Phylogeny and evolution of Asparagaceae subfamily Nolinoideae: new insights from plastid phylogenomics

Plastome Sequences Uncover the Korean Endemic Species Polygonatum grandicaule (Asparagaceae) as Part of the P. odoratum Complex

Background/Objectives:Polygonatum grandicaule Y.S.Kim, B.U.Oh & C.G.Jang (Asparagaceae Juss.), a Korean endemic species, has been described based on its erect stem, tubular perianth shape, and pedicel length. However, its taxonomic status remains unclear due to limited molecular data. Methods: This study presents the complete plastid genomes (plastomes) of two P. grandicaule individuals and its close relative, P. odoratum (Mill.) Druce var. thunbergii (C.Morren & Decne.) H.Hara. Results: The plastomes, ranging from 154,578 to 154,579 base pairs (bp), are identical to those of P. falcatum A.Gray, P. odoratum var. odoratum, and another Korean endemic species, P. infundiflorum Y.S.Kim, B.U.Oh & C.G.Jang. All contain 78 plastid protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes, except for the pseudogene infA. Phylogenetic analyses using 78 plastid PCGs and whole intergenic spacer (IGS) regions strongly support the three sections within Polygonatum Mill. and show that P. odoratum and its variety are nested within P. falcatum, P. grandicaule, and P. infundiflorum. Conclusions: Given the limited genomic variation and phylogenetic relationships, we propose treating P. falcatum, P. grandicaule, and P. infundiflorum as part of the P. odoratum complex, despite their morphological differences. This study offers valuable putative molecular markers for species identification and supports the application of plastome-based super-barcoding in the morphologically diverse genus Polygonatum.

Complete plastomes serve as desirable molecular makers for precise identification of Asparagus cochinchinensis (Asparagaceae) and nine other congeneric species frequently utilized as its adulterants

BACKGROUD

The processed tuberous roots of Asparagus cochinchinensis (Asparagaceae), known as Asparagi Radix, have long been used in East Asia (particularly in China) as traditional medicines and play an indispensable role in the pharmaceutical industry. However, the frequent adulteration of Asparagi Radix with processed tuberous roots obtained from nine other congeneric species could potentially compromise the quality control measures for related pharmaceutical products, while also posing challenges to the conservation and rational exploitation of the nine adulterant congeneric species that are also used as traditional ethnomedicines. Given this issue, this study aims to develop a molecular authentication method for the accurate identification of A. cochinchinensis and the nine congeneric adulterants, employing the genome skimming approach to generate complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) arrays as the candidate molecular markers.

RESULTS

Through comprehensive phylogenetic and genetic distance analyses based on extensive sampling at both inter- and intra-specific levels, the efficacy of the two candidate molecular markers was assessed by investigating whether their inter-specific genetic divergences align with the taxonomically delineated species boundaries.

CONCLUSION

The results indicated that complete plastomes exhibit superior performance for accurately identifying A. cochinchinensis (the botanical source of Asparagi Radix) and the nine congeneric adulterants, thus can serve as the optimal molecular markers for effective authentication of Asparagi Radix. The desirable discriminative power demonstrated by complete plastomes suggests that the PCR-free molecular authentication method developed in this study will not only contribute to the quality control of pharmaceutical products derived from Asparagi Radix but also facilitate the conservation efforts and rational exploitation of the nine Asparagus species commonly used as adulterants.

Plastid genome comparison and phylogenetic analyses of the Chinese group of medicinal species and related taxa within Asparagus genus

Background

Asparagus L. is a large genus widely distributed across the continents of the Old World. Among its members, approximately 14 species found in China are recognized as popular herbal medicines. However, accurate authentication of these medicinal species and their phylogenetic relationships with related taxa remains unresolved.

Methods

To identify simple sequence repeats (SSRs) and divergence hotspot regions appropriate for future authentication studies, as well as to infer the phylogenetic relationships among Asparagus species, we employed a plastid genome (plastome) dataset consisting of 25 Asparagus species (21 newly sequenced and four retrieved from GenBank), encompassing 12 Chinese medicinal species, for comparative and phylogenetic analyses.

Results

All Asparagus plastomes displayed a typical quadripartite structure with sizes ranging from 155,948 bp to 157,128 bp and harbored 114 unique genes (80 protein-coding genes, 30 tRNA genes, and four rRNA genes). IRscope and Mauve analyses indicated minimal structural variation among Asparagus plastomes. We detected between 79 to 95 SSRs across the plastomes; most were located in the large single-copy (LSC) region and primarily consisted of mono-nucleotide repeat sequences (especially A and T repeats). The genus displayed mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, but with variations in types and numbers among different species. Additionally, we identified 12 special SSR motifs and seven divergent hotspot regions that may serve as potential molecular markers for future identification efforts. Phylogenetic analyses yielded a robust phylogeny for Asparagus taxa, which were split into Clades I, II, and III. Notably, medicinal Asparagus species were mainly found in Clade III. Although the phylogenetic relationships of most Asparagus species aligned with previous study findings, the phylogenetic positions of A. munitus, A. subscandens, A. gobicus, and A. dauricus were newly determined.

Conclusions

The plastomes of Asparagus are largely conserved in terms of genome structure, size, gene content, and arrangement. Nevertheless, SSRs analyses revealed significant interspecific polymorphism within Asparagus. In addition, special SSR motifs and divergent hotspot regions identified from Asparagus plastomes provided reference for subsequent identification investigations. The plastome-based phylogeny provided preliminary insights into the relationships among the Chinese group of medicinal species and related taxa within Asparagus. Overall, this study offers a wealth of informative genetic resources pertinent to Asparagus, thereby enhancing our understanding of its evolution and laying a foundation for species identification, assessment of genetic population diversity, as well as the exploration and conservation of germplasm resources.

Morphology, phylogeography, phylogeny, and taxonomy of Cyclorhiza (Apiaceae)

Background

The genus Cyclorhiza is endemic to China and belongs to the Apiaceae family, which is widely distributed in the Himalaya-Hengduan Mountains (HHM) region. However, its morphology, phylogeny, phylogeography, taxonomy, and evolutionary history were not investigated due to insufficient sampling and lack of population sampling and plastome data. Additionally, we found that Seseli purpureovaginatum was not similar to Seseli members but resembled Cyclorhiza species in morphology, indicating that the taxonomic position of S. purpureovaginatum needs to be re-evaluated.

Methods

First, we observed the morphology of the genus. Second, we newly sequenced four plastomes and conducted comparative analyses. Third, we used the newly sequenced internal transcribed spacer (ITS) and chloroplast DNA (cpDNA) (matK, trnQ-rps16, and trnD-trnT) from 27 populations totaling 244 individuals to explore the genetic diversity and structure. Finally, we performed the phylogenetic analyses based on three datasets (plastome data, ITS sequences, and haplotypes) and estimated the origin and divergence time of the genus.

Results and discussion

The morphology of Cyclorhiza plants and S. purpureovaginatum was highly similar, and their plastomes in structure and features were conserved. The genus possessed high genetic diversity and significant lineage geographic structure, which may be associated with the long-term evolutionary history, complex terrain and habitat, and its sexual reproduction mode. The genus Cyclorhiza originated in the late Eocene (36.03 Ma), which was closely related to the early uplift of the Qinghai-Tibetan Plateau (QTP) and Hengduan Mountains (HDM). The diversification of the genus occurred in the late Oligocene (25.43 Ma), which was largely influenced by the colonization of the newly available climate and terrain. The phylogenetic results showed that Cyclorhiza species clustered into a separate clade and S. purpureovaginatum nested within Cyclorhiza. Cyclorhiza waltonii was sister to Cyclorhiza peucedanifolia, and Cyclorhiza puana clustered with S. purpureovaginatum. Thus, based on the morphology, plastome analyses, and phylogenetic evidence, S. purpureovaginatum should be transferred to Cyclorhiza. All these evidences further supported the monophyly of the genus after including S. purpureovaginatum. Finally, we clarified the generic limits of Cyclorhiza and provided a species classification key index for the genus. In conclusion, the study comprehensively investigated the morphology, phylogeography, phylogeny, taxonomy, and evolution of the genus Cyclorhiza for the first time.

Phylotranscriptomic analyses reveal the evolutionary complexity of Paris L. (Melanthiaceae), a morphologically distinctive genus with significant pharmaceutical importance

BACKGROUND AND AIMS

Previous phylogenetic studies on the pharmaceutically significant genus Paris (Melanthiaceae) have consistently revealed substantial cytonuclear discordance, yet the underlying mechanism responsible for this phenomenon remains elusive. This study aims to reconstruct a robust nuclear backbone phylogeny and elucidate the potential evolutionarily complex events contributing to previously observed cytonuclear discordance within Paris.

METHODS

Based on a comprehensive set of nuclear low-copy orthologous genes obtained from transcriptomic data, the intrageneric phylogeny of Paris, along with its phylogenetic relationships to allied genera, were inferred using coalescent and concatenated approaches. The analysis of gene tree discordance and reticulate evolution, in conjunction with an incomplete lineage sorting (ILS) simulation, was conducted to explore potential hybridization and ILS events in the evolutionary history of Paris and assess their contribution to the discordance of gene trees.

KEY RESULTS

The nuclear phylogeny unequivocally confirmed the monophyly of Paris and its sister relationship with Trillium, while widespread incongruences in gene trees were observed at the majority of internal nodes within Paris. The reticulate evolution analysis identified five instances of hybridization events in Paris, indicating that hybridization events might have occurred recurrently throughout the evolutionary history of Paris. In contrast, the ILS simulations revealed that only two internal nodes within section Euthyra experienced ILS events.

CONCLUSIONS

Our data suggest that the previously observed cytonuclear discordance in the phylogeny of Paris can primarily be attributed to recurrent hybridization events, with secondary contributions from infrequent ILS events. The recurrent hybridization events in the evolutionary history of Paris not only drove lineage diversification and speciation but also facilitated morphological innovation, and enhanced ecological adaptability. Therefore, artificial hybridization has great potential for breeding medicinal Paris species. These findings significantly contribute to our comprehensive understanding of the evolutionary complexity of this pharmaceutically significant plant lineage, thereby facilitating effective exploitation and conservation efforts.

Developing Asparagaceae1726: An Asparagaceae-specific probe set targeting 1726 loci for Hyb-Seq and phylogenomics in the family

Premise

Target sequence capture (Hyb-Seq) is a cost-effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low-copy orthologs, Hyb-Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726-a Hyb-Seq probe set targeting 1726 low-copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae-which will aid the often-challenging delineation and resolution of evolutionary relationships within Asparagaceae.

Methods

Here we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target-enriched data sets.

Results

We recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference.

Discussion

Asparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family.

Characterization, comparison, and phylogenetic analyses of chloroplast genomes of Euphorbia species

The genus Euphorbia (Euphorbiaceae) has near-cosmopolitan distribution and serves as a significant resource for both ornamental and medicinal purposes. Despite its economic importance, Euphorbia's taxonomy has long been challenged by the intricate nature of morphological traits exhibiting high levels of convergence. While molecular markers are essential for phylogenetic studies, their availability for Euphorbia has been limited. To address this gap, we conducted comparative analyses focusing on the chloroplast (CP) genomes of nine Euphorbia species, incorporating three newly sequenced and annotated accessions. In addition, phylogenetic informativeness and nucleotide diversity were computed to identify candidate markers for phylogenetic analyses among closely related taxa in the genus. Our investigation revealed relatively conserved sizes and structures of CP genomes across the studied species, with notable interspecific variations observed primarily in non-coding regions and IR/SC borders. By leveraging phylogenetic informativeness and nucleotide diversity, we identified rpoB gene as the optimal candidate for species delimitation and shallow-level phylogenetic inference within the genus. Through this comprehensive analysis of CP genomes across multiple taxa, our study sheds light on the evolutionary dynamics and taxonomic intricacies of Euphorbia, offering valuable insights into its CP genome evolution and taxonomy.

Assembly and comparative analysis of the first complete mitochondrial genome of the invasive water hyacinth, Eichhornia crassipes

Eichhornia crassipes is an aquatic plant in tropical and subtropical regions, renowned for its notorious invasive tendencies. In this study, we assembled the complete mitogenome of E. crassipes into a single circle molecule of 397,361 bp. The mitogenome has 58 unique genes, including 37 protein-coding genes (PCGs), 18 tRNA genes, three rRNA genes, and 47 % GC content. Sixteen (6.93 %) homologous fragments, ranging from 31 bp to 8548 bp, were identified, indicating the transfer of genetic material from chloroplasts to mitochondria. In addition, we detected positive selection in six PCGs (ccmB, ccmC, ccmFC, nad3, nad4 and sdh4), along with the identification of 782 RNA editing sites across 37 mt-PCGs. These findings suggest a potential contribution to the robust adaptation of this invasive plant to the stressful environment. Lastly, we inferred that phylogenetic conflicts of E. crassipes between the plastome and mitogenome may be attributed to the difference in nucleotide substitution rates between the two organelle genomes. In conclusion, our study provided vital genomic resources for further understanding the invasive mechanism of this species and exploring the dynamic evolution of mitogenomes within the monocot clade.

Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the 'woody clade' in Saxifragales

BACKGROUND

The "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence.

RESULTS

Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected.

CONCLUSIONS

Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.

Historical biogeography and evolutionary diversification of Lilium (Liliaceae): New insights from plastome phylogenomics

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.

Patterns of Carpel Structure, Development, and Evolution in Monocots

The phenomenon of heterochrony, or shifts in the relative timing of ontogenetic events, is important for understanding many aspects of plant evolution, including applied issues such as crop yield. In this paper, we review heterochronic shifts in the evolution of an important floral organ, the carpel. The carpels, being ovule-bearing organs, facilitate fertilisation, seed, and fruit formation. It is the carpel that provides the key character of flowering plants, angiospermy. In many angiosperms, a carpel has two zones: proximal ascidiate and distal plicate. When carpels are free (apocarpous gynoecium), the plicate zone has a ventral slit where carpel margins meet and fuse during ontogeny; the ascidiate zone is sac-like from inception and has no ventral slit. When carpels are united in a syncarpous gynoecium, a synascidiate zone has as many locules as carpels, whereas a symplicate zone is unilocular, at least early in ontogeny. In ontogeny, either the (syn)ascidiate or (sym)plicate zone is first to initiate. The two developmental patterns are called early and late peltation, respectively. In extreme cases, either the (sym)plicate or (syn)ascidiate zone is completely lacking. Here, we discuss the diversity of carpel structure and development in a well-defined clade of angiosperms, the monocotyledons. We conclude that the common ancestor of monocots had carpels with both zones and late peltation. This result was found irrespective of the use of the plastid or nuclear phylogeny. Early peltation generally correlates with ovules belonging to the (syn)ascidiate zone, whereas late peltation is found mostly in monocots with a fertile (sym)plicate zone.

The CAM lineages of planet Earth

BACKGROUND AND SCOPE

The growth of experimental studies of crassulacean acid metabolism (CAM) in diverse plant clades, coupled with recent advances in molecular systematics, presents an opportunity to re-assess the phylogenetic distribution and diversity of species capable of CAM. It has been more than two decades since the last comprehensive lists of CAM taxa were published, and an updated survey of the occurrence and distribution of CAM taxa is needed to facilitate and guide future CAM research. We aimed to survey the phylogenetic distribution of these taxa, their diverse morphology, physiology and ecology, and the likely number of evolutionary origins of CAM based on currently known lineages.

RESULTS AND CONCLUSIONS

We found direct evidence (in the form of experimental or field observations of gas exchange, day-night fluctuations in organic acids, carbon isotope ratios and enzymatic activity) for CAM in 370 genera of vascular plants, representing 38 families. Further assumptions about the frequency of CAM species in CAM clades and the distribution of CAM in the Cactaceae and Crassulaceae bring the currently estimated number of CAM-capable species to nearly 7 % of all vascular plants. The phylogenetic distribution of these taxa suggests a minimum of 66 independent origins of CAM in vascular plants, possibly with dozens more. To achieve further insight into CAM origins, there is a need for more extensive and systematic surveys of previously unstudied lineages, particularly in living material to identify low-level CAM activity, and for denser sampling to increase phylogenetic resolution in CAM-evolving clades. This should allow further progress in understanding the functional significance of this pathway by integration with studies on the evolution and genomics of CAM in its many forms.

Comprehensive Comparative Analyses of Aspidistra Chloroplast Genomes: Insights into Interspecific Plastid Diversity and Phylogeny

Limestone karsts are renowned for extremely high species richness and endemism. Aspidistra (Asparagaceae) is among the highly diversified genera distributed in karst areas, making it an ideal group for studying the evolutionary mechanisms of karst plants. The taxonomy and identification of Aspidistra species are mainly based on their specialized and diverse floral structures. Aspidistra plants have inconspicuous flowers, and the similarity in vegetative morphology often leads to difficulties in species discrimination. Chloroplast genomes possess variable genetic information and offer the potential for interspecies identification. However, as yet there is little information about the interspecific diversity and evolution of the plastid genomes of Aspidistra. In this study, we reported chloroplast (cp) genomes of seven Aspidistra species (A. crassifila, A. dolichanthera, A. erecta, A. longgangensis, A. minutiflora, A. nankunshanensis, and A. retusa). These seven highly-conserved plastid genomes all have a typical quartile structure and include a total of 113 unique genes, comprising 79 protein-coding genes, 4 rRNA genes and 30 tRNA genes. Additionally, we conducted a comprehensive comparative analysis of Aspidistra cp genomes. We identified eight divergent hotspot regions (trnC-GCA-petN, trnE-UUC-psbD, accD-psaI, petA-psbJ, rpl20-rps12, rpl36-rps8, ccsA-ndhD and rps15-ycf1) that serve as potential molecular markers. Our newly generated Aspidistra plastomes enrich the resources of plastid genomes of karst plants, and an investigation into the plastome diversity offers novel perspectives on the taxonomy, phylogeny and evolution of Aspidistra species.