Morphology and biogeography of Apiaceae subfamily Saniculoideae as inferred by phylogenetic analysis of molecular data

Seed dormancy, climate changes, desertification and soil use transformation threaten the Mediterranean endemic monospecific plant Petagnaea gussonei

This study investigated the germination capacity (endogenous factor) of Petagnaea gussonei (Spreng.) Rauschert, an endemic monospecific plant considered as a relict species of the ancient Mediterranean Tertiary flora. This investigation focused also on the temporal trends of soil-use, climate and desertification (exogenous factors) across the natural range of P. gussonei. The final germination percentage showed low values between 14 and 32%, the latter obtained with GA3 and agar at 10 °C. The rising temperatures in the study area will further increase the dormancy of P. gussonei, whose germination capacity was lower and slower at temperatures higher than 10 °C. A further limiting factor of P. gussonei is its dormancy, which seems to be morpho-physiological. Regarding climate trends, in the period 1931-2020, the average temperature increased by 0.5 °C, from 15.4 to 15.9 °C, in line with the projected climate changes throughout the twenty-first century across the Mediterranean region. The average annual rainfall showed a relatively constant value of c. 900 mm, but extreme events grew considerably in the period 1991-2020. Similarly, the land affected by desertification expanded in an alarming way, by increasing from 21.2% in 2000 to 47.3% in 2020. Soil-use changes created also a complex impacting mosaic where c. 40% are agricultural areas. The effective conservation of P. gussonei should be multilateral by relying on germplasm banks, improving landscape connectivity and vegetation cover, and promoting climate policies.

Phylogeny and diversification of genus Sanicula L. (Apiaceae): novel insights from plastid phylogenomic analyses

BACKGROUND

The genus Sanicula L. is a unique perennial herb that holds important medicinal values. Although the previous studies on Sanicula provided us with a good research basis, its taxonomic system and interspecific relationships have not been satisfactorily resolved, especially for those endemic to China. Moreover, the evolutionary history of this genus also remains inadequately understood. The plastid genomes possessing highly conserved structure and limited evolutionary rate have proved to be an effective tool for studying plant phylogeny and evolution.

RESULTS

In the current study, we newly sequenced and assembled fifteen Sanicula complete plastomes. Combined with two previously reported plastomes, we performed comprehensively plastid phylogenomics analyses to gain novel insights into the evolutionary history of this genus. The comparative results indicated that the seventeen plastomes exhibited a high degree of conservation and similarity in terms of their structure, size, GC content, gene order, IR borders, codon bias patterns and SSRs profiles. Such as all of them displayed a typical quadripartite structure, including a large single copy region (LSC: 85,074-86,197 bp), a small single copy region (SSC: 17,047-17,132 bp) separated by a pair of inverted repeat regions (IRs: 26,176-26,334 bp). And the seventeen plastomes had similar IR boundaries and the adjacent genes were identical. The rps19 gene was located at the junction of the LSC/IRa, the IRa/SSC junction region was located between the trnN gene and ndhF gene, the ycf1 gene appeared in the SSC/IRb junction and the IRb/LSC boundary was located between rpl12 gene and trnH gene. Twelve specific mutation hotspots (atpF, cemA, accD, rpl22, rbcL, matK, ycf1, trnH-psbA, ycf4-cemA, rbcL-accD, trnE-trnT and trnG-trnR) were identified that can serve as potential DNA barcodes for species identification within the genus Sanicula. Furthermore, the plastomes data and Internal Transcribed Spacer (ITS) sequences were performed to reconstruct the phylogeny of Sanicula. Although the tree topologies of them were incongruent, both provided strong evidence supporting the monophyly of Saniculoideae and Apioideae. In addition, the sister groups between Saniculoideae and Apioideae were strongly suggested. The Sanicula species involved in this study were clustered into a clade, and the Eryngium species were also clustered together. However, it was clearly observed that the sections of Sanicula involved in the current study were not respectively recovered as monophyletic group. Molecular dating analysis explored that the origin of this genus was occurred during the late Eocene period, approximately 37.84 Ma (95% HPD: 20.33-52.21 Ma) years ago and the diversification of the genus was occurred in early Miocene 18.38 Ma (95% HPD: 10.68-25.28 Ma).

CONCLUSION

The plastome-based tree and ITS-based tree generated incongruences, which may be attributed to the event of hybridization/introgression, incomplete lineage sorting (ILS) and chloroplast capture. Our study highlighted the power of plastome data to significantly improve the phylogenetic supports and resolutions, and to efficiently explore the evolutionary history of this genus. Molecular dating analysis explored that the diversification of the genus occurred in the early Miocene, which was largely influenced by the prevalence of the East Asian monsoon and the uplift of the Hengduan Mountains (HDM). In summary, our study provides novel insights into the plastome evolution, phylogenetic relationships, taxonomic framework and evolution of genus Sanicula.

Complete chloroplast of four Sanicula taxa (Apiaceae) endemic to China: lights into genome structure, comparative analysis, and phylogenetic relationships

BACKGROUND

The genus Sanicula comprises ca. 45 taxa, widely distributed from East Asia to North America, which is a taxonomically difficult genus with high medicinal value in Apiaceae. The systematic classification of the genus has been controversial for a long time due to varied characters in key morphological traits. China is one of the most important distributed centers, with ca. 18 species and two varieties. At present, chloroplast genomes are generally considered to be conservative and play an important role in evolutionary relationship study. To investigate the plastome evolution and phylogenetic relationships of Chinese Sanicula, we comprehensively analyzed the structural characteristics of 13 Chinese Sanicula chloroplasts and reconstructed their phylogenetic relationships.

RESULTS

In present study, four newly complete chloroplast genome of Sanicula taxa by using Illumina sequencing were reported, with the typical quadripartite structure and 155,396-155,757 bp in size. They encoded 126 genes, including 86 protein-coding genes, 32 tRNA genes and 8 rRNA genes. Genome structure, distributions of SDRs and SSRs, gene content, among Sanicula taxa, were similar. The nineteen intergenic spacers regions, including atpH-atpI, ndhC-trnM, petB-petD, petD-rpoA, petN-psbM, psaJ-rpl33, rbcL-accD, rpoB-trnC, rps16-trnQ, trnE-psbD, trnF-ndhJ, trnH-psbA, trnN-ndhF, trnS-psbZ, trnS-trnR, trnT-trnF, trnV-rps12, ycf3-trnS and ycf4-cemA, and one coding region (ycf1 gene) were the most variable. Results of maximum likelihood analysis based on 79 unique coding genes of 13 Chinese Sanicula samples and two Eryngium (Apiaceae-Saniculoideae) species as outgroup taxa revealed that they divided into four subclades belonged to two clades, and one subclade was consistent with previously traditional Sanicula section of its system. The current classification based on morphology at sect. Sanicla and Sect. Tuberculatae in Chinese Sanicula was not supported by analysis of cp genome phylogeny.

CONCLUSIONS

The chloroplast genome structure of Sanicula was similar to other angiosperms and possessed the typical quadripartite structure with the conserved genome arrangement and gene features. However, their size varied owing to expansion/contraction of IR/SC boundaries. The variation of non-coding regions was larger than coding regions of the chloroplast genome. Phylogenetic analysis within these Chinese Sanicula were determined using the 79 unique coding genes. These results could provide important data for systematic, phylogenomic and evolutionary research in the genus for the future studies.

Origin, evolution, breeding, and omics of Apiaceae: a family of vegetables and medicinal plants

Many of the world's most important vegetables and medicinal crops, including carrot, celery, coriander, fennel, and cumin, belong to the Apiaceae family. In this review, we summarize the complex origins of Apiaceae and the current state of research on the family, including traditional and molecular breeding practices, bioactive compounds, medicinal applications, nanotechnology, and omics research. Numerous molecular markers, regulatory factors, and functional genes have been discovered, studied, and applied to improve vegetable and medicinal crops in Apiaceae. In addition, current trends in Apiaceae application and research are also briefly described, including mining new functional genes and metabolites using omics research, identifying new genetic variants associated with important agronomic traits by population genetics analysis and GWAS, applying genetic transformation, the CRISPR-Cas9 gene editing system, and nanotechnology. This review provides a reference for basic and applied research on Apiaceae vegetable and medicinal plants.

Exceptional evolutionary lability of flower-like inflorescences (pseudanthia) in Apiaceae subfamily Apioideae

PREMISE

Pseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower-like inflorescences and their potential correlation with diversification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseudanthia and evaluate their potential association with changes in the size of floral display.

METHODS

The framework for our analyses consisted of a time-calibrated phylogeny of 1734 representatives of Apioideae and a morphological matrix of inflorescence traits encoded for 847 species. Macroevolutionary patterns in pseudanthia were inferred using Markov models of discrete character evolution and stochastic character mapping, and a principal component analysis was used to visualize correlations in inflorescence architecture. The interdependence between net diversification rates and the occurrence of pseudocorollas was analyzed with trait-independent and trait-dependent approaches.

RESULTS

Pseudanthia evolved in 10 major clades of Apioideae with at least 36 independent origins and 46 reversals. The morphospace analysis recovered differences in color and compactness between floral and hyperfloral pseudanthia. A correlation between pseudocorollas and size of inflorescence was also strongly supported. Contrary to our predictions, pseudanthia are not responsible for variation in diversification rates identified in this subfamily.

CONCLUSIONS

Our results suggest that pseudocorollas evolve as an answer to the trade-off between enlargement of floral display and costs associated with production of additional flowers. The high evolvability and architectural differences in apioid pseudanthia may be explained on the basis of adaptive wandering and evolutionary developmental biology.

The potential of Apiaceae species as sources of singular phytochemicals and plant-based pesticides

The Apiaceae Lindl. (=Umbelliferae Juss.), which includes several economical important vegetables, herbs, and spices, is one of the most numerous plant family. Umbelliferous crops (namely anise, fennel, carrot, coriander, parsley, etc.) are also valuable sources of botanical flavoring agents and fragrances. In addition, Apiaceae species yield a wide variety of distinctive specialized metabolites (i.e, volatile phenylpropanoids, furanocoumarins, sesquiterpene coumarins, polyacetylenes, and phthalides), some of them been described as uncommon natural phytochemicals exclusive of the family, which offers a great potential for bioprospection. Numerous studies have pointed out the outstanding biological activity of extracts and several classes of phytochemicals from Apiaceae species. Emphasis has been given to essential oils (EOs) and their constituents activities, most likely because this type of plant added value product benefits from a larger acceptance and application potential in integrated pest management (IPM) and integrated vector management (IVM) programs. Several species of the family offer a variety of unique compounds with great potential as biopesticidal and/or synergizing agents. Investigations covering their activity toward agricultural pests and phytopathogens have increased in the last years, nevertheless the interest remains strongly focus on arthropod species, predominantly those acting as vectors of human diseases. From our survey, it is patent the gap of knowledge concerning the potential molluscicidal properties of Apiaceae extracts/phytochemicals, as well as their herbicidal activities against invasive plant species. In this review, we propose to highlight the potential of Apiaceae species as suitable sources of bioactive phytochemicals with great relevance within the frame of plant-based pesticides R&D, and will discuss their applicability in real-world scenarios considering the recent developments regarding the design of stable formulations incorporating Apiaceae bioactive products. We expect that this review will encourage researchers to consider undervalued Apiaceae species as alternative sources of bioactive compounds and will give a contribute to the field by suggesting new research topics.

A transcriptome-based study on the phylogeny and evolution of the taxonomically controversial subfamily Apioideae (Apiaceae)

BACKGROUND AND AIMS

A long-standing controversy in the subfamily Apioideae concerns relationships among the major lineages, which has prevented a comprehensive study of their fruits and evolutionary history. Here we use single copy genes (SCGs) generated from transcriptome datasets to generate a reliable species tree and explore the evolutionary history of Apioideae.

METHODS

In total, 3351 SCGs were generated from 27 transcriptome datasets and one genome, and further used for phylogenetic analysis using coalescent-based methods. Fruit morphology and anatomy were studied in combination with the species tree. Eleven SCGs were screened out for dating analysis with two fossils selected for calibration.

KEY RESULTS

A well-supported species tree was generated with a topology [Chamaesieae, (Bupleureae, (Pleurospermeae, (Physospermopsis Clade, (Group C, (Group A, Group B)))))] that differed from previous trees. Daucinae and Torilidinae were not in the tribe Scandiceae and existed as sister groups to the Acronema Clade. Five branches (I-V) of the species tree showed low quartet support but strong local posterior probabilities. Dating analysis suggested that Apioideae originated around 56.64 Mya (95 % highest posterior density interval, 45.18-73.53 Mya).

CONCLUSIONS

This study resolves a controversial phylogenetic relationship in Apioideae based on 3351 SCGs and coalescent-based species tree estimation methods. Gene trees that contributed to the species tree may undergoing rapid evolutionary divergence and incomplete lineage sorting. Fruits of Apioideae might have evolved in two directions, anemochorous and hydrochorous, with epizoochorous as a derived mode. Molecular and morphological evidence suggests that Daucinae and Torilidinae should be restored to the tribe level. Our results provide new insights into the morphological evolution of this subfamily, which may contribute to a better understanding of species diversification in Apioideae. Molecular dating analysis suggests that uplift of the Qinghai-Tibetan Plateau (QTP) and climate changes probably drove rapid speciation and diversification of Apioideae in the QTP region.

Old sleeping Sicilian beauty: seed germination in the palaeoendemic Petagnaea gussonei (Spreng.) Rauschert (Saniculoideae, Apiaceae)

Petagnaea gussonei (Apiaceae) is a perennial herbaceous species endemic to northeast Sicily (Nebrodi Mountains). It is considered a remnant of the Sicilian Tertiary flora, and is endangered according to the Red List. There is no information in the literature about the germinability of its seeds, even though seed production is know to occur. The aim of this study was to obtain data to better understand seed germination of this species and its biological implications. Thus, several approaches were employed: vitality analyses, gibberellic acid supply, germination and soil microbial flora analyses via end-point and qPCR. The results suggest that seed germination occurs after ca. 1.5 years at a rate of ca. 11%. The seeds can be classified as physiologically dormant, and probably require prolonged cold stratification for germination. Because seed germination is low, it is likely that agamic reproduction represents an important mean for its conservation and survival. These results have important implications for P. gussonei survival and should be considered in possible re-introduction attempts aimed at restoring threatened populations.

A Southern Hemisphere origin for campanulid angiosperms, with traces of the break-up of Gondwana

BACKGROUND

New powerful biogeographic methods have focused attention on long-standing hypotheses regarding the influence of the break-up of Gondwana on the biogeography of Southern Hemisphere plant groups. Studies to date have often concluded that these groups are too young to have been influenced by these ancient continental movements. Here we examine a much larger and older angiosperm clade, the Campanulidae, and infer its biogeographic history by combining Bayesian divergence time information with a likelihood-based biogeographic model focused on the Gondwanan landmasses.

RESULTS

Our analyses imply that campanulids likely originated in the middle Albian (~105 Ma), and that a substantial portion of the early evolutionary history of campanulids took place in the Southern Hemisphere, despite their greater species richness in the Northern Hemisphere today. We also discovered several disjunctions that show biogeographic and temporal correspondence with the break-up of Gondwana.

CONCLUSIONS

While it is possible to discern traces of the break-up of Gondwana in clades that are old enough, it will generally be difficult to be confident in continental movement as the prime cause of geographic disjunctions. This follows from the need for the geographic disjunction, the inferred biogeographic scenario, and the dating of the lineage splitting events to be consistent with the causal hypothesis.

Evolution of morphological traits in Verbenaceae

PREMISE OF THE STUDY

A new infrafamilial circumscription of the Verbenaceae with eight tribes: Casselieae, Citharexyleae, Duranteae, Lantaneae, Neospartoneae, Petreeae, Priveae, and Verbeneae, has been recently proposed, on the basis of molecular phylogenetic studies. Two genera, Dipyrena and Rhaphithamnus, remain unplaced. The aim of this work is to reconstruct the evolutionary history of morphological characters traditionally employed in the classification of the Verbenaceae, with special attention to tribes Verbeneae and Lantaneae.

METHODS

Twenty-one characters, related to habit and vegetative morphology, inflorescence and floral morphology, ovary and fruit morphology, as well as chromosome number, were optimized over a molecular phylogeny of Verbenaceae.

KEY RESULTS

All tribes are supported by at least one morphological trait except tribes Duranteae and Citharexyleae. Suffrutescent habit, sessile flowers, and four cluses are synapomorphies for tribe Verbeneae. Gynoecium with short style and entire stigma are synapomorphic traits for tribe Lantaneae. Sessile flowers and unicarpellate ovaries are morphological synapomorphies for the new tribe Neospartoneae. Suffrutescent habit is a synapomorphic trait for tribe Priveae. Homothetic pleiobotrya and absence of the adaxial staminode are synapomorphic traits for tribe Casselieae. Undivided fleshy fruits are probably a synapomorphic trait for tribe Petreeae. Putative plesiomorphies for the ancestor of the Verbenaceae are discussed as well as synapomorphic traits within other Verbenaceae clades.

CONCLUSIONS

Many of the characters traditionally employed in classification have proven to be very homoplastic, or have been shown not to support relationships within the family. Moreover, traditional assumptions concerning character polarity have in some cases been shown to be incorrect.

Relative embryo length as an adaptation to habitat and life cycle in Apiaceae

• The factors driving the evolution of the relative embryo length in Apiaceae were examined. We tested the hypothesis that seeds with large relative embryo length, because of more rapid germination, are beneficial in dry and open habitats and for short-lived species. We also analyzed to what extent delayed germination as a result of embryo growth can be considered a dormancy mechanism. • Hypotheses were tested by correlating the relative embryo length with other plant traits, habitat and climatic variables. The adaptive nature of the relative embryo length was determined by comparing the performance of a pure drift, Brownian motion (BM) model of trait evolution with that of a selection-inertia, Ornstein-Uhlenbeck (OU) model. • A positive correlation of the relative embryo length with germination speed and negative correlations with the amount of habitat shade, longevity and precipitation were found. An OU model, in which the evolution of longer embryos corresponded to a transition to habitats of high light, or to a short life cycle, outperformed significantly a BM model. • The results indicated that the relative embryo length may have evolved as an adaptation to habitat and life cycle, whereas dormancy was mainly related to temperature at the sampling sites.