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Background  Platostoma palustre (Blume) A. J. Paton is a medicinal and edible plant in China, and polysaccharide is its main functional component, composed of various monosaccharides. This study aims to investigate the biosynthesis and regulatory mechanisms of polysaccharides in P. palustre . Results The results showed that increased red light intensity promoted the growth of P. palustre , and an increase in light intensity to a certain degree increased the concentrations of monosaccharides. Transcriptome sequencing showed that a total of 55 differentially expressed genes (DEGs) encoding enzymes involved in polysaccharide biosynthesis were identified as key functional genes. The pathways for polysaccharide biosynthesis in P. palustre were also reconstructed. Weighted gene coexpression network analysis (WGCNA) revealed 4 modules significantly correlated with 9 monosaccharides. Based on the high connectivities and expression levels, a total of 17 hub TFs, belonging to the B3_superfamily , AP2/ERF , bHLH , WRKY , and MYB families, were considered key regulatory genes. Additionally, protein interaction network analysis revealed that there were interactions between transcript_43348 ( B3_superfamily ) and transcript_20138 ( Sucrose synthase ,  SuSy ), between transcript_1530 ( B3_superfamily ) and transcript_35035 ( bHLH ), between transcript_1530 ( B3_superfamily ) and transcript_41067 ( Sucrose non-fermenting-1-related protein kinase 2 ,  SnRK2 ), and between transcript_52483 ( AP2/ERF ) and transcript_23314 ( ARR-B ). Conclusions This study laid the foundation for elucidating the biosynthesis and regulatory mechanisms of polysaccharides in P. palustre .

Background Fruit crops, including tropical and subtropical fruits like Avocado ( Persea americana ), Fig ( Ficus carica ), Date Palm ( Phoenix dactylifera ), Mango ( Mangifera indica ), Guava ( Psidium guajava ), Papaya ( Carica papaya ), Pineapple ( Ananas comosus ), and Banana ( Musa acuminata ) are economically vital, contributing significantly to global agricultural output, as classified by the FAO’s World Programme for the Census of Agriculture. Advancements in next-generation sequencing, have transformed fruit crop breeding by providing in-depth genomic and transcriptomic data. RNA sequencing enables high-throughput analysis of gene expression, and functional genomics, crucial for addressing horticultural challenges and enhancing fruit production. The genomic and expression data for key tropical and sub-tropical fruit crops is currently lacking a comprehensive expression atlas, revealing a significant gap in resources for horticulturists who require a unified platform with diverse datasets across various conditions and cultivars. Results The Fruit Expression Atlas (FEAtl), available at http://backlin.cabgrid.res.in/FEAtl/ , is a first-ever extensive and unified expression atlas for tropical and subtropical fruit crops developed using 3-tier architecture. The expressivity of coding and non-coding genes, encompassing 2,060 RNA-Seq samples across 91 tissue types and 177 BioProjects, it provides a comprehensive view of gene expression patterns for different tissues under various conditions. FEAtl features multiple tabs that cater to different aspects of the dataset, namely, Home , About , Analyze , Statistics , and Team and contains seven central functional modules: Transcript Information , Sample Information , Expression Profiles in FPKM and TPM , Functional Analysis , Genes Based on Tau Score , and Search for Specific Gene . The expression of a transcript of interest can be easily queried by searching by tissue ID and transcript type. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes. Conclusions This atlas represents a groundbreaking compilation of a wide array of information pertaining to eight distinct fruit crops and serves as a fundamental resource for comparative analysis among different fruit species and is a catalyst for functional genomic studies. Database availability: http://backlin.cabgrid.res.in/FEAtl/ .

Selenium is a beneficial element in agriculture, particularly for its potential to improve plant growth and stress tolerance at suitable concentrations. In this study, Phaseolus vulgaris was foliar-sprayed with selenium selenate (Se) or selenium nanoparticles (SeNP) at different concentrations during the vegetative stage; afterward, the seed yield was analyzed for metabolomics using 1 H, J -resolved and HSQC NMR data, and NMR databases. A total of 47 metabolites were identified with sugars being the major chemical class. In the control sample, the most abundant sugar was stachyose (14.6 ± 0.8 mM). Among the identified alkaloids, the concentration of trigonelline was the highest (0.6 ± 0.08 mM). Chemometric and cluster analyses distinctly differentiated the control from the Se and SeNP-treated samples. Treatments with SeNP resulted in elevated concentrations of sugars, carboxylic acids, and sulfur-containing amino acids compared to control and Se treated samples. Conversely, betaine levels were higher in Se samples. The presence of Se and SeNP significantly decreased the levels of several aliphatic amino acids, e.g. alanine. The addition of 50 µM SeNP upregulated the levels of trigonelline and syringate by 2-fold and 1.75-fold, respectively, relative to the control. Pathway analysis indicated the most significantly altered pathways due to SeNP addition were arginine biosynthesis and nitrogen metabolism. The pathways influenced by Se addition were glyoxylate and dicarboxylate metabolism as well as glycine-serine and threonine metabolism. This study proved that SeNP are more efficient than Se in enhancing the metabolic profile of Phaseolus vulgaris which will have implications for agricultural practices, focusing on the sustainability and nutritional enhancement of crops.

Background Arctium lappa L. is a medicinal edible homologous plant, commonly known as burdock or bardana, which belongs to the Asteraceae family and is abundant all over the world. Genetic diversity assessment is essential for A. lappa germplasm resource conservation and breeding. The assessment techniques include morphological, biochemical, and DNA marker analysis. However, the limited number of available DNA markers is insufficient to conduct related genetic diversity assessment studies. Results In this study, we conducted RNA sequencing of the A. lappa cultivar 'Yanagikawa Ideal' and developed SSR markers to characterize the genetic diversity and population structure of 56 A. lappa accessions and 8 wild relative accessions. A total of 4,851 simple sequence repeats (SSRs) loci were identified. The proportions of mono-, di- and tri-nucleotide repeat motifs were 30.40%, 21.50% and 33.10%, respectively. We developed and verified the reliability of 28 SSR core primer pairs through electronic polymerase chain reaction (ePCR) and the PCR amplification process. The polymorphism information content (PIC) values of the 28 SSR core primer pairs ranged from 0.246 to 0.848, with 14 pairs of SSR primers displaying high polymorphism (PIC > 0.5). The 28 SSR core primer pairs showed 100% mobility in Arctium tomentosum Miller and 96.43% mobility in Synurus deltoides (Aiton) Nakai, indicating their high versatility. The average Shannon information index (I) was 1.231, and the average observed heterozygosity (Ho) was 0.132, the average expected heterozygosity (He) was 0.564. The 64 accessions were divided into three clusters at a genetic distance of 0.558. AMOVA analysis shows 83% genetic variation within populations and 17% among populations, highlighting implications for conservation and breeding strategies. Conclusion Our study provides 28 newly high-quality SSR markers to enhance genetic resource conservation and breeding programs for A. lappa , as well as to support comparative genomics and cross-species breeding strategies for related species.

Background Low-coverage whole-genome sequencing (lcWGS) presents a cost-effective solution for genotyping, particularly in applications requiring high marker density and reduced costs. In this study, we evaluated lcWGS for eggplant genotyping using eight founder accessions from the first eggplant MAGIC population (MEGGIC). We tested various sequencing coverages and minimum depth of coverage thresholds with two SNP callers, Freebayes and GATK. Reference SNP panels were used to estimate the percentage of common biallelic SNPs (i.e., true positives) relative to the low coverage datasets (accuracy) and the SNP panels themselves (sensitivity). Furthermore, the percentage of true positives with the same genotype across both datasets was calculated to assess genotypic concordance. Results Sequencing coverages as low as 1X and 2X achieved high accuracy but lacked sufficient sensitivity and genotypic concordance. However, 3X sequencing reached approximately 10% less sensitivity than 5X while maintaining genotypic concordance above 90% at any depth of coverage threshold. Freebayes outperformed GATK in terms of sensitivity and genotypic concordance. Therefore, we used this software to conduct a pilot test with some MEGGIC lines from the fifth generation of selfing, comparing their datasets with a gold standard. Sequencing coverages as low as 1X identified a substantial number of true positives, with 3X significantly increasing the yield, particularly at moderate depth of coverage thresholds. Additionally, at least 30% of the true positives were consistently genotyped in all lines when using coverages greater than 2X, regardless of the depth of coverage threshold applied. Conclusions This study highlights the importance of using a gold standard to reduce false positives and demonstrates that lcWGS, with proper filtering, is a valuable alternative to high-coverage sequencing for eggplant genotyping, with potential applications to other crops.

Background Yam is a globally significant crop with both culinary and medicinal value. Anthocyanin, an important secondary metabolite, plays a key role in determining the nutritional quality of yams. However, the research on the light-induced anthocyanins accumulation in yams remains limited. In this study, we revealed light-induced anthocyanin biosynthesis and identified transcription factors associated with anthocyanin-related pathways in yam. These findings enhance our understanding of the molecular mechanisms underlying light-mediated anthocyanin regulation in yams. Results Significant variations in color were observed in the stems, leaves, and tuber roots of the two yam varieties ‘Xuwen’ and ‘Luhe’. Under light conditions, the total anthocyanin content in ‘Xuwen’ tuber roots was significantly higher than that under dark conditions. The targeted metabolomics analysis of anthocyanins identified that procyanidin and cyanidin glycosides, such as cyanidin-3-O-(sinapoyl)sophoroside, cyanidin-3-O-sophoroside, procyanidin B1, procyanidin B3, and quercetin-3-O-glucoside, were the primary anthocyanin components. These compounds were responsible for the observed differences in anthocyanin content between the two varieties and were significantly influenced by light conditions. The non-targeted metabolomics analysis further revealed that light also induce the biosynthesis of flavonoids. Transcriptome analysis showed significant differences in the expression levels of MYB, ERF, and WRKY transcription factors (TFs) between the two yam varieties, with these expressions being strongly influenced by light conditions. The association analysis of the anthocyanin metabolome, candidate TFs, and structural genes involved in anthocyanin biosynthesis revealed significant correlations. Specifically, MYB ( Dioal.09G044700 and Dioal.12G068700 ) and WRKY ( Dioal.20G040900 and Dioal.12G062900 ) showed strong correlations with procyanidins, anthocyanins, and the structural genes associated with anthocyanin biosynthesis. RT-qPCR confirmed that the expression patterns of these four TFs, strongly induced by light, were consistent with the expression of structural genes involved in anthocyanin biosynthesis. Conclusions The results of this study provide useful insights into the regulation of light on anthocyanin accumulation in yam, and will be helpful for yam breeding and cultivation practices.

Background Common bean ( Phaseolus vulgaris L.) is a thermophilic crop, and exposure to cold stress can significantly impact their yield and quality. To elucidate the impact of cold stress on cold-tolerant ‘Wei Yuan’ (WY) and cold-sensitive ‘Bai Bu Lao’ (BBL) of common bean, the mechanism of cold tolerance was studied by physiological and biochemical and multi-omics analysis. Results In this study, lower relative conductivity and higher malondialdehyde content after cold stress endowed ‘WY’ seedlings with cold tolerance. A total of 11,837 differentially expressed genes (DEGs) and 923 differential metabolites (DEMs) were identified by transcriptome and metabolomics analysis. Joint analysis showed that under cold stress, DEGs and DEMs in common beans are extensively engaged in sugar, amino acid and isoflavonoid biosynthesis, flavone and flavonol biosynthesis, and plant hormone signal translation, especially related to isoflavone biosynthesis. In addition, it was also found that bHLH and MYB family transcription factors may be involved in the cold signal transduction of common bean. Conclusions The above results will provide a theoretical basis for the cold tolerance mechanism of common beans and provide help for the screening of cold-tolerant resources of common beans. Clinical trial number Not applicable.

Background Red raspberry ( Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast genome (plastome) have been reported, while there is a lack of genetic information on its mitogenome. We sequenced and assembled the complete mitogenome of R. idaeus , and conducted a series of genetic investigations comparing it with the nuclear and chloroplast genomes, so as to better gain a comprehensive understanding of the species’ genetic background. Results The mitogenome is represented by one circular chromosome of 438,947 bp. Twenty-four core genes, nine variable genes, 26 tRNAs, and three rRNAs were annotated. A total of 52 SSRs and 38 tandem repeat sequences were identified. 533 pairs of dispersed repeats were detected, among which three pairs were found to have mediated the homologous recombination, resulting in one major conformation and seven minor conformations. Furthermore, 52 homologous sequences between the mitogenome and plastome were identified, including six complete protein-coding genes and 12 tRNA genes. We also detected 828 homologous fragments between the nuclear genome and mitogenome, including one trn M-CAU gene. Conclusions In this study, we presented the mitogenome of R. idaeus for the first time based on data obtained from Illumina and Oxford Nanopore sequencing platforms. Key characteristics of the mitogenome were examined, including its gene composition, repetitive elements, and homologous DNA fragments. Additionally, we identified multiple recombination events in the mitogenome mediated by repetitive sequences The high-quality and well-annotated mitogenome for the known fruit red raspberry will provide essential genetic information for species classification, evolution analysis, and even genetic improvement in Rubus in the future.

Gloriosa L. possesses exceptional ornamental value, with its floral hues exhibiting a wide range of variations. In this study, we employed sophisticated colorimetry, Ultra Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS), and transcriptome sequencing to investigate the phenotypic expression of tepal colors, the composition of carotenoids and anthocyanins, and the differential gene expression in four Gloriosa varieties during their full bloom phase. Our findings revealed that the redness of the tepals, indicated by higher a * values, increased with the intensity of the red hue, while lighter colors corresponded to higher L * values. Metabolomic analysis identified 50 carotenoids and 60 anthocyanins. It was observed that carotenoids primarily influence the yellow and orange color of Gloriosa tepals, with β -carotene, lutein, and zeaxanthin being the predominant carotenoids. Anthocyanins serve as the principal coloring agents in the orange, red and purple tepals of Gloriosa . High levels and proportions of cyanidins and pelargonidins are key contributors to the formation of red and purple tepals, while high levels and proportions of peonidins also play a significant role in purple coloration. In contrast, the presence of high levels and proportions of pelargonidins alone is a crucial factor in the formation of orange tepals. Transcriptomic data unearthed 57 and 92 candidate differentially expressed genes (DEGs) belong to carotenoid and anthocyanin biosynthesis pathway, respectively, with PSY , PDS , DFR , and ANS genes considered as critical genes for the differential accumulation of pigments of Gloriosa tepals. Weighted gene co-expression network analysis (WGCNA) revealed significant co-expression patterns between 217 transcription regulatory factors (TFs) and 8 carotenoid biosynthesis genes, and between 194 TFs and 41 anthocyanin biosynthesis genes. qRT-PCR verified the expression patterns of four carotenoid biosynthesis-related genes, eight anthocyanin biosynthesis-related genes, and three transcription regulatory factors. It was found that Cluster-121969.6 ( MYB ) gene is specifically expressed in the tepals of the four varieties (compared to stems and leaves) and shows a high consistency with the trend of anthocyanin content changes. This research provides new insights into the mechanisms underlying the formation of diverse floral colors in Gloriosa tepals.

Background Anthocyanins are a group of polyphenolic pigments that play essential biological roles and significantly influence the quality of agricultural produce. Bioinformatics approaches were employed to predict and identify potential genes involved in the sequestration of anthocyanins in Zicaitai ( Brassica rapa var. purpuraria ) utilizing data from the transcriptome database. Results In this study 0-hour light (dark) and 8-hour light treatments of Zicaitai were examined using transcriptome analysis. RNA-seq analysis indicates that 24 important anthocyanin biosynthesis genes, including 5 PAL , 3 4CL , 3 CHS , 3 CHI , 2 F3H , 1 DFR , 2 ANS , and 5 UGFT were significantly differentially expressed between 0-hour and 8-hour light treatment. The transcript levels of the glutathione S-transferase gene, BrGSTF12 , were significantly higher at 8 h compared to 0 h. BrGSTF12 expression level correlated with the patterns of anthocyanins content in each tissue of Zicaitai. Functional complementation in the Arabidopsis tt19 mutant further demonstrated that BrGSTF12 was involved in the transport of anthocyanins. Additionally, expression analysis showed that BrMYB114 levels were significantly elevated at 8 h, and dual-luciferase assays confirmed that BrMYB114 effectively trans-activated the promoter of the BrGSTF12 gene. Conclusion This study provides molecular evidence supporting the regulatory roles of BrGSTF12 and BrMYB114 in enhancing anthocyanin accumulation in Zicaitai under light induction. The findings contribute to a deeper understanding of the mechanisms behind anthocyanin biosynthesis and transport, offering valuable insights that could aid in breeding anthocyanin-rich crops, and paving the way for new opportunities in crop development.