Chloranthales remain the last major mesangiosperm lineage without a nuclear genome assembly. We therefore assemble a high-quality chromosome-level genome of Chloranthus spicatus to resolve enigmatic evolutionary relationships, as well as explore patterns of genome evolution among the major lineages of mesangiosperms (eudicots, monocots, magnoliids, Chloranthales, and Ceratophyllales). We find that synteny is highly conserved between genomic regions of Amborella, Vitis, and Chloranthus. We identify an ancient single whole-genome duplication (WGD) (κ) prior to the divergence of extant Chloranthales. Phylogenetic inference shows Chloranthales as sister to magnoliids. Furthermore, our analyses indicate that ancient hybridization may account for the incongruent phylogenetic placement of Chloranthales + magnoliids relative to monocots and eudicots in nuclear and chloroplast trees. Long genes and long introns are found to be prevalent in both Chloranthales and magnoliids compared to other angiosperms. Overall, our findings provide an improved context for understanding mesangiosperm relationships and evolution and contribute a valuable genomic resource for future investigations.

Chloranthus genome provides insights into the early diversification of angiosperms.

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.

/pdf/insights-into-angiosperm-evolution-floral-development-and-4ar83n45i4.pdf

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

The global consumption of plant-based cosmetics has shown spectacular growth in recent years because of rising consumer awareness regarding the long-term health benefits of natural ingredients. As the global demand for herbal cosmetics increases, there are ample opportunities for Sri Lanka as a tropical Asian country to expand its productions and global exports along with its unique biodiversity and inherited traditional knowledge. Therefore, the present review attempts to give an overview of the widely used medicinal plants in the global herbal cosmetic industry and strengths, challenges, and possible solutions for the development of the herbal cosmetic industry of Sri Lanka. Information was collected using electronic search (using Pub Med, Science Direct, Web of Science, Google Scholar, TEEAL, and Scopus) for articles published in peer-reviewed journals, industrial reports, market surveys, and library search for local books on ethnobotany. Important plant-derived ingredients used in the global herbal cosmetic industry are essential oils, colorants, oils, fats, and waxes. The traditional usage of 108 medicinal plant species (belonging to 58 families) in cosmetic treatments was identified from the local books of Sri Lanka. Of these, 49 plant species were reported as new ingredients for the herbal cosmetic industry. However, the lack of ethnobotanical and ethnopharmacological surveys to identify the cosmetic potential plants, insufficient or absence of continuous supply of raw materials for production in line with the existing demand, the lack of quality control of raw materials and finished cosmetic products, improper systematic cultivation systems for medicinal plants, poor postharvest practices, and the lack of innovations are major challenges encountered in Sri Lanka for the development of the herbal cosmetic industry. In conclusion, addressing these vital knowledge gaps is a timely requirement of the country for the sustainable development of the herbal cosmetic industry in Sri Lanka. Furthermore, assembling of the multidisciplinary cooperation of botanists, chemists, toxicologists, researchers, and biologists is crucial to analyze the interesting functional properties, efficacy, and effectiveness of documented medicinal plants with cosmetic potential.

/pdf/global-perspective-of-plant-based-cosmetic-industry-and-dzrxi8ii.pdf

Global Perspective of Plant-Based Cosmetic Industry and Possible Contribution of Sri Lanka to the Development of Herbal Cosmetics

Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.

/pdf/the-current-developments-in-medicinal-plant-genomics-enabled-2s6to8jv.pdf

The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites’ Biosynthesis

Wintersweet (Chimonanthus praecox) is one of the most important ornamental plants, whose color is mainly determined by the middle tepals. However, the molecular mechanisms underlying the intriguing flower color development among different wintersweet groups are still largely unknown. In addition, wintersweet belongs to magnoliids, and the issue remains as to how to determine the phylogenetic position of magnoliids conclusively. Here, the whole genome of red flower wintersweet, a new wintersweet type, was sequenced and assembled with high-quality. The genome comprised 11 super-scaffolds (chromosomes) with a total size of 737.03 Mb. Based on the analyses of the long branch attraction (LBA), incomplete lineage sorting (ILS), sparse taxon sampling and other factors, we suggest that a bifurcating tree may not fully represent the complex early diversification of the angiosperms, and that magnoliids are most likely to be the sister of the eudicots. The wintersweet genome appears to have undergone two rounds of whole-genome duplication (WGD) events: a younger WGD event representing an independent event specific to the Calycanthaceae species; and an ancient WGD event shared by Laurales. By integrating genomic, transcriptomic, and metabolomic data, CpANS1 and transcription factor CpMYB1 were considered to play key roles in regulating tepal color development, whereas CpMYB1 needs to form a complex with bHLH and WD40 to fully perform its regulatory function. The present study not only provided novel insights into the evolution of magnoliids and the molecular mechanism for flower color development, but also laid the foundation for subsequent functional genomics study and molecular breeding of wintersweet.

The red flower wintersweet genome provides insights into the evolution of magnoliids and the molecular mechanism for tepal color development

Magnolia biondii Pamp. (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China. Determining the genome sequence of M. biondii would help resolve the phylogenetic uncertainty of magnoliids and improve the understanding of individual trait evolution within the Magnolia genus. We assembled a chromosome-level reference genome of M. biondii using ~67, ~175, and ~154 Gb of raw DNA sequences generated via Pacific Biosciences single-molecule real-time sequencing, 10X Genomics Chromium, and Hi-C scaffolding strategies, respectively. The final genome assembly was ~2.22 Gb, with a contig N50 value of 269.11 kb and a BUSCO complete gene percentage of 91.90%. Approximately 89.17% of the genome was organized into 19 chromosomes, resulting in a scaffold N50 of 92.86 Mb. The genome contained 47,547 protein-coding genes, accounting for 23.47% of the genome length, whereas 66.48% of the genome length consisted of repetitive elements. We confirmed a WGD event that occurred very close to the time of the split between the Magnoliales and Laurales. Functional enrichment of the Magnolia-specific and expanded gene families highlighted genes involved in the biosynthesis of secondary metabolites, plant–pathogen interactions, and responses to stimuli, which may improve the ecological fitness and biological adaptability of the lineage. Phylogenomic analyses revealed a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots. The genome sequence of M. biondii could lead to trait improvement, germplasm conservation, and evolutionary studies on the rapid radiation of early angiosperms.

/pdf/the-genome-of-magnolia-biondii-pamp-provides-insights-into-4ie764i9or.pdf

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids.

Magnolia biondii Pamp (Magnoliaceae, magnoliids) is a phylogenetically, economically, and medicinally important ornamental tree species widely grown and cultivated in the north-temperate regions of China Contributing a genome sequence for M biondii will help resolve phylogenetic uncertainty of magnoliids and further understand individual trait evolution in Magnolia We assembled a chromosome-level reference genome of M biondii using ~67, ~175, and ~154 Gb of raw DNA sequences generated by Pacific Biosciences Single-molecule Real-time sequencing, 10X genomics Chromium, and Hi-C scaffolding strategies, respectively The final genome assembly was ⍰222 Gb with a contig N50 of 26911 Kb and a BUSCO complete gene ratio of 9190% About 8917% of the genome length was organized to 19 chromosomes, resulting in a scaffold N50 of 9286 Mb The genome contained 48,319 protein-coding genes, accounting for 2297% of the genome length, in contrast to 6648% of the genome length for the repetitive elements We confirmed a Magnoliaceae specific WGD event that might have probably occurred shortly after the split of Magnoliaceae and Annonaceae Functional enrichment of the Magnolia specific and expanded gene families highlighted genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, and response to stimulus, which may improve ecological fitness and biological adaptability of the lineage Phylogenomic analyses recovered a sister relationship of magnoliids and Chloranthaceae, which are sister to a clade comprising monocots and eudicots The genome sequence of M biondii could empower trait improvement, germplasm conservation, and evolutionary studies on rapid radiation of early angiosperms

/pdf/the-genome-assembly-and-annotation-of-magnolia-biondii-pamp-1q1duxah4t.pdf

The genome assembly and annotation of Magnolia biondii Pamp., a phylogenetically, economically, and medicinally important ornamental tree species

O_LIThe Qinghai-Tibet Plateau (QTP) encompasses areas with a remarkably high degree of biodiversity, harboring exceptional species-rich radiations. How these radiations formed by interacting with geology, climate and ecology remains seldom examined. C_LIO_LIWe investigate the roles of abiotic (environmental) and biotic (species-intrinsic) factors in driving radiating diversification of Saussurea (Asteraceae) by deploying a number of time-dependent, paleoenvironment-dependent and trait-dependent models, as well as ecological distribution data. C_LIO_LIWe show that three main clades of Saussurea begin to diversify in the Miocene almost simultaneously, with increasing diversification rates toward the present and negative dependence to paleotemperature. Acceleration in diversification rates are correlated with adaptive traits, as well climate lability, niche breadth and species range. C_LIO_LIWe conclude that fluctuation of paleoclimate along with complex QTP environments provided opportunities for increased diversification rates of Saussurea with diverse adaptive traits, highlighting the importance of combinations of clade-specific traits and ecological niches in driving rapid radiation. C_LI

/pdf/insights-into-the-drivers-of-radiating-diversification-in-4rsfaav6ey.pdf

Insights into the drivers of radiating diversification in biodiversity hotspots using Saussurea (Asteraceae) as a case

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The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids.

The genome assembly and annotation of Magnolia biondii Pamp., a phylogenetically, economically, and medicinally important ornamental tree species

Insights into the drivers of radiating diversification in biodiversity hotspots using Saussurea (Asteraceae) as a case