Dissecting the genome of star fruit (Averrhoa carambola L.)

Whole genome sequencing of Castanea mollissima and molecular mechanisms of sugar and starch synthesis

The chestnut tree exhibits self-incompatibility, where the selection of the male parent (pollen xenia) significantly affects seed starch metabolism, as well as fruit yield and quality. Despite its importance, the molecular mechanisms underlying pollen xenia remains largely unknown. In this study, we utilized the 'Lan You' variety of C. mollissima to construct a high-quality reference genome. As a result, a first Telomere-to-telomere (T2T) gap-free genome for this species was successfully assembled. A total of 560 transcription factors and 22 structural genes were identified as consistent across the TO-GCNs, indicating a consistent regulation pattern in the co-expression of genes involved in starch accumulation. These networks were further divided into three sub-networks: T1, T2, and T3. Among these, the T1 and T2 sub-networks exhibited a higher number of structural genes with consistent regulation patterns and were closely associated with sugar biosynthesis. The gene SBE (Camol08G0254600) was identified as the hub gene with the highest degree of connectivity, encoding a key rate-limiting enzyme in the amylopectin biosynthesis pathway. This study provides a foundation for further research on C. mollissima population genetics, genetic improvement, and strategies aimed at enhancing yield and quality.

Chromosome-level Alstonia scholaris genome unveils evolutionary insights into biosynthesis of monoterpenoid indole alkaloids

Alstonia scholaris of the Apocynaceae family is a medicinal plant with a rich source of bioactive monoterpenoid indole alkaloids (MIAs), which possess anti-cancer activity like vinca alkaloids. To gain genomic insights into MIA biosynthesis, we assembled a high-quality chromosome-level genome for A. scholaris using nanopore and Hi-C data. The 444.95 Mb genome contained 35,488 protein-coding genes. A total of 20 chromosomes were assembled with a scaffold N50 of 21.75 Mb. The genome contained a cluster of strictosidine synthases and tryptophan decarboxylases with synteny to other species and a saccharide-terpene cluster involved in the monoterpenoid biosynthesis pathway of the MIA upstream pathway. The multi-omics data of A. scholaris provide a valuable resource for understanding the evolutionary origins of MIAs and for discovering biosynthetic pathways and synthetic biology efforts for producing pharmaceutically useful alkaloids.

Chromosome-scale genomes of commercial timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis)

Wood is the most important natural and endlessly renewable source of energy. Despite the ecological and economic importance of wood, many aspects of its formation have not yet been investigated. We performed chromosome-scale genome assemblies of three timber trees (Ochroma pyramidale, Mesua ferrea, and Tectona grandis) which exhibit different wood properties such as wood density, hardness, growth rate, and fiber cell wall thickness. The combination of 10X, stLFR, Hi-Fi sequencing and HiC data led us to assemble high-quality genomes evident by scaffold N50 length of 55.97 Mb (O. pyramidale), 22.37 Mb (M. ferrea) and 14.55 Mb (T. grandis) with >97% BUSCO completeness of the assemblies. A total of 35774, 24027, and 44813 protein-coding genes were identified in M. ferrea, T. grandis and O. pyramidale, respectively. The data generated in this study is anticipated to serve as a valuable genetic resource and will promote comparative genomic analyses, and it is of practical importance in gaining a further understanding of the wood properties in non-model woody species.

Integration of Volatilomics and Metabolomics Unveils Key Flavor-Related Biological Pathways in Different Carambola Cultivars

Carambola is a tropical fruit that is highly sought after by consumers due to its unique flavor, star shape, and nutritional value. Enhancing the flavor quality of this fruit can increase the consumer acceptance and market demand. However, flavor is an intrinsic characteristic of fruits. Its decoding requires in-depth knowledge based on recognizing key biological pathways relevant to flavor formation and development. In this study, the volatile and non-volatile metabolites contributing to the flavor variation of five carambola cultivars were investigated by a novel strategy combining GC-MS/O-based volatilomics with LC-MS-based metabolomics. Several significant flavor-related pathways, involving biosynthesis or metabolism of amino acids, terpenoids, fatty acids, sugar and organic acid, and flavonoids were identified based on the enrichment analysis of important volatile and non-volatile metabolites. The results indicated that there were metabolites in the flavor-related pathways being up- or downregulated, leading to the differences in flavor traits of different carambola cultivars. This study could provide a valuable reference for breeders and researchers of interest in the mechanisms underlying the regulation of flavor, which would ultimately lead to the creation of carambola cultivars with more attractive flavor profiles and pleasurable consuming experiences.

An optimized FACS-free single-nucleus RNA sequencing (snRNA-seq) method for plant science research

Recently, single-cell RNA sequencing (scRNA-seq) provides unprecedented power for accurately understanding gene expression regulatory mechanisms. However, scRNA-seq studies have limitations in plants, due to difficulty in protoplast isolation that requires enzymatic digestion of the cell walls from various plant tissues. Therefore, to overcome this problem, we developed a nuclei isolation approach that does not rely on Fluorescence Activated Cell Sorting (FACS). We validated the robustness of the FACS-free single-nucleus RNA sequencing (snRNA-seq) methodology in mature Arabidopsis plant tissue by comparing it to scRNA-seq results based on protoplasts extracted from the same batch of leaf materials. Sequencing results demonstrated the high quality of snRNA-seq data, as well as its utility in cell type classification and marker gene identification. This approach also showed several advantages, including the ability to use frozen samples, taking less suspension preparation time, and reducing biased cellular coverage and dissociation-induced transcriptional artifacts. Surprisingly, snRNA-seq detected two epidermal pavement cell clusters, while scRNA-seq only had one. Furthermore, we hypothesized that these two epidermal cells represent the top and lower epidermis based on differences in expression patterns of cluster-specific expressed genes. In summary, this study has advanced the application of snRNA-seq in Arabidopsis leaves and confirmed the advantages of snRNA-seq in plant research.

A draft genome of the medicinal plant Cremastra appendiculata (D. Don) provides insights into the colchicine biosynthetic pathway

Cremastra appendiculata (D. Don) Makino is a rare terrestrial orchid with a high market value as an ornamental and Chinese traditional medicinal herb with a wide range of pharmacological properties. The pseudobulbs of C. appendiculata are one of the primary sources of the famous traditional Chinese medicine "Shancigu", which has been clinically used for treating many diseases, especially, as the main component to treat gout. The lack of genetic research and genome data restricts the modern development and clinical use of C. appendiculata. Here, we report a 2.3 Gb chromosome-level genome of C. appendiculata. We identify a series of candidates of 35 candidate genes responsible for colchicine biosynthesis, among which O-methyltransferase (OMT) gene exhibits an important role in colchicine biosynthesis. Co-expression analysis reveal purple and green-yellow module have close relationships with pseudobulb parts and comprise most of the colchicine pathway genes. Overall, our genome data and the candidate genes reported here set the foundation to decipher the colchicine biosynthesis pathways in medicinal plants.

Nutrient-Mediated Perception and Signalling in Human Metabolism: A Perspective of Nutrigenomics

The interaction between selective nutrients and linked genes involving a specific organ reveals the genetic make-up of an individual in response to a particular nutrient. The interaction of genes with food opens opportunities for the addition of bioactive compounds for specific populations comprising identical genotypes. The slight difference in the genetic blueprints of humans is advantageous in determining the effect of nutrients and their metabolism in the body. The basic knowledge of emerging nutrigenomics and nutrigenetics can be applied to optimize health, prevention, and treatment of diseases. In addition, nutrient-mediated pathways detecting the cellular concentration of nutrients such as sugars, amino acids, lipids, and metabolites are integrated and coordinated at the organismal level via hormone signals. This review deals with the interaction of nutrients with various aspects of nutrigenetics and nutrigenomics along with pathways involved in nutrient sensing and regulation, which can provide a detailed understanding of this new leading edge in nutrition research and its potential application to dietetic practice.

Perspectives and recent progress of genome-wide association studies (GWAS) in fruits

BACKGROUND

Earlier next-generation sequencing technologies are being vastly used to explore, administer, and investigate the gene space with accurate profiling of nucleotide variations in the germplasm. OVERVIEW AND PROGRESS: Recently, novel advancements in high-throughput sequencing technologies allow a genotyping-by-sequencing approach that has opened up new horizons for extensive genotyping exploiting single-nucleotide-polymorphisms (SNPs). This method acts as a bridge to support and minimize a genotype to phenotype gap allowing genetic selection at the genome-wide level, named genomic selection that could facilitate the selection of traits also in the pomology sector. In addition to this, genome-wide genotyping is a prerequisite for genome-wide association studies that have been used successfully to discover the genes, which control polygenic traits including the genetic loci, associated with the trait of interest in fruit crops.

AIMS AND PROSPECTS

This review article emphasizes the role of genome-wide approaches to unlock and explore the genetic potential along with the detection of SNPs affecting the phenotype of fruit crops and highlights the prospects of genome-wide association studies in fruits.

The Effects of Star Fruit (Averrhoa carambola Linn.) Extract on Body Mass Index, Fasting Blood Glucose, and Triglyceride Levels in Male Rats with Obesity and Type 2 Diabetes Mellitus

BACKGROUND: Obesity is the main risk factor of diabetes by which induces insulin resistance. Epicatechin gallate can virtually interact with sodium-glucose co-transporter 2 as same as dapagliflozin and is found in green tea and star fruits. AIM: This study aimed to investigate the effects of methanol extract of star fruit (MES) on body weight (BW), body mass index (BMI), fasting blood glucose (FBG), and triglyceride levels in male rats with obesity and type 2 diabetes mellitus (T2DM). METHODS: Twenty-four male Sprague-Dawley rats were randomly assigned to normal and high-fat diet (HFD) groups. Obesity was induced with a HFD diet for 5 weeks and followed by induction of T2DM with 230 mg/kg BW nicotinamide and 65 mg/kg BW streptozotocin injections. Twenty-one obesity and T2DM rats were randomly assigned to negative control (n = 3) and the remaining rats in the MES1-3 groups, which were given 250, 500, and 1000 mg/kg BW/day MES. Data of BW, BMI, FBG, and triglyceride levels were collected at day 1, 14, and 28 interventions. Data were statistically analyzed using parametric and non-parametric tests with p < 0.05 considered significant. RESULTS: The MES3 group (282.56 ± 10.75 g) had significantly lower mean BW than the MES2 group (331.33 ± 13.17 g, p = 0.035). The duration of MES administration significantly decreased BW (p = 0.009) and BMI (p = 0.034) compared with the negative control. The mean triglyceride levels in MES1 (93.72 ± 53.69 mg/dl, p = 0.020), MES2 (71.98 ± 35.72 mg/dl, p = 0.025), and MES3 (56.68 ± 16.37 mg/dl, p = 0.020) groups significantly lower than the control group (1042.13 ± 681.74 mg/dl) on day 14. The mean FBG levels in MES1 (437.85 ± 33.04 mg/dl) and MES2 (353 ± 33.04 mg/dl) groups were also lower than the control group (470.97 ± 33.04 mg/dl). CONCLUSION: Administrations of 250, 500, and 1000 mg/kg BW/day MES decrease BW, BMI, and triglyceride level but increase FBG level in male rats with obesity and T2DM for 14 and 28 days.

The chromosome-scale genomes of Dipterocarpus turbinatus and Hopea hainanensis (Dipterocarpaceae) provide insights into fragrant oleoresin biosynthesis and hardwood formation

Dipterocarpaceae are typical tropical plants (dipterocarp forests) that are famous for their high economic value because of their production of fragrant oleoresins, top-quality timber and usage in traditional Chinese medicine. Currently, the lack of Dipterocarpaceae genomes has been a limiting factor to decipher the fragrant oleoresin biosynthesis and gain evolutionary insights into high-quality wood formation in Dipterocarpaceae. We generated chromosome-level genome assemblies for two representative Dipterocarpaceae species viz. Dipterocarpus turbinatus Gaertn. f. and Hopea hainanensis Merr. et Chun. Our whole-genome duplication (WGD) analysis revealed that Dipterocarpaceae underwent a shared WGD event, which showed significant impacts on increased copy numbers of genes related to the biosynthesis of terpene, BAHD acyltransferases, fatty acid and benzenoid/phenylpropanoid, which probably confer to the formation of their characteristic fragrant oleoresin. Additionally, compared with common soft wood plants, the expansion of gene families was also found to be associated with wood formation, such as in CESA (cellulose synthase), CSLE (cellulose synthase-like protein E), laccase and peroxidase in Dipterocarpaceae genomes, which might also contribute to the formation of harder, stronger and high-density timbers. Finally, an integrative analysis on a combination of genomic, transcriptomic and metabolic data from different tissues provided further insights into the molecular basis of fragrant oleoresins biosynthesis and high-quality wood formation of Dipterocarpaceae. Our study contributes the first two representative genomes for Dipterocarpaceae, which are valuable genetic resources for further researches on the fragrant oleoresins and superior-quality timber, genome-assisted breeding and improvement, and conservation biology of this family.

Genome-wide identification and expression profile of YABBY genes in Averrhoa carambola

Background

Members of the plant-specific YABBY gene family are thought to play an important role in the development of leaf, flower, and fruit. The YABBY genes have been characterized and regarded as vital contributors to fruit development in Arabidopsis thaliana and tomato, in contrast to that in the important tropical economic fruit star fruit (Averrhoa carambola), even though its genome is available.

Methods

In the present study, a total of eight YABBY family genes (named from AcYABBY1 to AcYABBY8) were identified from the genome of star fruit, and their phylogenetic relationships, functional domains and motif compositions, physicochemical properties, chromosome locations, gene structures, protomer elements, collinear analysis, selective pressure, and expression profiles were further analyzed.

Results

Eight AcYABBY genes (AcYABBYs) were clustered into five clades and were distributed on five chromosomes, and all of them had undergone negative selection. Tandem and fragment duplications rather than WGD contributed to YABBY gene number in the star fruit. Expression profiles of AcYABBYs from different organs and developmental stages of fleshy fruit indicated that AcYABBY4 may play a specific role in regulating fruit size. These results emphasize the need for further studies on the functions of AcYABBYs in fruit development.

The Clausena lansium (Wampee) genome reveal new insights into the carbazole alkaloids biosynthesis pathway

Clausena lansium (Lour.) Skeels (Rutaceae), recognized as wampee, is a widely distributed fruit tree which is utilized as a folk-medicine for treatment of several common diseases. However, the genomic information about this medicinally important species is still lacking. Therefore, we assembled the first genome of Clausena genus with a total length of 310.51 Mb and scaffold N50 of 2.24 Mb by using 10× Genomics technology. Further annotation revealed a total of 34,419 protein-coding genes, while repetitive elements covered 39.08% (121.36 Mb) of the genome. The Clausena and Citrus genus were found to diverge around 22 MYA, and also shared an ancient whole-genome triplication event with Vitis. Furthermore, multi-tissue transcriptomic analysis enabled the identification of genes involved in the synthesis of carbazole alkaloids. Altogether, these findings provided new insights into the genome evolution of Wampee species and highlighted the possible role of key genes involved in the carbazole alkaloids biosynthetic pathway.

Traditional Uses, Phytochemical Constituents and Pharmacological Properties of Averrhoa carambola L.: A Review

Averrhoa carambola L. (star fruit) is an edible fruit that is extensively cultivated in southern China, Southeast Asia, India, and northern South America. It has a sweet and juicy taste and is frequently used in fruit salads and fruit platters, as a garnish in cocktail drinks and beverages, or squeezed into juice and served as a beverage. Traditionally, it has been used for treating diabetes and diabetic nephropathy, arthralgia, vomiting, lithangiuria, coughing, hangovers, and chronic paroxysmal headache for thousands of years. Currently, approximately 132 compounds have been isolated from A. carambola. Among them, flavonoids, benzoquinone, and their glycosides have been considered as biologically active substances, which are responsible for various biological activities. Pharmacological studies have revealed that crude extracts or monomeric compounds from A. carambola exhibit multiple bioactivities, such as anti-oxidant, anti-hyperglycemic, anti-obesity, anti-hyperlipidemic, anti-tumor, anti-inflammatory, hepatoprotective, cardioprotective, anti-hypertensive, neuroprotective, and others. Thus, A. carambola is a valuable treatment in Chinese medicine with therapeutic potential for multiple diseases, especially diabetes and diabetes-related diseases. Even though it is a very promising candidate in the development of functional food and the pharmaceutical industry, reports on its bioactivities have only been conducted in vivo and in vitro and there is a gap in research regarding clinical settings and safety. This review therefore provides a comprehensive and systematic overview of current progress on botany, ethnopharmacology, phytochemistry, pharmacology, and toxicity of A. carambola, providing a valuable reference for further developments and applications of A. carambola in the pharmaceutical industry and functional food.

Chromosome-scale genome assembly provides insights into the evolution and flavor synthesis of passion fruit (Passiflora edulis Sims)

Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7 Mb chromosome-scale genome assembly of passion fruit, with 98.91% (~1327.18 Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that 'alpha-linolenic acid metabolism', 'metabolic pathways', and 'secondary metabolic pathways' were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.

Review on the Development and Applications of Medicinal Plant Genomes

With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.