not nested within the Taxaceae and is characterized by a unique set of characters including morphology, anatomy, embryology, and chemistry. The family Cephalotaxaceae shows transitional characters between the Cupressaceae and the Taxaceae; the family possesses female cones with a primary cone axis bearing 5-8 pairs of decussate bracts, which is similar to the typical female cones of the Cupressaceae, on the one hand, and may have given rise to the reduced female cone of the Taxaceae with one terminal ovule partially or completely enclosed in a fleshy aril. In parallel, the compound male cone of the Cephalotaxaceae evolved into the seemingly "simple" male cones of the Taxaceae by means of reduction, elimination, and fusion.

Detailed seed cone morpho-anatomy of the Prumnopityoid clade: an insight into the origin and evolution of Podocarpaceae seed cones

BACKGROUND AND AIMS

Seed cone traits are significant for understanding the evolutionary history of conifers. Podocarpaceae has fleshy cones with a distinct morphology compared with other conifers. However, we have a poor understanding of the seed cone morphology of the Prumnopityoid clade and within Podocarpaceae. This study presents detailed seed cone morpho-anatomy and the evolution of fleshy structures traits in the Prumnopityoid clade.

METHODS

We investigated the detailed seed cone morpho-anatomy of selected species from the nine genera using the histological method. The evolution of morpho-anatomical traits was assessed using ancestral state reconstruction methods.

KEY RESULTS

The Prumnopityoid clade has evolved fleshy seed cones using different functional structures (e.g. aril, epimatium, bracts or receptaculum) and fleshiness is an ancestral trait in the clade. An epimatium is present in all genera except Phyllocladus, but with different structural morphologies (e.g. a fleshy asymmetrical cup-like epimatium or an epimatium that is fused with the integument, forming a fleshy sarcotesta-like seed coat). In all species with fleshy sarcotesta-like seed coats, the endotesta is hard and woody, forming a sclerotesta-like structure and the epimatium and exotesta are fused, forming a fleshy sarcotesta-like structure.

CONCLUSIONS

This study highlights that the Prumnopityoid clade has an amazing diversity of structures and complex evolutionary patterns. Fleshiness is an ancestral trait of the clade and has been achieved via diverse evolutionary pathways and structures. This clade has four distinct seed cone types, i.e. drupe-like, receptaculate, arilloid and dacrydioid cones, based on morpho-anatomical structures and traits. The macrofossil record also demonstrates the presence of several structures and traits.

Recent advances on phylogenomics of gymnosperms and a new classification

Living gymnosperms comprise four major groups: cycads, Ginkgo, conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes and single-copy nuclear genes, for reconstruction of solid phylogenetic trees. Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics. Here, we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms. This new classification includes three classes (Cycadopsida, Ginkgoopsida, and Pinopsida), five subclasses (Cycadidae, Ginkgoidae, Cupressidae, Pinidae, and Gnetidae), eight orders (Cycadales, Ginkgoales, Araucariales, Cupressales, Pinales, Ephedrales, Gnetales, and Welwitschiales), 13 families, and 86 genera. We also described six new tribes including Acmopyleae Y. Yang, Austrocedreae Y. Yang, Chamaecyparideae Y. Yang, Microcachrydeae Y. Yang, Papuacedreae Y. Yang, and Prumnopityeae Y. Yang, and made 27 new combinations in the genus Sabina.

Phytochemical and biological studies on rare and endangered plants endemic to China. Part XXII. Structurally diverse diterpenoids from the leaves and twigs of the endangered conifer Torreya jackii and their bioactivities

A phytochemical investigation on the MeOH extract of the leaves and twigs of the endangered conifer Torreya jackii Chun led to the isolation and characterization of 21 structurally diverse diterpenoids. Among them, six are previously undescribed, including four abietane-type (torreyins A-D, resp.) and two labdane-type diterpenoids (torreyins E and F). Their structures and absolute configurations were determined by a combination of spectroscopic methods, calculated/experimental electronic circular dichroism (ECD) data, and single-crystal X-ray diffraction analyses. In particular, torreyins A-C are rare 11,12-seco-abietane type diterpenoids possessing a dilactone moiety, and their biosynthetic pathway starting from a co-occurring abietane derivative (i.e., cyrtophyllone B) was briefly proposed. Among the isolates, 7-oxo-dehydroabietic acid and 15-methoxy-7,13-abietadien-18-oic acid showed considerable inhibitory effects against acetyl-coenzyme A carboxylase 1 (ACC1) and protein tyrosine phosphatase 1 B (PTP1B), with IC₅₀ values of 3.1 and 6.8 μM, respectively.

Fleshy or dry: transcriptome analyses reveal the genetic mechanisms underlying bract development in Ephedra

BACKGROUND

Gnetales have a key phylogenetic position in the evolution of seed plants. Among the Gnetales, there is an extraordinary morphological diversity of seeds, the genus Ephedra, in particular, exhibits fleshy, coriaceous or winged (dry) seeds. Despite this striking diversity, its underlying genetic mechanisms remain poorly understood due to the limited studies in gymnosperms. Expanding the genomic and developmental data from gymnosperms contributes to a better understanding of seed evolution and development.

RESULTS

We performed transcriptome analyses on different plant tissues of two Ephedra species with different seed morphologies. Anatomical observations in early developing ovules, show that differences in the seed morphologies are established early in their development. The transcriptomic analyses in dry-seeded Ephedra californica and fleshy-seeded Ephedra antisyphilitica, allowed us to identify the major differences between the differentially expressed genes in these species. We detected several genes known to be involved in fruit ripening as upregulated in the fleshy seed of Ephedra antisyphilitica.

CONCLUSIONS

This study allowed us to determine the differentially expressed genes involved in seed development of two Ephedra species. Furthermore, the results of this study of seeds with the enigmatic morphology in Ephedra californica and Ephedra antisyphilitica, allowed us to corroborate the hypothesis which suggest that the extra envelopes covering the seeds of Gnetales are not genetically similar to integument. Our results highlight the importance of carrying out studies on less explored species such as gymnosperms, to gain a better understanding of the evolutionary history of plants.

Morpho-anatomical affinities and evolutionary relationships of three paleoendemic podocarp genera based on seed cone traits

BACKGROUND AND AIMS

The three relict genera Pherosphaera, Microcachrys and Saxegothaea in Podocarpaceae produce quite distinct seed cone types in comparison with other genera and do not form a clade along with Acmopyle. The detailed seed cone morpho-anatomy of these three relict genera and affinities with other podocarps are poorly known. This study aims to understand the seed cone morpho-anatomy and affinities among these three disjunct relict genera and with other podocarps.

METHODS

We comparatively analysed the seed cone morpho-anatomical traits of the three podocarps genera and used ancestral state reconstruction to understand the evolution of these traits.

KEY RESULTS

We described the seed cone morpho-anatomical structures of the three relict genera in detail. The three genera produce aggregated multiovulate cones. Both Microcachrys and Saxegothaea have an asymmetrical free cup-like epimatium. Both species of Pherosphaera lack an epimatium. The ancestral state reconstruction implies that the presence of an epimatium is an ancestral trait in podocarps and is independently lost in Pherosphaera and Phyllocladus. The seed cones are fleshy in Microcachrys and non-fleshy in Saxegothaea and Pherosphaera. The seed cone macrofossils of both extinct and living podocarps also show the presence of an epimatium and fleshiness in podocarps.

CONCLUSIONS

Altogether, the morpho-anatomy suggests that Pherosphaera, Microcachrys and Saxegothaea present affinities with each other and other podocarps, but the reconstruction of the ancestral seed cone in Podcarpaceae is quite complex due to multiple convergent evolutions of several structures. These structures (e.g. epimatium, aril and receptaculum) are of low taxonomic value but of great evolutionary and ecological significance, and are responsive adaptations to ever-changing environmental conditions.

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

BACKGROUND

Elucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors underlying its occurrence. Adaptive genetic variation is common in tree species, especially widely distributed long-lived species. Pseudotaxus chienii can occupy diverse habitats with environmental heterogeneity and thus provides an ideal material for investigating the process of population adaptive evolution. Here, we characterize genetic and expression variation patterns and investigate adaptive genetic variation in P. chienii populations.

RESULTS

We generated population transcriptome data and identified 13,545 single nucleotide polymorphisms (SNPs) in 5037 unigenes across 108 individuals from 10 populations. We observed lower nucleotide diversity (π = 0.000701) among the 10 populations than observed in other gymnosperms. Significant negative correlations between expression diversity and nucleotide diversity in eight populations suggest that when the species adapts to the surrounding environment, gene expression and nucleotide diversity have a reciprocal relationship. Genetic structure analyses indicated that each distribution region contains a distinct genetic group, with high genetic differentiation among them due to geographical isolation and local adaptation. We used FST outlier, redundancy analysis, and latent factor mixed model methods to detect molecular signatures of local adaptation. We identified 244 associations between 164 outlier SNPs and 17 environmental variables. The mean temperature of the coldest quarter, soil Fe and Cu contents, precipitation of the driest month, and altitude were identified as the most important determinants of adaptive genetic variation. Most candidate unigenes with outlier signatures were related to abiotic and biotic stress responses, and the monoterpenoid biosynthesis and ubiquitin-mediated proteolysis KEGG pathways were significantly enriched in certain populations and deserve further attention in other long-lived trees.

CONCLUSIONS

Despite the strong population structure in P. chienii, genomic data revealed signatures of divergent selection associated with environmental variables. Our research provides SNPs, candidate unigenes, and biological pathways related to environmental variables to facilitate elucidation of the genetic variation in P. chienii in relation to environmental adaptation. Our study provides a promising tool for population genomic analyses and insights into the molecular basis of local adaptation.

Omic analysis of the endangered Taxaceae species Pseudotaxus chienii revealed the differences in taxol biosynthesis pathway between Pseudotaxus and Taxus yunnanensis trees

BACKGROUND

Taxol is an efficient anticancer drug accumulated in Taxus species. Pseudotaxus chienii is an important member of Taxaceae, however, the level of six taxoids in P. chienii is largely unknown.

RESULTS

High accumulation of 10-DAB, taxol, and 7-E-PTX suggested that P. chienii is a good taxol-yielding species for large-scale cultivation. By the omics approaches, a total of 3,387 metabolites and 61,146 unigenes were detected and annotated. Compared with a representative Taxus tree (Taxus yunnanensis), most of the differentially accumulated metabolites and differential expressed genes were assigned into 10 primary and secondary metabolism pathways. Comparative analyses revealed the variations in the precursors and intermediate products of taxol biosynthesis between P. chienii and T. yunnanensis. Taxusin-like metabolites highly accumulated in P. chienii, suggesting a wider value of P. chienii in pharmaceutical industry.

CONCLUSIONS

In our study, the occurrence of taxoids in P. chienii was determined. The differential expression of key genes involved in the taxol biosynthesis pathway is the major cause of the differential accumulation of taxoids. Moreover, identification of a number of differentially expressed transcription factors provided more candidate regulators of taxol biosynthesis. Our study may help to reveal the differences between Pseudotaxus and Taxus trees, and promote resource utilization of the endangered and rarely studied P. chienii.

Ephedra as a gymnosperm evo-devo model lineage

Established model systems in the flowering plants have greatly advanced our understanding of plant developmental biology, facilitating in turn its investigation across diverse land plants. The reliance on a limited number of model organisms, however, constitutes a barrier for future progress in evolutionary developmental biology (evo-devo). In particular, a more thorough understanding of seed plant character evolution and of its genetic and developmental basis has been hampered in part by a lack of gymnosperm model systems, since most are trees with decades-long generation times. Guided by the premise that future model organisms should be selected based on their character diversity, rather than simply phylogenetic "position," we highlight biological questions of potential interest that can be addressed via comparative studies in Ephedra (Gnetales). In addition to having relatively small genomes and shorter generation times in comparison to most other gymnosperms, Ephedra are amenable to investigations on the evolution of the key reproductive seed plant innovations of pollination and seed dispersal, as well as on polyploidy, and adaptation to extreme environments.

Evolution and patterning of the ovule in seed plants

The ovule and its developmental successor, the seed, together represent a highly characteristic feature of seed plants that has strongly enhanced the reproductive and dispersal potential of this diverse group of taxa. Ovules encompass multiple tissues that perform various roles within a highly constrained space, requiring a complex cascade of genes that generate localized cell proliferation and programmed cell death during different developmental stages. Many heritable morphological differences among lineages reflect relative displacement of these tissues, but others, such as the second (outer) integuments of angiosperms and Gnetales, represent novel and apparently profound and independent innovations. Recent studies, mostly on model taxa, have considerably enhanced our understanding of gene expression in the ovule. However, understanding its evolutionary history requires a comparative and phylogenetic approach that is problematic when comparing extant angiosperms not only with phylogenetically distant extant gymnosperms but also with taxa known only from fossils. This paper reviews ovule characters across a phylogenetically broad range of seed plants in a dynamic developmental context. It discusses both well-established and recent theories of ovule and seed evolution and highlights potential gaps in comparative data that will usefully enhance our understanding of evolutionary transitions and developmental mechanisms.

Colourful cones: how did flower colour first evolve?

Angiosperms that are biotically pollinated typically produce flowers with bright and contrasting colours that help to attract pollinators and hence contribute to the reproductive success of the species. This colourful array contrasts with the much less multicoloured reproductive structures of the four living gymnosperm lineages, which are mostly wind pollinated, though cycads and Gnetales are predominantly pollinated by insects that feed on surface fluids from the pollination drops. This review examines the possible evolutionary pathways and cryptic clues for flower colour in both living and fossil seed plants. It investigates how the ancestral flowering plants could have overcome the inevitable trade-off that exists between attracting pollinators and minimizing herbivory, and explores the possible evolutionary and biological inferences from the colours that occur in some living gymnosperms. The red colours present in the seed-cone bracts of some living conifers result from accumulation of anthocyanin pigments; their likely primary function is to help protect the growing plant tissues under particular environmental conditions. Thus, the visual cue provided by colour in flower petals could have first evolved as a secondary effect, probably post-dating the evolution of bee colour vision but occurring before the subsequent functional accumulation of a range of different flower pigments.