Differential color development and response to light deprivation of fig (Ficus carica L.) syconia peel and female flower tissues: transcriptome elucidation

Independent flavonoid and anthocyanin biosynthesis in the flesh of a red-fleshed table grape revealed by metabolome and transcriptome co-analysis

BACKGROUND

Red flesh is a desired fruit trait, but the regulation of red flesh formation in grape is not well understood. 'Mio Red' is a seedless table grape variety with light-red flesh and blue-purple skin. The skin color develops at veraison whereas the flesh color develops at a later stage of berry development. The flesh and skin flavonoid metabolomes and transcriptomes were analyzed.

RESULTS

A total of 161 flavonoids were identified, including 16 anthocyanins. A total of 66 flavonoids were found at significantly different levels in the flesh and skin (fold change ≥ 2 or ≤ 0.5, variable importance in projection (VIP) ≥ 1). The main anthocyanins in the flesh were pelargonidin and peonidin, and in the skin were peonidin, delphinidin, and petunidin. Transcriptome comparison revealed 57 differentially expressed structural genes of the flavonoid-metabolism pathway (log₂fold change ≥ 1, FDR < 0.05, FPKM ≥ 1). Two differentially expressed anthocyanin synthase (ANS) genes were annotated, ANS2 (Vitvi02g00435) with high expression in flesh and ANS1 (Vitvi11g00565) in skin, respectively. One dihydro flavonol 4-reductase (DFR, Vitvi18g00988) gene was differentially expressed although high in both skin and flesh. Screened and correlation analysis of 12 ERF, 9 MYB and 3 bHLH genes. The Y1H and dual luciferase assays showed that MYBA1 highly activates the ANS2 promoter in flesh and that ERFCBF6 was an inhibitory, EFR23 and bHLH93 may activate the DFR gene. These genes may be involved in the regulation of berry flesh color.

CONCLUSIONS

Our study revealed that anthocyanin biosynthesis in grape flesh is independent of that in the skin. Differentially expressed ANS, MYB and ERF transcription factors provide new clues for the future breeding of table grapes that will provide the health benefits as red wine.

First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq

Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F₁ mapping populations, whose female parents were a genotype of a so called 'ponpon' and of a 'double flower' varieties, while the common male parental ('Cipro') was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F₁ population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.

Integrated Physiological, Transcriptomic, and Metabolomic Analyses of the Response of Peach to Nitrogen Levels during Different Growth Stages

This study performed physiological, transcriptome, and metabolite analyses of peach fruit under different nitrogen (N) conditions at different growth stages. Nitrogen management directly affected the yield, fruit quality, and metabolites of peach in different growth stages. Different fertilizing time influenced yield and leaf N concentration. RNA-Seq was used to analyze the influence of N levels at the fruit pit hardening (PH) and fruit expansion (FE) stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed differentially expressed genes (DEGs) related to carbon and nitrogen metabolite processes. Metabolome analysis shows that applying different nitrogen fertilizers at different growth stages of peach mainly affected metabolites related to carbon and amino acids. This research provides insight into the metabolic processes underlying different N responses during different growth stages and provides a foundation to improve the efficiency of N use in peach.

Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L

WD40 proteins serve as crucial regulators in a broad spectrum of plant developmental and physiological processes, including anthocyanin biosynthesis. However, in fig (Ficus carica L.), neither the WD40 family nor any member involved in anthocyanin biosynthesis has been elucidated. In the present study, 204 WD40 genes were identified from the fig genome and phylogenetically classified into 5 clusters and 12 subfamilies. Bioinformatics analysis prediction localized 109, 69, and 26 FcWD40 proteins to the cytoplasm, nucleus and other cellular compartments, respectively. RNA-seq data mining revealed 127 FcWD40s expressed at FPKM > 10 in fig fruit. Most of these genes demonstrated higher expression in the early stages of fruit development. FcWD40-97 was recruited according to three criteria: high expression in fig fruit, predicted nuclear localization, and closest clustering with TTG1s identified in other plants. FcWD40-97, encoding 339 amino acids including 5 WD-repeat motifs, showed 88.01 and 87.94% amino acid sequence similarity to apple and peach TTG1, respectively. The gene is located on fig chromosome 4, and is composed of 1 intron and 2 exons. Promoter analysis revealed multiple light-responsive elements, one salicylic acid-responsive element, three methyl jasmonate-responsive elements, and one MYB-binding site involved in flavonoid biosynthesis gene regulation. FcWD40-97 was in the FPKM > 100 expression level group in fig fruit, and higher expression was consistently found in the peel compared to the flesh at the same development stages. Expression level did not change significantly under light deprivation, whereas in leaves and roots, its expression was relatively low. Transient expression verified FcWD40-97's localization to the nucleus. Yeast two-hybrid (Y2H) and biomolecular fluorescence complementation (BiFC) assays revealed that FcWD40-97 interacts with FcMYB114, FcMYB123, and FcbHLH42 proteins in vitro and in vivo, showing that FcWD40-97 functions as a member of the MYB-bHLH-WD40 (MBW) complex in anthocyanin-biosynthesis regulation in fig. We therefore renamed FcWD40-97 as FcTTG1. Our results provide the first systematic analysis of the FcWD40 family and identification of FcTTG1 in fig pigmentation.

Integrated Metabolome and Transcriptome Analysis of Fruit Flavor and Carotenoids Biosynthesis Differences Between Mature-Green and Tree-Ripe of cv. "Golden Phoenix" Mangoes (Mangifera indica L.)

The commodity value of fruits is directly affected by fruit flavor and color. Secondary metabolites, such as amino acids, organic acids, esters, and β-carotene, are important synthetic products, which are of great significance in the flavor formation of mango fruits. In this study, a total of 309 different metabolites, consisting of organic acids, amino acids, phenolic acids, and saccharides, and a further 84 types of volatile organic compounds (VOCs) were identified in differential levels in TR vs. MG mango fruit stages. The major volatile compounds found were ester [2(3H)-furanone, 5-ethyldihydro; N-(2,5-ditrifluoromethylbenzoyl)-D-alanine, pentyl ester; and Octanoic acid, ethyl ester], aldehyde (benzaldehyde, 3-ethyl, and nonanal), and phenol [2-(1,1-dimethylethyl)-6-(1-methylethyl) phenol]. The analysis of carotenoid contents identified 68 carotenoids and we report for the first-time significant contents of zeaxanthin palmitate and (E/Z)-phytoene in mango fruits. α-carotene was a further major contributor to carotene contents with lesser contributions from 5,6epoxy-lutein-caprate-palmitate, β-carotene, lutein oleate, and β-cryptoxanthin. What is more, lutein content was significantly decreased in TR vs. MG fruit. RT-qPCR analysis revealed that relative to the MG stage, the expression of carotenogenic genes GGPS, PSY, LCYB, and ZEP was downregulated in TR mango fruit, whereas the transcript levels of PSD, CHYB, and NCED were downregulated. Additionally, the transcription level of some transcription factors (MYB, bHLH, and NAC) was highly correlated with pigment content in the pulp and may be responsible for carotenoid accumulation. The results describe major differences in metabolic pathways during the transition from MG to the TR stage of fruit ripening that are likely to contribute alterations in fruit flavor and provide several associated genes to be further studied in mango fruit.

AGAMOUS Gene as a New Sex-Identification Marker in Fig (Ficus carica L.) Is More Efficient Than RAN1

Fig is an ancient gynodioecious fruit tree with females for commercial fruit production and hermaphrodites (males) sometimes used as pollen providers. An early sex-identification method would improve breeding efficiency. Three AGAMOUS (AG) genes were recruited from the Ficus carica genome using AG sequences from Ficus microcarpa and Ficus hispida. FcAG was 5230 bp in length, with 7 exons and 6 introns, and a 744-bp coding sequence. The gene was present in both female and male fig genomes, with a 15-bp deletion in the 7th exon. The other two AG genes (FcAG2-Gall_Stamen and FcAG3-Gall_Stamen) were male-specific, without the 15-bp deletion (759-bp coding sequence), and were only expressed in the gall and stamen of the male fig fruit. Using the deletion as the forward primer (AG-Marker), male plants were very efficiently identified by the presence of a 146-bp PCR product. The previously reported fig male and female polymorphism gene RESPONSIVE-TO-ANTAGONIST1 (RAN1) was also cloned and compared between male and female plants. Fifteen SNPs were found in the 3015-bp protein-coding sequence. Among them, 12 SNPs were identified as having sex-differentiating capacity by checking the sequences of 27 known male and 24 known female cultivars. A RAN1-Marker of 608 bp, including 6 SNPs, was designed, and a PCR and sequencing-based method was verified with 352 fig seedlings from two hybrid populations. Our results confirmed that the newly established AG-Marker is as accurate as the RAN1-Marker, and provide new clues to understanding Ficus sex determination.

Metabolome and transcriptome analysis of flavor components and flavonoid biosynthesis in fig female flower tissues (Ficus carica L.) after bagging

BACKGROUND

Bagging can improve the appearance of fruits and increase the food safety and commodification, it also has effects on intrinsic quality of the fruits, which was commonly reported negative changes. Fig can be regarded as a new model fruit with its relatively small genome size and long fruit season.

RESULTS

In this study, widely targeted metabolomics based on HPLC MS/MS and RNA-seq of the fruit tissue of the 'Zibao' fig before and after bagging were analyzed to reveal the metabolites changes of the edible part of figs and the underneath gene expression network changes. A total of 771 metabolites were identified in the metabolome analysis using fig female flower tissue. Of these, 88 metabolites (including one carbohydrate, eight organic acids, seven amino acids, and two vitamins) showed significant differences in fruit tissue before and after bagging. Changes in 16 structural genes, 13 MYB transcription factors, and endogenous hormone (ABA, IAA, and GA) metabolism and signal transduction-related genes in the biosynthesis pathway of flavonoids after bagging were analyzed by transcriptome analysis. KEGG enrichment analysis also determined significant differences in flavonoid biosynthesis pathways in female flower tissue before and after bagging.

CONCLUSIONS

This work provided comprehensive information on the composition and abundance of metabolites in the female flower tissue of fig. The results showed that the differences in flavor components of the fruit before and after bagging could be explained by changes in the composition and abundance of carbohydrates, organic acids, amino acids, and phenolic compounds. This study provides new insights into the effects of bagging on changes in the intrinsic and appearance quality of fruits.

Ethephon induces coordinated ripening acceleration and divergent coloration responses in fig (Ficus carica L.) flowers and receptacles

The regulatory landscape of ethephon-accelerated fig ripening is revealed; flowers and receptacles exhibit opposite responses in anthocyanin accumulation; PG, PL and EXP are suggested key genes in fig softening. Ethephon is used to accelerate fig-fruit ripening for improvement of harvesting efficiency, but the underlying molecular mechanism is still unclear. To elucidate the detailed biological mechanism of ethylene-accelerated fig ripening, fruit in phase II (the lag phase on the double sigmoid growth curve) were treated with ethephon, and reached commercial ripeness 6 days earlier than the nontreated controls. Transcriptomes of flowers and the surrounding receptacles-which together make up the pseudocarp in fig fruit-were analyzed. There were 5189, 5818 and 2563 differentially expressed genes (DEGs) 2, 4 and 6 days after treatment (DAT) in treated compared to control fruit, screened by p-adjust < 0.05 and |log2(fold change) |≥ 2. The DEGs were significantly enriched in plant hormone metabolism and signal transduction, cell-wall modification, sugar accumulation and anthocyanin accumulation pathways. DEGs in the first three pathway categories demonstrated an overall similar expression change in flowers and receptacles, whereas DEGs in anthocyanin pigmentation revealed divergent transcript abundance. Specifically, in both flowers and receptacles, ethephon significantly upregulated 1-aminocyclopropane-1-carboxylate oxidase and downregulated most of the ethylene-response factor genes; polygalacturonase, pectate lyase and expansin were mainly upregulated; two acid beta-fructofuranosidases were upregulated. However, structural genes in the anthocyanin-synthesis pathway were mainly downregulated in female flowers 2 and 4 DAT, whereas they were upregulated in the receptacles. Our study reveals the regulatory landscape of the two tissues of fig fruit in ethylene-induced ripening; the differentially expressed pathways and genes provide valuable resources for the mining of target genes for crucial biological and commercial trait improvement.

Papain-Like Cysteine Protease Gene Family in Fig (Ficus carica L.): Genome-Wide Analysis and Expression Patterns

The papain-like cysteine proteases (PLCPs) are the most abundant family of cysteine proteases in plants, with essential roles in biotic/abiotic stress responses, growth and senescence. Papain, bromelain and ficin are widely used in food, medicine and other industries. In this study, 31 PLCP genes (FcPCLPs) were identified in the fig (Ficus carica L.) genome by HMM search and manual screening, and assigned to one of nine subfamilies based on gene structure and conserved motifs. SAG12 and RD21 were the largest subfamilies with 10 and 7 members, respectively. The FcPCLPs ranged from 1,128 to 5,075 bp in length, containing 1-10 introns, and the coding sequence ranged from 624 to 1,518 bp, encoding 207-505 amino acids. Subcellular localization analysis indicated that 24, 2, and 5 PLCP proteins were targeted to the lysosome/vacuole, cytoplasm and extracellular matrix, respectively. Promoter (2,000 bp upstream) analysis of FcPLCPs revealed a high number of plant hormone and low temperature response elements. RNA-seq revealed differential expression of 17 FcPLCPs in the inflorescence and receptacle, and RD21 subfamily members were the major PLCPs expressed in the fruit; 16 and 5 FcPLCPs responded significantly to ethylene and light, respectively. Proteome analyses revealed 18 and 5 PLCPs in the fruit cell soluble proteome and fruit latex, respectively. Ficins were the major PLCP in fig fruit, with decreased abundance in inflorescences, but increased abundance in receptacles of commercial-ripe fruit. FcRD21B/C and FcALP1 were aligned as the genes encoding the main ficin isoforms. Our study provides valuable multi-omics information on the FcPLCP family and lays the foundation for further functional studies.

Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Fig (Ficus carica L.)

The basic helix-loop-helix (bHLH) transcription factor family is the second largest transcription factor family in plants, and participates in various plant growth and development processes. A total of 118 bHLH genes were identified from fig (Ficus carica L.) by whole-genome database search. Phylogenetic analysis with Arabidopsis homologs divided them into 25 subfamilies. Most of the bHLHs in each subfamily shared a similar gene structure and conserved motifs. Seventy-two bHLHs were found expressed at fragments per kilobase per million mapped (FPKM) > 10 in the fig fruit; among them, 15 bHLHs from eight subfamilies had FPKM > 100 in at least one sample. bHLH subfamilies had different expression patterns in the female flower tissue and peel during fig fruit development. Comparing green and purple peel mutants, 13 bHLH genes had a significantly different (≥ 2-fold) expression. Light deprivation resulted in 68 significantly upregulated and 22 downregulated bHLH genes in the peel of the fruit. Sixteen bHLH genes in subfamily III were selected by three sets of transcriptomic data as candidate genes related to anthocyanin synthesis. Interaction network prediction and yeast two-hybrid screening verified the interaction between FcbHLH42 and anthocyanin synthesis-related genes. The transient expression of FcbHLH42 in tobacco led to an apparent anthocyanin accumulation. Our results confirm the first fig bHLH gene involved in fruit color development, laying the foundation for an in-depth functional study on other FcbHLH genes in fig fruit quality formation, and contributing to our understanding of the evolution of bHLH genes in other horticulturally important Ficus species.

Anthocyanin accumulation is initiated by abscisic acid to enhance fruit color during fig (Ficus carica L.) ripening

Fig fruit is well-known for its attractive flavor, color, and nutritional and medicinal value. Anthocyanin contributes to the fruit's color and constitutes a high percentage of the total antioxidant content of the fig fruit. We quantified the major anthocyanins and characterized the expression levels of anthocyanin-biosynthesis and transcription factor genes in fruit treated on-tree with exogenous abscisic acid (ABA) or ethephon, or the ABA inhibitors nordihydroguaiaretic acid (NDGA) or fluridone. The major anthocyanins cyanidin 3-O-glucoside and cyanidin 3-O-rutinoside were found in significantly higher quantities in exogenous ABA- and ethephon-treated fruit, with early dark purple color compared to the controls. On the other hand, NDGA- and fluridone-treated fruit had significantly lower amounts of anthocyanins, with less purple color coverage than controls. Expression levels of the anthocyanin-biosynthesis genes FcPAL, FcCHS2, FcCHI, FcF3H, FcDFR, FcANS, FcUFGT and Fc3RT were upregulated by exogenous ABA and ethephon treatment, and downregulated by NDGA and fluridone treatment. The MYB-bHLH-WD40 complex-related genes of ripe fig fruit were identified. In particular, FcMYB113 was strongly upregulated by exogenous ABA and ethephon, and strongly downregulated by NDGA and fluridone. In addition, moderate upregulation of FcGL3 and FcWD40 was observed with exogenous ABA and ethephon treatment, and moderate downregulation in NDGA- and fluridone-treated fruit. These results indicate that ABA can initiate anthocyanin biosynthesis, which ultimately improves the color and nutritional value of fig fruit, enhancing their attractiveness to consumers.

Transcriptomic analysis of flower color variation in the ornamental crabapple (Malus spp.) half-sib family through Illumina and PacBio Sequel sequencing

Ornamental crabapple is an important woody ornamental plant with flower colors ranging from white to pink to red, and the degree of redness is directly related to the anthocyanin content. To explore the molecular mechanism leading to the variation in flower color in ornamental crabapple, transcriptome sequencing using the Illumina and PacBio Sequel platforms revealed the difference in gene expression between the petals of plants with white and red flowers in the half-sib family. In total, the analysis identified 603 differentially expressed genes (DEGs), including 449 upregulated and 154 downregulated genes. GO and KEGG enrichment analyses of the DEGs showed that the oxidation-reduction process and catalytic activity were more active in red petals, and most of the DEGs were involved in secondary metabolite synthesis and plant hormone signaling. Among the 603 DEGs, 10 were enriched as structural genes. Transcription factors related to anthocyanin synthesis and five genes related to anthocyanin transport and degradation were highly expressed in red petals. In addition, this study found that five AUX gene signals were differentially expressed in the two petal types. The discovery of these DEGs indicates that plant endogenous hormones also exert a regulatory effect on flower color.

Transcriptomic Analysis of Ficus carica Peels with a Focus on the Key Genes for Anthocyanin Biosynthesis

Fig (Ficus carica L.), a deciduous fruit tree of the Moraceae, provides ingredients for human health such as anthocyanins. However, little information is available on its molecular structure. In this study, the fig peels in the yellow (Y) and red (R) stages were used for transcriptomic analyses. Comparing the R with the Y stage, we obtained 6224 differentially expressed genes, specifically, anthocyanin-related genes including five CHS, three CHI, three DFR, three ANS, two UFGT and seven R2R3-MYB genes. Furthermore, three anthocyanin biosynthetic genes, i.e., FcCHS1, FcCHI1 and FcDFR1, and two R2R3-MYB genes, i.e., FcMYB21 and FcMYB123, were cloned; sequences analysis and their molecular characteristics indicated their important roles in fig anthocyanin biosynthesis. Heterologous expression of FcMYB21 and FcMYB123 significantly promoted anthocyanin accumulation in both apple fruits and calli, further suggesting their regulatory roles in fig coloration. These findings provide novel insights into the molecular mechanisms behind fig anthocyanin biosynthesis and coloration, facilitating the genetic improvement of high-anthocyanin cultivars and other horticultural traits in fig fruits.