The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids

Evolutionary trajectories and subfunctionalization of 2 key methyltransferase regulator subfamilies in plants

DNA methylation, a conserved epigenetic mark in both plants and animals, plays a critical role in growth, development, and adaptability. This study explores the origin, evolution, and functional diversification of 2 key methyltransferase regulators, DNAJ-domain-containing protein 1/2/3 (DNAJ1/2/3) and SU(VAR)3-9 HOMOLOG 1/3 (SUVH1/3), in plants. By analyzing genomic data from 21 algae and 86 land plants, we discovered that DNAJ1/2/3 originated within Magnoliopsida, while SUVH1/3 emerged in ferns and evolved through retrotransposition. Both protein families have undergone multiple duplication events and positive selection throughout plant evolution, resulting in their expansion and functional divergence. In dicotyledons, DNAJ1/2/3 diverged into 3 subclades, whereas SUVH1/3 underwent a common duplication event in its ancestral lineage, resulting in 2 subgroups. Structural domain analysis revealed that the evolution of PHD fingers in DNAJ1/2/3 and AT domains in SUVH1/3, under selective pressure, enhanced their interaction capabilities and contributed to the formation of complexes involved in DNA methylation and demethylation regulation. Expression profile analysis across various plant taxa demonstrated tissue-specific expression patterns, with higher expression levels observed in meristematic tissues and active cell regions. These findings elucidate the evolutionary patterns of DNAJ1/2/3 and SUVH1/3 and offer insights into their functional diversification in plants.

Evolutionary history of magnoliid genomes and benzylisoquinoline alkaloid biosynthesis

Benzylisoquinoline alkaloids (BIAs) are important metabolites synthesized in early-diverging eudicots and magnoliids, yet the genetic basis of BIA biosynthesis in magnoliids remains unclear. Here, we decode the genomes of two magnoliid species, Saruma henryi and Aristolochia manshuriensis, and reconstruct the ancestral magnoliid karyotype and infer the chromosomal rearrangement history following magnoliid diversification. Metabolomic, transcriptomic, and phylogenetic analyses reveal the intermediate chemical components and genetic basis of BIA biosynthesis in A. manshuriensis. Although the core enzymes involved in BIA synthesis appear to be largely conserved between early-diverging eudicots and magnoliids, the biosynthetic pathways in magnoliids seem to exhibit greater flexibility. Significantly, our investigation of the evolutionary history of BIA biosynthetic genes revealed that almost all were duplicated before the emergence of extant angiosperms, with only early-diverging eudicots and magnoliids preferentially retaining these duplicated genes, thereby enabling the biosynthesis of BIAs in these groups.

Benzoxanthenone Lignans Related to Carpanone, Polemanone, and Sauchinone: Natural Origin, Chemical Syntheses, and Pharmacological Properties

Medicinal plants from the genus Saururus are commonly used to treat inflammatory pathologies. They contain numerous bioactive compounds, notably the polycyclic lignan sauchinone from the species Saururus chinensis. An in-depth analysis of benzoxanthenone lignans related to sauchinone, and the analogous products carpanone and polemannones, has been carried out. The review reports the product's isolation, biosynthetic pathway, and chemical strategies to synthesize benzoxanthenones via liquid- and solid-phase syntheses. The metabolic and pharmacokinetic properties of sauchinone are discussed. At the pharmacological level, sauchinone is a potent blocker of the production of pro-inflammatory mediators, such as nitric oxide and prostaglandin E2, and an efficient antioxidant agent. The properties of sauchinone can be exploited to combat multiple pathologies, such as liver injuries, renal dysfunction, osteoarthritis, inflammatory bowel disease, ulcerative colitis, and cancers. The capacity of the natural product to inhibit tumor cell proliferation and to reduce migration/invasion of cancer cells and the development of metastases is underlined, together with the regulation of the epithelial-mesenchymal transition and immune checkpoints. Altogether, the review offers a complete survey of the chemical and biochemical properties of sauchinone-type benzoxanthenones.

Comprehensive Genomic Dataset of Chinese Lizardtail Herb and Comparative Genomic Analysis Provide Insights Into Its Paleo-Polyploidization Event

The Chinese lizardtail herb, Saururus chinensis, holds a prominent position in traditional Chinese medicine. In this study, we present a comprehensive genomic dataset for S. chinensis. Furthermore, comparative genomic analysis indicates that the extant genome of S. chinensis retains extensive traces of a paleo-tetraploidization event. These traces are observable at both the macroscopic level of chromosomes and the microscopic level within specific gene families, such as the PEL (pseudo-etiolation in light) gene family. Additionally, our findings further suggest that this paleo-tetraploidization event drives an expansion of the PEL gene family in the S. chinensis genome, potentially facilitating its neo- and sub-functionalization, and thereby contributing to the evolutionary adaptability of this species.

The parsley genome assembly and DNA methylome shed light on apigenin biosynthesis in the Apiaceae

Parsley [Petroselinum crispum (Mill.)] is a medicinal and edible vegetable of the Apiaceae family that is rich in apigenin. The Apiaceae family is well known for its diverse secondary metabolites. As a high-quality reference genome is lacking for parsley, the evolution and apigenin biosynthesis in Apiaceae have remained unexplored. Here, we report the chromosome-level genome sequence of parsley, consisting of 1.85 Gb that mainly arose from the expansion of long terminal repeats. Whole-genome bisulfite sequencing revealed a significantly higher number of hypermethylated differentially expressed genes in leaf blades and petioles than in root tissues. Moreover, we identified and characterized chalcone isomerase (CHI) genes, encoding key enzymes involved in apigenin biosynthesis in parsley. We also established that the APETALA2 family transcription factor Pcrispum_6.2855 (PcAP2) binds to the (Pcrispum_11.4764) PcCHI promoter and promotes apigenin accumulation. In conclusion, our work presents a multiomics data resource for understanding apigenin biosynthesis and its transcriptional regulation in parsley, in addition to shedding light on the evolution of parsley within the Apiaceae.

Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris

The traditional Chinese medicinal plant Prunella vulgaris contains numerous triterpene saponin metabolites, notably ursolic and oleanolic acid saponins, which have significant pharmacological values. Despite their importance, the genes responsible for synthesizing these triterpene saponins in P. vulgaris remain unidentified. This study used a comprehensive screening methodology, combining phylogenetic analysis, gene expression assessment, metabolome-transcriptome correlation and co-expression analysis, to identify candidate genes involved in triterpene saponins biosynthesis. Nine candidate genes - two OSCs, three CYP716s and four UGT73s - were precisely identified from large gene families comprising hundreds of members. These genes were subjected to heterologous expression and functional characterization, with enzymatic activity assays confirming their roles in the biosynthetic pathway, aligning with bioinformatics predictions. Analysis revealed that these genes originated from a whole-genome duplication (WGD) event in P. vulgaris, highlighting the potential importance of WGD for plant metabolism. This study addresses the knowledge gap in the biosynthesis of triterpene saponins in P. vulgaris, establishing a theoretical foundation for industrial production via synthetic biology. Additionally, we present an efficient methodological protocol that integrates evolutionary principles and bioinformatics techniques in metabolite biosynthesis research. This approach holds significant value for studies focused on unraveling various biosynthetic pathways.

SWATH-MS based proteomics reveals the role of photosynthesis related proteins and secondary metabolic pathways in the colored leaves of sweet olive (Osmanthus fragrans)

Colored leaves, a notable horticultural trait, have high research and ornamental value. The evergreen sweet olive (Osmanthus fragrans), one of the top ten traditional flowers in China, has been cultivated for more than two thousand years. However, in recent years, an increasing number of O. fragrans cultivars with colored leaves have been cultivated for their ornamental value. To study the molecular mechanism underlying the observed changes in leaf color, we selected O. fragrans 'Yinbi Shuanghui' (Y), which has yellow-white leaves, and O. fragrans 'Sijigui' (S), which has green leaves, as materials. Pigment content measurement showed that the chlorophyll, carotenoid and anthocyanin contents in Y were lower than in S. According to the SWATH-MS sequencing results, a total of 3,959 proteins were quantitatively identified, 1,300 of which were differentially expressed proteins (DEPs), including 782 up-regulated and 518 down-regulated proteins in Y compared to S. Functional enrichment analysis of DEPs revealed that down-regulated expression of photosynthesis related proteins may lead to the inhibition of chlorophyll synthesis in Y, this may be the main cause of leaf color change. Moreover, a protein interaction prediction model also showed that proteins such as PetC, PsbO, PsbP, and PsbQ were key proteins in the interaction network, and the up-regulated proteins participating in the anthocyanin and carotenoid pathways may be related to the formation of yellow-white leaves. Taken together, our findings represent the first SWATH-MS-based proteomic report on colored leaf O. fragrans and reveal that chlorophyll synthesis and secondary metabolism pathways contribute to the changes in leaf color.

A near-complete assembly of the Houttuynia cordata genome provides insights into the regulatory mechanism of flavonoid biosynthesis in Yuxingcao

Houttuynia cordata, also known as Yuxingcao in Chinese, is a perennial herb in the Saururaceae family. It is highly regarded for its medicinal properties, particularly in treating respiratory infections and inflammatory conditions, as well as boosting the human immune system. However, a lack of genomic information has hindered research on the functional genomics and potential improvements of H. cordata. In this study, we present a near-complete assembly of H. cordata genome and investigate the biosynthetic pathway of flavonoids, specifically quercetin, using genomics, transcriptomics, and metabolomics analyses. The genome of H. cordata diverged from that of Saururus chinensis around 33.4 million years ago; it consists of 2.24 Gb with 76 chromosomes (4n = 76) and has undergone three whole-genome duplication (WGD) events. These WGDs played a crucial role in shaping the H. cordata genome and influencing the gene families associated with its medicinal properties. Through metabolomics and transcriptomics analyses, we identified key genes involved in the β-oxidation process for biosynthesis of houttuynin, one of the volatile oils responsible for the plant's fishy smell. In addition, using the reference genome, we identified genes involved in flavonoid biosynthesis, particularly quercetin metabolism, in H. cordata. This discovery has important implications for understanding the regulatory mechanisms that underlie production of active pharmaceutical ingredients in traditional Chinese medicine. Overall, the high-quality genome assembly of H. cordata serves as a valuable resource for future functional genomics research and provides a solid foundation for genetic improvement of H. cordata for the benefit of human health.

The chromosome-level genomes of the herbal magnoliids Warburgia ugandensis and Saururus chinensis

Warburgia ugandensis and Saururus chinensis are two of the most important medicinal plants in magnoliids and are widely utilized in traditional Kenya and Chinese medicine, respectively. The absence of higher-quality reference genomes has hindered research on the medicinal compound biosynthesis mechanisms of these plants. We report the chromosome-level genome assemblies of W. ugandensis and S. chinensis, and generated 1.13 Gb and 0.53 Gb genomes from 74 and 27 scaffolds, respectively, using BGI-DIPSEQ, Nanopore, and Hi-C sequencing. The scaffold N50 lengths were 82.97 Mb and 48.53 Mb, and the assemblies were anchored to 14 and 11 chromosomes of W. ugandensis and S. chinensis, respectively. In total, 24,739 and 20,561 genes were annotated, and 98.5% and 98% of the BUSCO genes were fully represented, respectively. The chromosome-level genomes of W. ugandensis and S. chinensis will be valuable resources for understanding the genetics of these medicinal plants, studying the evolution of magnoliids and angiosperms and conserving plant genetic resources.

Chromosome-level genome assembly of the threatened resource plant Cinnamomum chago

Cinnamomum chago is a tree species endemic to Yunnan province, China, with potential economic value, phylogenetic importance, and conservation priority. We assembled the genome of C. chago using multiple sequencing technologies, resulting in a high-quality, chromosomal-level genome with annotation information. The assembled genome size is approximately 1.06 Gb, with a contig N50 length of 92.10 Mb. About 99.92% of the assembled sequences could be anchored to 12 pseudo-chromosomes, with only one gap, and 63.73% of the assembled genome consists of repeat sequences. In total, 30,497 genes were recognized according to annotation, including 28,681 protein-coding genes. This high-quality chromosome-level assembly and annotation of C. chago will assist us in the conservation and utilization of this valuable resource, while also providing crucial data for studying the evolutionary relationships within the Cinnamomum genus, offering opportunities for further research and exploration of its diverse applications.

The high-quality genome of Cryptotaenia japonica and comparative genomics analysis reveals anthocyanin biosynthesis in Apiaceae

Cryptotaenia japonica, a traditional medicinal and edible vegetable crops, is well-known for its attractive flavors and health care functions. As a member of the Apiaceae family, the evolutionary trajectory and biological properties of C. japonica are not clearly understood. Here, we first reported a high-quality genome of C. japonica with a total length of 427 Mb and N50 length 50.76 Mb, was anchored into 10 chromosomes, which confirmed by chromosome (cytogenetic) analysis. Comparative genomic analysis revealed C. japonica exhibited low genetic redundancy, contained a higher percentage of single-cope gene families. The homoeologous blocks, Ks, and collinearity were analyzed among Apiaceae species contributed to the evidence that C. japonica lacked recent species-specific WGD. Through comparative genomic and transcriptomic analyses of Apiaceae species, we revealed the genetic basis of the production of anthocyanins. Several structural genes encoding enzymes and transcription factor genes of the anthocyanin biosynthesis pathway in different species were also identified. The CjANSa, CjDFRb, and CjF3H gene might be the target of Cjaponica_2.2062 (bHLH) and Cjaponica_1.3743 (MYB). Our findings provided a high-quality reference genome of C. japonica and offered new insights into Apiaceae evolution and biology.