Complete chloroplast genomes of Asparagus aethiopicus L., A. densiflorus (Kunth) Jessop 'Myers', and A. cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congenerics

Comparative metabolites profiling of different solvent extracts of Asparagus species cladodes using liquid chromatography-mass spectrometry-based metabolomics and molecular networking

INTRODUCTION

Asparagus species are naturally distributed worldwide and are known for their pharmacological properties that offer cures for various ailments. However, the metabolic choreography of these Asparagus species is not well characterized, and the compounds contributing to their bioactivities remain unknown.

OBJECTIVE

This study aimed to profile and compare the metabolomes of three Asparagus species cladodes using different solvent extractions.

METHODS

An ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry-based metabolomics and molecular networking approach was used to study the effects of different solvents (ethyl acetate, methanol, and chloroform) with varying polarity on metabolites extraction and identification of bioactive compounds from three Asparagus species cladodes (Asparagus falcatus, Asparagus plumosus, and Asparagus densiflorus 'Meyersii').

RESULTS

Multivariate statistical analyses (mainly principal component analysis) revealed a significant separation between the three solvents and the three species, indicating notable metabolic differences. A total of 118 metabolites were identified in the three species extracted with the different solvents, with methanolic and chloroform extracts containing more metabolites compared with ethyl acetate extracts. These metabolites were identified as belonging to the flavonoids, cinnamic acids, organooxygen compounds, steroids, fatty acids, benzenes, and glycerophospholipids compound classes. Furthermore, these compounds classes were differentially distributed among the three species, indicating chemical/chemotaxis differences between the compared species. Chloroform and methanol are recommended as the optimal solvents to obtain a high content of phytochemical compounds from Asparagus species cladodes.

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.

Correction: Complete chloroplast genomes of Asparagus aethiopicus L., A. densiflorus (Kunth) Jessop 'Myers', and A. cochinchinensis (Lour.) Merr.: Comparative and phylogenetic analysis with congenerics

[This corrects the article DOI: 10.1371/journal.pone.0266376.].

Young evolutionary origins of dioecy in the genus Asparagus

PREMISE

Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking.

METHODS

We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature.

RESULTS

We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers.

CONCLUSIONS

Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.

Comparative and phylogenetic analysis of Asparagus meioclados Levl. and Asparagus munitus Wang et S. C. Chen plastomes and utility of plastomes mutational hotspots

Tiandong is a vital traditional Chinese herbal medicine. It is derived from the tuber root of the Asparagus cochinchinensis according to the Pharmacopoeia of the people's republic of China (2020 Edition). On account of the similar morphology, Asparagus meioclados and Asparagus munitus were used as Tian-Dong in southwest China. Chloroplast (cp) genomes are highly active genetic components of plants and play an extremely important role in improving the efficiency of the identification of plant species. To differentiate the medicinal plants belonging to the genus Asparagus, we sequenced and analyzed the complete plastomes (plastid genomes) of A. meioclados and A. munitus and obtained two plastomes whose length changed to 156,515 bp and 156,381 bp, respectively. A total of 111 unique genes have been detected in plastome, which included 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. In plastomes of A. meioclados and A. munitus, 14,685 and 14,987 codons were detected, among which 9942 and 10,207 had the relative synonymous codon usage (RSCU) values higher than 1, respectively. A. meioclados and A. munitus have 26 SSRs patterns, among which A. meioclados was 25 and A. munitus 21. The average Ka/Ks value was 0.36, and positive selection was detected in genes of the photosynthetic system (ndhF and rbcL) in Asparagus species. To perform the comparative analysis of plastomes, the two newly sequenced plastomes of the A. meioclados and A. munitus species were compared with that of A. cochinchinensis, and 12 hotspots, including 5 coding regions and 7 inter-genomic regions, were identified. Based on the whole plastome of Asparagus, 2 divergent hotspots (accD and rpl32-trnL-UAG) and 1 international barcode fragment (rbcL) were screened, which may be used as particular molecular markers for the identification of Asparagus species. In addition, we determined the phylogenetic relationship between A. meioclados and A. munitus in the genus Asparagus. This study enriches our knowledge of the molecular evolutionary relationships of the Asparagus genus and provides treasured data records for species identification, molecular breeding, and evolutionary analysis of this genus.

The Complete Chloroplast Genomes of Nine Smilacaceae Species from Hong Kong: Inferring Infra- and Inter-Familial Phylogeny

The Smilacaceae is a cosmopolitan family consisting of 200-370 described species. The family includes two widely accepted genera, namely Smilax and Heterosmilax. Among them, the taxonomical status of Heterosmilax has been continuously challenged. Seven Smilax and two Heterosmilax species can be found in Hong Kong, with most of them having medicinal importance. This study aims to revisit the infra-familial and inter-familial relationships of the Smilacaceae using complete chloroplast genomes. The chloroplast genomes of the nine Smilacaceae species from Hong Kong were assembled and annotated, which had sizes of 157,885 bp to 159,007 bp; each of them was identically annotated for 132 genes, including 86 protein-coding genes, 38 transfer RNA genes, and 8 ribosomal RNA genes. The generic status of Heterosmilax was not supported because it was nested within the Smilax clade in the phylogenetic trees, echoing previous molecular and morphological studies. We suggest delimitating the genus Heterosmilax as a section under the genus Smilax. The results of phylogenomic analysis support the monophyly of Smilacaceae and the exclusion of Ripogonum from the family. This study contributes to the systematics and taxonomy of monocotyledons, authentication of medicinal Smilacaceae, and conservation of plant diversity.

The garden asparagus (Asparagus officinalis L.) mitochondrial genome revealed rich sequence variation throughout whole sequencing data

Garden asparagus (Asparagus officinalis L.) is a horticultural crop with high nutritional and medical value, considered an ideal plant for sex determination research among many dioecious plants, whose genomic information can support genetic analysis and breeding programs. In this research, the entire mitochondrial genome of A. officinalis was sequenced, annotated and assembled using a mixed Illumina and PacBio data. The garden asparagus circular mitochondrial genome measures 492,062 bp with a GC value of 45.9%. Thirty-six protein-coding genes, 17 tRNA and 6 rRNA genes were annotated, among which 8 protein-coding genes contained 16 introns. In addition, 254 SSRs with 10 complete tandem repeats and 293 non-tandem repeats were identified. It was found that the codons of edited sites located in the amino acids showed a leucine-formation trend, and RNA editing sites mainly caused the mutual transformation of amino acids with the same properties. Furthermore, 72 sequence fragments accounting for 20,240 bp, presentating 4.11% of the whole mitochondrial genome, were observed to migrate from chloroplast to mitochondrial genome of A. officinalis. The phylogenetic analysis showed that the closest genetic relationship between A. officinalis with onion (Allium cepa) inside the Liliaceae family. Our results demonstrated that high percentage of protein-coding genes had evolutionary conservative properties, with Ka/Ks values less than 1. Therefore, this study provides a high-quality garden asparagus mitochondrial genome, useful to promote better understanding of gene exchange between organelle genomes.

Asparagus cochinchinensis: A review of its botany, traditional uses, phytochemistry, pharmacology, and applications

Asparagus cochinchinensis (Lour.) Merr. (A. cochinchinensis) is a traditional herbal medicine that is used to treat constipation, fever, pneumonia, stomachache, tracheitis, rhinitis, cataract, acne, urticaria. More than 90 compounds have been identified from different structural types in A. cochinchinensis, including steroidal saponins, C21-steroides, lignans, polysaccharides, amino acids, etc. These bioactive ingredients make A. cochinchinensis remarkable for its pharmacological effects on anti-asthma, anti-inflammatory, anti-oxidation, anti-tumor, improving Alzheimer’s disease, neuroprotection, gut health-promoting and so on. Moreover, A. cochinchinensis also plays an important role in food, health product, cosmetic, and other fields. This review focused on the research publications of A. cochinchinensis and aimed to summarize the advances in the botany, traditional uses, phytochemistry, pharmacology, and applications which will provide reference for the further studies and applications of A. cochinchinensis.