Full-length transcriptome sequencing provides insights into the evolution of apocarotenoid biosynthesis in Crocus sativus

Crocus genome reveals the evolutionary origin of crocin biosynthesis

Crocus sativus (saffron) is a globally autumn-flowering plant, and its stigmas are the most expensive spice and valuable herb medicine. Crocus specialized metabolites, crocins, are biosynthesized in distant species, Gardenia (eudicot) and Crocus (monocot), and the evolution of crocin biosynthesis remains poorly understood. With the chromosome-level Crocus genome assembly, we revealed that two rounds of lineage-specific whole genome triplication occurred, contributing important roles in the production of carotenoids and apocarotenoids. According to the kingdom-wide identification, phylogenetic analysis, and functional assays of carotenoid cleavage dioxygenases (CCDs), we deduced that the duplication, site positive selection, and neofunctionalization of Crocus-specific CCD2 from CCD1 members are responsible for the crocin biosynthesis. In addition, site mutation of CsCCD2 revealed the key amino acids, including I143, L146, R161, E181, T259, and S292 related to the catalytic activity of zeaxanthin cleavage. Our study provides important insights into the origin and evolution of plant specialized metabolites, which are derived by duplication events of biosynthetic genes.

Metabolites profiling reveals the dynamic changes of non-volatiles in Pu-erh during Ganpu tea processing

Ganpu is an unique tea product made by Pu-erh tea and citrus peel. In this study, the non-volatiles changes of Pu-erh during Ganpu tea processing were fully analyzed by UPLC-ESI-MS/MS. Total 276 significantly differential metabolites in Pu-erh during Ganpu processing were detected (P < 0.05, VIP > 1), and their change trend were clustered into 8 subclasses by K-means analysis. Metabolites of Pu-erh present at various processes were revealed. 72 differential metabolites (P < 0.05, VIP > 1 and fold change ≥2 or ≤0.5) between any two stages were identified and fixation was the key step with 61 differential metabolites. 39 flavonoids and 2 lignans and coumarins were significantly decreased after fixation, while 5 terpenoids, 3 amino acids, 1 organic acids, 2 nucleotides and derivatives and newly detected jasminoside A (Log2FC = 9.90), picrocrocin (Log2FC = 9.90) and nomilinic acid (Log2FC = 7.56) were significantly increased. The results provided valuable information about the effect of Ganpu processing on dynamic changes of non-volatiles in Pu-erh.

Histology, physiology, and transcriptomic and metabolomic profiling reveal the developmental dynamics of annual shoots in tree peonies (Paeonia suffruticosa Andr.)

The development of tree peony annual shoots is characterized by "withering", which is related to whether there are bud points in the leaf axillaries of annual shoots. However, the mechanism of "withering" in tree peony is still unclear. In this study, Paeonia ostii 'Fengdan' and P. suffruticosa 'Luoyanghong' were used to investigate dynamic changes of annual shoots through anatomy, physiology, transcriptome, and metabolome. The results demonstrated that the developmental dynamics of annual shoots of the two cultivars were comparable. The withering degree of P. suffruticosa 'Luoyanghong' was higher than that of P. ostii 'Fengdan', and their upper internodes of annual flowering shoots had a lower degree of lignin deposition, cellulose, C/N ratio, showing no obvious sclerenchyma, than the bottom ones and the whole internodes of vegetative shoot, which resulted in the "withering" of upper internodes. A total of 36 phytohormone metabolites were detected, of which 33 and 31 were detected in P. ostii 'Fengdan' and P. suffruticosa 'Luoyanghong', respectively. In addition, 302 and 240 differentially expressed genes related to lignin biosynthesis, carbon and nitrogen metabolism, plant hormone signal transduction, and zeatin biosynthesis were screened from the two cultivars. Furtherly, 36 structural genes and 40 transcription factors associated with the development of annual shoots were highly co-expressed, and eight hub genes involved in this developmental process were identified. Consequently, this study explained the developmental dynamic on the varied annual shoots through multi-omics, providing a theoretical foundation for germplasm innovation and the mechanized harvesting of tree peony annual shoots.

A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges

In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.

Inference of Ancient Polyploidy Using Transcriptome Data

Polyploidizations, or whole-genome duplications (WGDs), in plants have increased biological complexity, facilitated evolutionary innovation, and likely enabled adaptation under harsh conditions. Besides genomic data, transcriptome data have been widely employed to detect WGDs, due to their efficient accessibility to the gene space of a species. Age distributions based on synonymous substitutions (so-called K_S age distributions) for paralogs assembled from transcriptome data have identified numerous WGDs in plants, paving the way for further studies on the importance of WGDs for the evolution of seed and flowering plants. However, it is still unclear how transcriptome-based age distributions compare to those based on genomic data. In this chapter, we implemented three different de novo transcriptome assembly pipelines with two popular assemblers, i.e., Trinity and SOAPdenovo-Trans. We selected six plant species with published genomes and transcriptomes to evaluate how assembled transcripts from different pipelines perform when using K_S distributions to detect previously documented WGDs in the six species. Further, using genes predicted in each genome as references, we evaluated the effects of missing genes, gene family clustering, and de novo assembled transcripts on the transcriptome-based K_S distributions. Our results show that, although the transcriptome-based K_S distributions differ from the genome-based ones with respect to their shapes and scales, they are still reasonably reliable for unveiling WGDs, except in species where most duplicates originated from a recent WGD. We also discuss how to overcome some possible pitfalls when using transcriptome data to identify WGDs.

Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis

Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C. However, the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions. Here, we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv. 'Hongyang', named Hongyang v4.0, which is the first to achieve two de novo haploid-resolved haplotypes, HY4P and HY4A. HY4P and HY4A have a total length of 606.1 and 599.6 Mb, respectively, with almost the entire telomeres and centromeres assembled in each haplotype. In comparison with Hongyang v3.0, the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions, resulting in ~38.6-39.5 Mb extra sequences, which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A, respectively. Furthermore, our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres. Globally, centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer (Ach-CEN153) with different copy numbers among chromosomes. Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids, but also have genetic features for participation in the regulation of cell division. The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.

Development and validation of SSR markers related to flower color based on full-length transcriptome sequencing in Chrysanthemum

Chrysanthemum (Chrysanthemum moriforlium Ramat.) is one of the most popular flowers worldwide, with very high ornamental and economic values. However, the limitations of available DNA molecular markers and the lack of full genomic sequences hinder the study of genetic diversity and the molecular breeding of chrysanthemum. Here, we developed simple sequence repeat (SSR) from the full-length transcriptome sequences of chrysanthemum cultivar 'Hechengxinghuo'. A total of 11,699 SSRs with mono-, di-, tri-, tetra-, penta- and hexanucleotide repeats were identified, of which eight out of eighteen SSR loci identified based on sixteen transcripts participated in carotenoid metabolism or anthocyanin synthesis were validated as polymorphic SSR markers. These SSRs were used to classify 117 chrysanthemum accessions with different flower colors at the DNA and cDNA levels. The results showed that four SSR markers of carotenoid metabolic pathway divided 117 chrysanthemum accessions into five groups at cDNA level and all purple chrysanthemum accessions were in the group III. Furthermore, the SSR marker CHS-3, LCYE-1 and 3MaT may be related to green color and the PSY-1b marker may be related to yellow color. Overall, our work may be provide a novel method for mining SSR markers associated with specific traits.

Morphological, molecular and phytochemical variations induced by colchicine and EMS chemical mutagens in Crocus sativus L

•

The highest expression level of the ALDH, BGL, and CCD2 genes was found in 0.025% colchicine for 12 h treatment.

•

The content of crocetin esters, picrocrocin, and safranal in colchicine treatments was changed.

•

The stigmas of the C. sativus flowers with two, four, five, and six threads were observed.

•

Various differences in morphological traits were observed in both colchicine and ethyl methanesulfonate (EMS) treatments.

•

The lowest survival rate of corms was related to ethyl methanesulfonate (EMS) treatments.

Crocus sativus L., also known as saffron, is one of the most important medicinal and spice plants throughout the world. The plant is a rich source of apocarotenoids such as crocetin esters, picrocrocin, and safranal. The purpose of this study was to investigate the effect of colchicine and ethyl methanesulfonate (EMS) mutagens on possible inducing new variation in C. sativus. Accordingly, corms were exposed to EMS (0.1% and 0.2%) and colchicine (0.05% and 0.025%) for three incubation times. The lowest survival rate of corms was related to EMS treatments. The relative expression of ALDH, BGL, and CCD2 genes under 0.025% colchicine treatment for 12 h revealed a 2 fold increase compared with the control. The flow cytometric measurements (FCM) of the nuclear DNA content of the colchicine-treated plants did not reveal any significant changes in 2C DNA content. The results, manifest the potential of mutagens to create new variations in the plant.

Understanding saffron biology using omics- and bioinformatics tools: stepping towards a better Crocus phenome

Saffron is a unique plant in many aspects, and its cellular processes are regulated at multiple levels. The genetic makeup in the form of eight chromosome triplets (2n = 3x = 24) with a haploid genetic content (genome size) of 3.45 Gbp is decoded into different types of RNA by transcription. The RNA then translates into peptides and functional proteins, sometimes involving post-translational modifications too. The interactions of the genome, transcriptome, proteome and other regulatory molecules ultimately result in the complex set of primary and secondary metabolites of saffron metabolome. These complex interactions manifest in the form of a set of traits 'phenome' peculiar to saffron. The phenome responds to the environmental changes occurring in and around saffron and modify its response in respect of growth, development, disease response, stigma quality, apocarotenoid biosynthesis, and other processes. Understanding these complex relations between different yet interconnected biological activities is quite challenging in saffron where classical genetics has a very limited role owing to its sterility, and the absence of a whole-genome sequence. Omics-based technologies are immensely helpful in overcoming these limitations and developing a better understanding of saffron biology. In addition to creating a comprehensive picture of the molecular mechanisms involved in apocarotenoid synthesis, stigma biogenesis, corm activity, and flower development, omics-technologies will ultimately lead to the engineering of saffron plants with improved phenome.

Insights into the plateau adaptation of Salvia castanea by comparative genomic and WGCNA analyses

INTRODUCTION

Salvia castanea, a wild plant species is adapted to extreme Qinghai-Tibetan plateau (QTP) environments. It is also used for medicinal purposes due to high ingredient of tanshinone IIA (T-IIA). Despite its importance to Chinese medicinal industry, the mechanisms associated with secondary metabolites accumulation (i.e. T-IIA and rosmarinic acid (RA)) in this species have not been characterized. Also, the role of special underground tissues in QTP adaptation of S. castanea is still unknown.

OBJECTIVES

We explored the phenomenon of periderm-like structure in underground stem center of S. castanea with an aim to unravel the molecular evolutionary mechanisms of QTP adaptation in this species.

METHODS

Morphologic observation and full-length transcriptome of S. castanea plants were conducted. Comparative genomic analyses of S. castanea with other 14 representative species were used to reveal its phylogenetic position and molecular evolutionary mechanisms. RNA-seq and WGCNA analyses were applied to understand the mechanisms of high accumulations of T-IIA and RA in S. castanea tissues.

RESULTS

Based on anatomical observations, we proposed a "trunk-branches" developmental model to explain periderm-like structure in the center of underground stem of S. castanea. Our study suggested that S. castanea branched off from cultivated Danshen around 16 million years ago. During the evolutionary process, significantly expanded orthologous gene groups, 24 species-specific and 64 positively selected genes contributed to morphogenesis and QTP adaptation in S. castanea. RNA-seq and WGCNA analyses unraveled underlying mechanisms of high accumulations of T-IIA and RA in S. castanea and identified NAC29 and TGA22 as key transcription factors.

CONCLUSION

We proposed a "trunk-branches" developmental model for the underground stem in S. castanea. Adaptations to extreme QTP environment in S. castanea are associated with accumulations of high secondary metabolites in this species.

Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds

The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.

The Relation between Drying Conditions and the Development of Volatile Compounds in Saffron (Crocus sativus)

Saffron is derived from the stigmas of the flower Crocus sativus L. The drying process is the most important post-harvest step for converting C. sativus stigmas into saffron. The aim of this review is to evaluate saffron's post-harvest conditions in the development of volatile compounds and its aroma descriptors. It describes saffron's compound generation by enzymatic pathways and degradation reactions. Saffron quality is described by their metabolite's solubility and the determination of picrocrocin, crocins, and safranal. The drying process induce various modifications in terms of color, flavor and aroma, which take place in the spice. It affects the aromatic species chemical profile. In the food industry, saffron is employed for its sensory attributes, such as coloring, related mainly to crocins (mono-glycosyl esters or di-glycosyl polyene).

The chromosome-scale reference genome of Rubus chingii Hu provides insight into the biosynthetic pathway of hydrolyzable tannins

Rubus chingii Hu (Fu-Pen-Zi), a perennial woody plant in the Rosaceae family, is a characteristic traditional Chinese medicinal plant because of its unique pharmacological effects. There are abundant hydrolyzable tannin (HT) components in R. chingii that provide health benefits. Here, an R. chingii chromosome-scale genome and related functional analysis provide insights into the biosynthetic pathway of HTs. In total, sequence data of 231.21 Mb (155 scaffolds with an N50 of 8.2 Mb) were assembled into seven chromosomes with an average length of 31.4 Mb, and 33 130 protein-coding genes were predicted, 89.28% of which were functionally annotated. Evolutionary analysis showed that R. chingii was most closely related to Rubus occidentalis, from which it was predicted to have diverged 22.46 million years ago (Table S8). Comparative genomic analysis showed that there was a tandem gene cluster of UGT, carboxylesterase (CXE) and SCPL genes on chromosome 02 of R. chingii, including 11 CXE, eight UGT, and six SCPL genes, which may be critical for the synthesis of HTs. In vitro enzyme assays indicated that the proteins encoded by the CXE (LG02.4273) and UGT (LG02.4102) genes have tannin hydrolase and gallic acid glycosyltransferase functions, respectively. The genomic sequence of R. chingii will be a valuable resource for comparative genomic analysis within the Rosaceae family and will be useful for understanding the biosynthesis of HTs.

The Beneficial Effects of Saffron Extract on Potential Oxidative Stress in Cardiovascular Diseases

Saffron is commonly used in traditional medicines and precious perfumes. It contains pharmacologically active compounds with notably potent antioxidant activity. Saffron has a variety of active components, including crocin, crocetin, and safranal. Oxidative stress plays an important role in many cardiovascular diseases, and its uncontrolled chain reaction is related to myocardial injury. Numerous studies have confirmed that saffron exact exhibits protective effects on the myocardium and might be beneficial in the treatment of cardiovascular disease. In view of the role of oxidative stress in cardiovascular disease, people have shown considerable interest in the potential role of saffron extract as a treatment for a range of cardiovascular diseases. This review analyzed the use of saffron in the treatment of cardiovascular diseases through antioxidant stress from four aspects: antiatherosclerosis, antimyocardial ischemia, anti-ischemia reperfusion injury, and improvement in drug-induced cardiotoxicity, particularly anthracycline-induced. Although data is limited in humans with only two clinically relevant studies, the results of preclinical studies regarding the antioxidant stress effects of saffron are promising and warrant further research in clinical trials. This review summarized the protective effect of saffron in cardiovascular diseases and drug-induced cardiotoxicity. It will facilitate pharmacological research and development and promote utilization of saffron.

Screening of Key Proteins Affecting Floral Initiation of Saffron Under Cold Stress Using iTRAQ-Based Proteomics

BACKGROUND

Saffron crocus (Crocus sativus) is an expensive and valuable species that presents preventive and curative effects. This study aimed to screen the key proteins affecting the floral initiation of saffron under cold stress and thus increasing yield by regulating the temperature.

RESULTS

Protein expression profiles in flowering and non-flowering saffron buds were established using isobaric tags for relative or absolute quantitation (iTRAQ). A total of 5,624 proteins were identified, and 201 differentially abundant protein species (DAPs) were further obtained between the flowering and non-flowering groups. The most important functions of the upregulated DAPs were "sucrose metabolic process," "lipid transport," "glutathione metabolic process," and "gene silencing by RNA." Downregulated DAPs were significantly enriched in "starch biosynthetic process" and several oxidative stress response pathways. Three new flower-related proteins, CsFLK, CseIF4a, and CsHUA1, were identified in this study. The following eight key genes were validated by real-time qPCR in flowering and non-flowering top buds from five different growth phases: floral induction- and floral organ development-related genes CsFLK, CseIF4A, CsHUA1, and CsGSTU7; sucrose synthase activity-related genes CsSUS1 and CsSUS2; and starch synthase activity-related genes CsGBSS1 and CsPU1. These findings demonstrate the important roles played by sucrose/starch biosynthesis pathways in floral development at the mRNA level. During normal floral organ development, the sucrose contents in the top buds of saffron increased, and the starch contents decreased. In contrast, non-flowering buds showed significantly decreased sucrose contents under cold stress and no significant changes in starch contents compared with those in the dormancy stage.

CONCLUSION

In this report, the protein profiles of saffron under cold stress and a normal environment were revealed for the first time by iTRAQ. A possible "reactive oxygen species-antioxidant system-starch/sugar interconversion flowering pathway" was established to explain the phenomenon that saffron does not bloom due to low temperature treatment.

Bio-synthesis of food additives and colorants-a growing trend in future food

Food additives and colorants are extensively used in the food industry to improve food quality and safety during processing, storage and packing. Sourcing of these molecules is predominately through three means: extraction from natural sources, chemical synthesis, and bio-production, with the first two being the most utilized. However, growing demands for sustainability, safety and "natural" products have renewed interest in using bio-based production methods. Likewise, the move to more cultured foods and meat alternatives requires the production of new additives and colorants. The production of bio-based food additives and colorants is an interdisciplinary research endeavor and represents a growing trend in future food. To highlight the potential of microbial hosts for food additive and colorant production, we focus on current advances for example molecules based on their utilization stage and bio-production yield as follows: (I) approved and industrially produced with high titers; (II) approved and produced with decent titers (in the g/L range), but requiring further engineering to reduce production costs; (III) approved and produced with very early stage titers (in the mg/L range); and (IV) new/potential candidates that have not been approved but can be sourced through microbes. Promising approaches, as well as current challenges and future directions will also be thoroughly discussed for the bioproduction of these food additives and colorants.

Lignin provides mechanical support to herbaceous peony (Paeonia lactiflora Pall.) stems

Stem bending caused by mechanical failure is a major constraint for high-quality herbaceous peony (Paeonia lactiflora Pall.) cut flowers, but little is known about the underlying factors. In this study, two P. lactiflora cultivars, Xixia Yingxue (bending) and Hong Feng (upright), were used to investigate differences in stem bending. The results showed that the stem mechanical strength of Hong Feng was significantly higher than that of Xixia Yingxue, and the thickening of the secondary cell wall and the number of thickened secondary cell wall layers in Hong Feng were significantly higher than those in Xixia Yingxue. Moreover, compared with Xixia Yingxue, Hong Feng showed greater lignification of the cell wall and lignin deposition in the cell walls of the sclerenchyma, vascular bundle sheath and duct. All three types of lignin monomers were detected. The S-lignin, G-lignin, and total lignin contents and the activities of several lignin biosynthesis-related enzymes were higher in Hong Feng than in the other cultivar, and the S-lignin content was closely correlated with stem mechanical strength. In addition, 113,974 full-length isoforms with an average read length of 2106 bp were obtained from the full-length transcriptome of P. lactiflora stems, and differential expression analysis was performed based on the comparative transcriptomes of these two cultivars. Ten lignin biosynthesis-related genes, including 26 members that were closely associated with lignin content, were identified, and multiple upregulated and downregulated transcription factors were found to positively or negatively regulate lignin biosynthesis. Consequently, lignin was shown to provide mechanical support to P. lactiflora stems, providing useful information for understanding the formation of P. lactiflora stem strength.

Prospects and progress on crocin biosynthetic pathway and metabolic engineering

Crocins are a group of highly valuable apocarotenoid-derived pigments mainly produced in Crocus sativus stigmas and Gardenia jasminoides fruits, which display great pharmacological activities for human health, such as anticancer, reducing the risk of atherosclerosis, and preventing Alzheimer's disease. However, traditional sources of crocins are no longer sufficient to meet current demands. The recent clarification of the crocin biosynthetic pathway opens up the possibility of large-scale production of crocins by synthetic metabolic engineering methods. In this review, we mainly introduce the crocin biosynthetic pathway, subcellular route, related key enzymes, and its synthetic metabolic engineering, as well as its challenges and prospects, with a view to providing useful references for further studies on the synthetic metabolic engineering of crocins.