A draft genome, resequencing, and metabolomes reveal the genetic background and molecular basis of the nutritional and medicinal properties of loquat (Eriobotrya japonica (Thunb.) Lindl)

Chromosome-scale genome, together with transcriptome and metabolome, provides insights into the evolution and anthocyanin biosynthesis of Rubus rosaefolius Sm. (Rosaceae)

Rubus rosaefolius is a kind of red raspberry possessing high nutritional and pharmaceutical value. Here we present a chromosome-level draft genome of R. rosaefolius. Of the total 131 assembled scaffolds, 70 with a total size of 219.02 Mb, accounting for 99.33% of the estimated genome size, were anchored to seven pseudochromosomes. We traced a whole-genome duplication (WGD) event shared among members of the Rosaceae family, from which were derived 5090 currently detectable duplicated gene pairs (dgps). Of the WGD-dgps 75.09% underwent purifying selection, and approximately three-quarters of informative WGD-dgps expressed their two paralogs with significant differences. We detected a wide variety of anthocyanins in the berries of R. rosaefolius, and their total concentration remained relatively stable during berry development but increased rapidly during the ripening stage, mainly because of the contributions of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6″-O-malonyl)glucoside. We identified many structural genes that encode enzymes, such as RrDFR, RrF3H, RrANS, and RrBZ1, and play key roles in anthocyanin biosynthesis. The expression of some of these genes significantly increased or decreased with the accumulation of pelargonidin-3-O-glucoside and pelargonidin-3-O-(6″-O-malonyl)glucoside. We also identified some transcription factors and specific methylase-encoding genes that may play a role in regulating anthocyanin biosynthesis by targeting structural genes. In conclusion, our findings provide deeper insights into the genomic evolution and molecular mechanisms underlying anthocyanin biosynthesis in berries of R. rosaefolius. This knowledge may significantly contribute to the targeted domestication and breeding of Rubus species.

Transcriptome and biochemical analyses reveal phenolic compounds-mediated flavor differences in loquat (Eriobotrya japonica Lindl.) cultivars Chunhua No.1 and Dawuxing

The novel loquat cultivar 'Chunhua No.1' (CH1) is a promising commercial cultivar. However, CH1 has texture characteristics different from those of common loquat, and its formation mechanism remains unclear. Here, we first identified the phenolic compounds of CH1 and its parent ('Dawuxing', DWX) and the effect on texture formation. The special presence of stone cells explained the flavor differences in CH1. Chlorogenic acid, neochlorogenic acid, and coniferyl alcohol were the main phenolic compounds in loquat, and the high content of coniferyl alcohol was a potential factor for the rough texture of CH1. Transcriptome reveals that phenylpropanoid metabolism was activated during CH1 fruit texture formation. Kyoto Encyclopedia of Genes and Genomes (KEGG) identified 51 structural genes involved in phenylpropanoid biosynthesis, and Weighted Gene Co-expression Network Analysis (WGCNA) identified four structural genes and 88 transcription factors. These findings provide new insights into the phenolic metabolism and flavor formation of loquat fruit.

DataColor: unveiling biological data relationships through distinctive color mapping

In the era of rapid advancements in high-throughput omics technologies, the visualization of diverse data types with varying orders of magnitude presents a pressing challenge. To bridge this gap, we introduce DataColor, an all-encompassing software solution meticulously crafted to address this challenge. Our aim is to empower users with the ability to handle a wide array of data types through an assortment of tools, while simultaneously streamlining parameter selection for rapid insights and detailed enhancements. DataColor stands as a robust toolkit, encompassing 23 distinct tools coupled with over 600 parameters. The defining characteristic of this toolkit is its adept utilization of the color spectrum, allowing for the representation of data spanning diverse types and magnitudes. Through the integration of advanced algorithms encompassing data clustering, normalization, squarified layouts, and customizable parameters, DataColor unveils an abundance of insights that lay hidden within the intricate relationships embedded in the data. Whether you find yourself navigating the analysis of expansive datasets or embarking on the quest to visualize intricate patterns, DataColor stands as the comprehensive and potent solution. We extend the availability of DataColor to all users at no cost, accessible through the following link: https://github.com/frankgenome/DataColor.

Genome-Wide Identification and Expression Analysis of the SBP-Box Gene Family in Loquat Fruit Development

The loquat (Eriobotrya japonica L.) is a special evergreen tree, and its fruit is of high medical and health value as well as having stable market demand around the world. In recent years, research on the accumulation of nutrients in loquat fruit, such as carotenoids, flavonoids, and terpenoids, has become a hotspot. The SBP-box gene family encodes transcription factors involved in plant growth and development. However, there has been no report on the SBP-box gene family in the loquat genome and their functions in carotenoid biosynthesis and fruit ripening. In this study, we identified 28 EjSBP genes in the loquat genome, which were unevenly distributed on 12 chromosomes. We also systematically investigated the phylogenetic relationship, collinearity, gene structure, conserved motifs, and cis-elements of EjSBP proteins. Most EjSBP genes showed high expression in the root, stem, leaf, and inflorescence, while only five EjSBP genes were highly expressed in the fruit. Gene expression analysis revealed eight differentially expressed EjSBP genes between yellow- and white-fleshed fruits, suggesting that the EjSBP genes play important roles in loquat fruit development at the breaker stage. Notably, EjSBP01 and EjSBP19 exhibited completely opposite expression patterns between white- and yellow-fleshed fruits during fruit development, and showed a close relationship with SlCnr involved in carotenoid biosynthesis and fruit ripening, indicating that these two genes may participate in the synthesis and accumulation of carotenoids in loquat fruit. In summary, this study provides comprehensive information about the SBP-box gene family in the loquat, and identified two EjSBP genes as candidates involved in carotenoid synthesis and accumulation during loquat fruit development.

A telomere-to-telomere reference genome provides genetic insight into the pentacyclic triterpenoid biosynthesis in Chaenomeles speciosa

Chaenomeles speciosa (2n = 34), a medicinal and edible plant in the Rosaceae, is commonly used in traditional Chinese medicine. To date, the lack of genomic sequence and genetic studies has impeded efforts to improve its medicinal value. Herein, we report the use of an integrative approach involving PacBio HiFi (third-generation) sequencing and Hi-C scaffolding to assemble a high-quality telomere-to-telomere genome of C. speciosa. The genome comprised 650.4 Mb with a contig N50 of 35.5 Mb. Of these, 632.3 Mb were anchored to 17 pseudo-chromosomes, in which 12, 4, and 1 pseudo-chromosomes were represented by a single contig, two contigs, and four contigs, respectively. Eleven pseudo-chromosomes had telomere repeats at both ends, and four had telomere repeats at a single end. Repetitive sequences accounted for 49.5% of the genome, while a total of 45 515 protein-coding genes have been annotated. The genome size of C. speciosa was relatively similar to that of Malus domestica. Expanded or contracted gene families were identified and investigated for their association with different plant metabolisms or biological processes. In particular, functional annotation characterized gene families that were associated with the biosynthetic pathway of oleanolic and ursolic acids, two abundant pentacyclic triterpenoids in the fruits of C. speciosa. Taken together, this telomere-to-telomere and chromosome-level genome of C. speciosa not only provides a valuable resource to enhance understanding of the biosynthesis of medicinal compounds in tissues, but also promotes understanding of the evolution of the Rosaceae.

Whole-Genome Resequencing Reveals the Diversity of Patchouli Germplasm

As an important medicinal and aromatic plant, patchouli is distributed throughout most of Asia. However, current research on patchouli's genetic diversity is limited and lacks genome-wide studies. Here, we have collected seven representative patchouli accessions from different localities and performed whole-genome resequencing on them. In total, 402,650 single nucleotide polymorphisms (SNPs) and 153,233 insertions/deletions (INDELs) were detected. Based on these abundant genetic variants, patchouli accessions were primarily classified into the Chinese group and the Southeast Asian group. However, the accession SP (Shipai) collected from China formed a distinct subgroup within the Southeast Asian group. As SP has been used as a genuine herb in traditional Chinese medicine, its unique molecular markers have been subsequently screened and verified. For 26,144 specific SNPs and 16,289 specific INDELs in SP, 10 of them were validated using Polymerase Chain Reaction (PCR) following three different approaches. Further, we analyzed the effects of total genetic variants on genes involved in the sesquiterpene synthesis pathway, which produce the primary phytochemical compounds found in patchouli. Eight genes were ultimately investigated and a gene encoding nerolidol synthetase (PatNES) was chosen and confirmed through biochemical assay. In accession YN, genetic variants in PatNES led to a loss of synthetase activity. Our results provide valuable information for understanding the diversity of patchouli germplasm resources.

Insights into the nutritional properties and molecular basis of biosynthesis of amino acids and vitamins of Gastrodia elata offered by metabolomic and transcriptomic analysis

Gastrodia elata Blume (GE), a traditional and precious Chinese medicinal material, has been approved as a functional food. However, understanding GE's nutritional properties and its molecular basis remains limited. Here, metabolomic and transcriptomic analyses were performed on young and mature tubers of G. elata.f.elata (GEEy and GEEm) and G. elata.f.glauca (GEGy and GEGm). A total of 345 metabolites were detected, including 76 different amino acids and their derivatives containing all human essential amino acids (e.g., l-(+)-lysine, l-leucine), 13 vitamins (e.g., nicotinamide, thiamine), and 34 alkaloids (e.g., spermine, choline). GEGm has higher amino acid accumulation than GEEy, GEEm and GEGy, and vitamin contents were also slightly different in all four samples. Implying that GE, especially GEGm, is a kind of excellent complementary food as amino acid nutrition provider. From assembled 21,513 transcripts (genes) based on the transcriptome, we identified many genes that encode enzymes (e.g., pfkA, bglX, tyrAa, lysA, his B, aroA), which are responsible for the biosynthesis of amino acids and enzymes (e.g., nadA, URH1, NAPRT1, punA, rsgA) that related to vitamins metabolism. A total of 16 pairs of the differentially expressed genes (DEG) and differentially accumulated metabolites (DAM) (e.g., gene-tia006709 coding GAPDH and l-(+)-arginine, and gene-tia010180 coding tyrA and l-(+)-arginine) and three DEG-DAM pairs (e.g., gene-tia015379 coding NadA and nicotinate d-ribonucleoside) show significant similar positive or negative correlation based on three, and two comparisons of GEEy vs. GEGy, GEGy vs. GEGm, GEEy vs. GEGy and GEEm vs. GEGm, which involved into amino acid biosynthesis, and nicotinate nicotinamide metabolism, respectively. These results prove that the enzyme coded by these DEG promotes (positive correlation) or inhibits (negative correlation) the biosynthesis of parallel DAM in GE. Overall, the data and corresponding analysis in this study provide new insights into the nutritional properties of GE and the related molecular basis.

Antimicrobial and Antioxidant Properties of Theobroma cacao, Bourreria huanita, Eriobotrya japonica, and Elettaria cardamomum - Traditional Plants Used in Central America

The search for alternative naturally occurring antimicrobial agents will always continue, especially when emerging diseases like COVID-19 provide an urgency to identify and develop safe and effective ways to prevent or treat these infections. The purpose of this study was to evaluate the potential antimicrobial activity as well as antioxidant properties of commercial samples from four traditional medicinal plants used in Central America: Theobroma cacao, Bourreria huanita, Eriobotrya japonica, and Elettaria cardamomum. Ethanolic extracts were prepared from commercial products derived from the seeds or flowers of these plants. Total phenolics and antioxidant activity were assessed using commercial kits. The cytotoxicity and antiviral activity against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) were evaluated using the XTT colorimetric assay and a SARS-CoV-2 delta pseudoviral model. The half-maximal cytotoxic concentration (CC50) and half-maximal effective concentration (EC50) were used to calculate the therapeutic index (TI). Additionally, the antibacterial activity against Escherichia coli and Staphylococcus epidermidis was tested using a spectrophotometric method. The extracts showed total phenolics in the range of 0.06 to 1.85 nM/μL catechin equivalents, with T. cacao bean extract showing the highest content. The antioxidant activity showed values between 0.02 and 0.44 mM Trolox equivalents. T. cacao bean extract showed the highest antioxidant activity. Most plant extracts showed zero to moderate selective antiviral activity; however, one T. cacao beans sample showed excellent antiviral activity against SARS-CoV-2 with a TI value of 30.3, and one sample of E. japonica showed selective antiviral activity with a TI value of 18.7. Significant inhibition of E. coli and S. epidermidis by an E. japonica ethanolic extract (p<0.001) was observed using a spectrophotometric method that monitors bacterial growth over time. Additionally, ethanolic extracts of E. cardamomum showed significant inhibition of S. epidermidis growth (p<0.001). The results warrant further investigation of the antimicrobial and antioxidant properties of these plant extracts.

Organic Acid Accumulation and Associated Dynamic Changes in Enzyme Activity and Gene Expression during Fruit Development and Ripening of Common Loquat and Its Interspecific Hybrid

Loquats have gained increasing attention from consumers and growers for their essential nutrients and unusual phenology, which could help plug a gap period at market in early spring. Fruit acid is a critical contributor to fruit quality. The dynamic changes in organic acid (OA) during fruit development and ripening of common loquat (Dawuxing, DWX) and its interspecific hybrid (Chunhua, CH) were compared, as well as the corresponding enzyme activity and gene expression. At harvest, titratable acid was significantly lower (p ≤ 0.01) in CH (0.11%) than in DWX loquats (0.35%). As the predominant OA compound, malic acid accounted for 77.55% and 48.59% of the total acid of DWX and CH loquats at harvest, followed by succinic acid and tartaric acid, respectively. PEPC and NAD-MDH are key enzymes that participate in malic acid metabolism in loquat. The OA differences in DWX loquat and its interspecific hybrid could be attributed to the coordinated regulation of multiple genes and enzymes associated with OA biosynthesis, degradation, and transport. The data obtained in this work will serve as a fundamental and important basis for future loquat breeding programs and even for improvements in loquat cultural practices.

Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat

Wild loquats (Eriobotrya japonica Lindl.) provide remarkable genetic resources for studying domestication and breeding improved varieties. Herein, we generate the first high-quality chromosome-level genome assembly of wild loquat, with 45 791 predicted protein-coding genes. Analysis of comparative genomics indicated that loquat shares a common ancestor with apple and pear, and a recent whole-genome duplication event occurred in loquat prior to its divergence. Genome resequencing showed that the loquat germplasms can be distinctly classified into wild and cultivated groups, and the commercial cultivars have experienced allelic admixture. Compared with cultivated loquats, the wild loquat genome showed very few selected genomic regions and had higher levels of genetic diversity. However, whole-genome scans of selective sweeps were mainly related to fruit quality, size, and flesh color during the domestication process. Large-scale transcriptome and metabolome analyses were further performed to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in wild and cultivated loquats at various fruit development stages. Unlike those in wild loquat, the key DEGs and DAMs involved in carbohydrate metabolism, plant hormone signal transduction, flavonoid biosynthesis, and carotenoid biosynthesis were significantly regulated in cultivated loquats during fruit development. These high-quality reference genome, resequencing, and large-scale transcriptome/metabolome data provide valuable resources for elucidating fruit domestication and molecular breeding in loquat.

Genome-wide analysis of the WOX gene family and the role of EjWUSa in regulating flowering in loquat (Eriobotrya japonica)

The WUSCHEL (WUS)-related homeobox (WOX) gene family plays a crucial role in stem cell maintenance, apical meristem formation, embryonic development, and various other developmental processes. However, the identification and function of WOX genes have not been reported in perennial loquat. In this study, 18 EjWOX genes were identified in the loquat genome. Chromosomal localization analysis showed that 18 EjWOX genes were located on 12 of 17 chromosomes. Gene structure analysis showed that all EjWOX genes contain introns, of which 11 EjWOX genes contain untranslated regions. There are 8 pairs of segmental duplication genes and 0 pairs of tandem duplication genes in the loquat WOX family, suggesting that segmental duplications might be the main reason for the expansion of the loquat WOX family. A WOX transcription factor gene named EjWUSa was isolated from loquat. The EjWUSa protein was localized in the nucleus. Protein interactions between EjWUSa with EjWUSa and EjSTM were verified. Compared with wild-type Arabidopsis thaliana, the 35S::EjWUSa transgenic Arabidopsis showed early flowering. Our study provides an important basis for further research on the function of EjWOX genes and facilitates the molecular breeding of loquat early-flowering varieties.

Genome-Wide Analysis of SAUR Gene Family Identifies a Candidate Associated with Fruit Size in Loquat (Eriobotrya japonica Lindl.)

Fruit size is an important fruit quality trait that influences the production and commodity values of loquats (Eriobotrya japonica Lindl.). The Small Auxin Upregulated RNA (SAUR) gene family has proven to play a vital role in the fruit development of many plant species. However, it has not been comprehensively studied in a genome-wide manner in loquats, and its role in regulating fruit size remains unknown. In this study, we identified 95 EjSAUR genes in the loquat genome. Tandem duplication and segmental duplication contributed to the expansion of this gene family in loquats. Phylogenetic analysis grouped the SAURs from Arabidopsis, rice, and loquat into nine clusters. By analyzing the transcriptome profiles in different tissues and at different fruit developmental stages and comparing two sister lines with contrasting fruit sizes, as well as by functional predictions, a candidate gene (EjSAUR22) highly expressed in expanding fruits was selected for further functional investigation. A combination of Indoleacetic acid (IAA) treatment and virus-induced gene silencing revealed that EjSAUR22 was not only responsive to auxin, but also played a role in regulating cell size and fruit expansion. The findings from our study provide a solid foundation for understanding the molecular mechanisms controlling fruit size in loquats, and also provide potential targets for manipulation of fruit size to accelerate loquat breeding.

Total Sesquiterpenoids of Loquat Leaves Alleviated High-Fat Diet-Induced Obesity by Targeting Fecal Metabolic Profiling and Gut Microbiota Composition

In the present study, we demonstrated that whether the gut microbiota and related metabolites contribute to the therapeutic effect of total sesquiterpenoids (TSs) from loquat leaves on obesity. A 4-week high fat diet was used to induce obesity which was then treated with TSs for another 4 weeks. TSs remarkedly reduced the weight of body and white adipose and the levels of total cholesterol (TC) and triglyceride (TG) in serum. We also found that TSs restored the diversity and richness of gut microbiota. In addition, TSs administration affected the relative abundance of seven key genera. Meanwhile, TSs were determined to affect the metabolism of the host through detecting the metabolites in feces. By applying KEGG and the correlation analysis with gut microbiota, 10 differential metabolites were identified to be the key. The results in this work proved that TSs inhibited obesity by remodeling gut microbiota and related metabolites.

Applications of Genomic Tools in Plant Breeding: Crop Biofortification

Crop breeding has mainly been focused on increasing productivity, either directly or by decreasing the losses caused by biotic and abiotic stresses (that is, incorporating resistance to diseases and enhancing tolerance to adverse conditions, respectively). Quite the opposite, little attention has been paid to improve the nutritional value of crops. It has not been until recently that crop biofortification has become an objective within breeding programs, through either conventional methods or genetic engineering. There are many steps along this long path, from the initial evaluation of germplasm for the content of nutrients and health-promoting compounds to the development of biofortified varieties, with the available and future genomic tools assisting scientists and breeders in reaching their objectives as well as speeding up the process. This review offers a compendium of the genomic technologies used to explore and create biodiversity, to associate the traits of interest to the genome, and to transfer the genomic regions responsible for the desirable characteristics into potential new varieties. Finally, a glimpse of future perspectives and challenges in this emerging area is offered by taking the present scenario and the slow progress of the regulatory framework as the starting point.

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.