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The genus Ficus of the family Moraceae, is one of the largest genera of angiosperms, with diverse pharmaceutical applications and biological activities. The traditional approaches based on the morphological traits have been frequently implemented for taxonomical identification of the different taxa of Ficus , however, encompassing these features are quite laborious, due to the dependence of these phenotypic traits on the environmental conditions. So, authenticating the taxonomical identity of the Ficus taxa with molecular barcoding and metabolic profiling, as relatively stable traits, could be a relevant approach for confirming the traditional phenotypic traits of this genus. Nine species of the genus Ficus namely F. amplissima Sm., F. benjamina L. F. binnendijkii , F. drupacea var. pubescens , F. elastica Roxb., F. microcarpa L., F. religiosa L., F. tinctoria subsp. gibbosa and F. virens var. sublancelata in Egypt, were selected for this study. From the anatomical features, three species of subsection Urostigma, F. religiosa , F. virens var. sublanceolata have cystoliths on the abaxial layer, whereas in F. amplissima it was on the adaxial layer. The UPGMA dendrogram of the studied Ficus taxa has been generated from the 21 anatomical characters, categorized the studied taxa into two clusters (I and II) of average distance ~ 3.5, each cluster has been further divided into subclusters I and II. The sub-cluster I includes F. religiosa , F. virens var. sublanceolata and F. tinctoria subsp. gibbosa were grouped together to subsection Urostigma, while the sub-cluster II of the cluster I includes F. benjamina and F. amplissima . From the DNA barcoding analysis, three clusters I, II and III were emerged, the cluster I includes F. benjamina , F. binnendjikee , and F. amplissima . The cluster II, F. virens var. sublanceolata and F. religiosa that belong to subsection Urostigma, while, the cluster III includes F. elastica and F. drupacea var. pubescens , F. microcarpa that belongs to subsection Conosycea. From the metabolic profiling of Ficus species, the major compounds; H-cycloprop-azulen-7-ol, 3,7,11,15-Tetramethyl-2-hexadecen-1-ol, 2-(9-octadecenyloxy), pentadecanoic acid, phytol, sitosterol and 9,12-octadecadienoic acid were the common among the taxa, with an obvious fluctuation, that could be a chemotaxonomic markers for these species of Ficus . Based on the metabolic profiling, two distinct clusters I and II were evolved, the cluster I involve F. elastica , F. benjamina , F. drupacea var. pubescens , F. amplissima , while, the cluster II had F. tinctoria subsp. gibbosa and F. religiosa . The fluctuation on the metabolites of the tested Ficus species could be a metabolic fingerprint for each species. So, the delamination of the tested plants based on their anatomical traits was typically matched to the separation based on the ITS sequence analysis.

Furanocoumarins (FCs) are plant-specialized metabolites with potent allelochemical properties. The distribution of FCs is scattered with a chemotaxonomical tendency towards four distant families with highly similar FC pathways. The mechanism by which this pathway emerged and spread in plants has not been elucidated. Furanocoumarin biosynthesis was investigated in Ficus carica (fig, Moraceae), focusing on the first committed reaction catalysed by an umbelliferone dimethylallyltransferase (UDT). Comparative RNA-seq analysis among latexes of different fig organs led to the identification of a UDT. The phylogenetic relationship of this UDT to previously reported Apiaceae UDTs was evaluated. The expression pattern of F. carica prenyltransferase 1 (FcPT1) was related to the FC contents in different latexes. Enzymatic characterization demonstrated that one of the main functions of FcPT1 is UDT activity. Phylogenetic analysis suggested that FcPT1 and Apiaceae UDTs are derived from distinct ancestors, although they both belong to the UbiA superfamily. These findings are supported by significant differences in the related gene structures. This report describes the identification of FcPT1 involved in FC biosynthesis in fig and provides new insights into multiple origins of the FC pathway and, more broadly, into the adaptation of plants to their environments.

The genus (Moraceae) is a large and ecologically important group, known for its intricate fig-wasp pollination mutualism and role as a keystone resource in tropical ecosystems. Despite its significance, the phylogenetic relationships within remain partially unresolved, necessitating more comprehensive genomic data. Chloroplast (cp) genomes are valuable resources for plant phylogenetic and comparative genomic studies. Here, we sequenced, assembled, and comparatively analyzed the complete chloroplast genomes of seven species, including , , , , , , and . The complete cp genomes were successfully assembled, ranging in size from 160,340 bp to 160,669 bp, and exhibited a typical quadripartite structure with highly conserved gene content and arrangement. Critically, while some of these species have previously published plastomes, our assemblies consistently encoded 130 genes, contrasting with reported gene counts ( , 129 for (NC_059898), 119 for (KY635880), 131 for (MT093220)) in earlier studies. Numerous repeat sequences and simple sequence repeats (SSRs) were identified, predominantly in non-coding regions, which serve as valuable resources for developing novel genetic markers. Analysis of codon usage revealed a strong bias towards A/T endings, a common feature in plant cp genomes. While inverted repeat (IR) boundary regions were largely conserved, minor variations, including partial gene duplications ( 19, 2), were observed. Comparative genome alignment and nucleotide diversity analysis showed high sequence conservation, with most variations concentrated in single-copy and non-coding regions. We identified three hypervariable regions ( A, A - D, and B - C-GCA) with elevated nucleotide diversity (Pi > 0.012, A up to 0.0141), suggesting their utility as candidate DNA barcodes for . Phylogenetic analysis using 79 protein-coding genes from 26 species robustly supported the monophyly of and resolved the seven newly sequenced species into two well-supported clades, consistent with previous classifications. Our study provides new, consistently assembled and rigorously annotated chloroplast genome data for , including clarified data for previously studied species with notable gene content discrepancies. These data identify candidate molecular markers with potential applications for systematics and population genetics, and offer robust insights into relationships among sampled taxa. These data will facilitate future studies of evolution and conservation when complemented by broader taxon sampling and nuclear/mitochondrial data.

Due to maternal inheritance and minimal rearrangement, the chloroplast genome is an important genetic resource for evolutionary studies. However, the evolutionary dynamics and phylogenetic performance of chloroplast genomes in closely related species are poorly characterized, particularly in taxonomically complex and species-rich groups. The taxonomically unresolved Ficus sarmentosa species complex (Moraceae) comprises approximately 20 taxa with unclear genetic background. In this study, we explored the evolutionary dynamics, hotspot loci, and phylogenetic performance of thirteen chloroplast genomes (including eleven newly obtained and two downloaded from NCBI) representing the F . sarmentosa complex. Their sequence lengths, IR boundaries, repeat sequences, and codon usage were compared. Both sequence length and IR boundaries were found to be highly conserved. All four categories of long repeat sequences were found across all 13 chloroplast genomes, with palindromic and forward sequences being the most common. The number of simple sequence repeat (SSR) loci varied from 175 ( F . dinganensis and F . howii ) to 190 ( F . polynervis ), with the dinucleotide motif appearing the most frequently. Relative synonymous codon usage (RSCU) analysis indicated that codons ending with A/T were prior to those ending with C/T. The majority of coding sequence regions were found to have undergone negative selection with the exception of ten genes ( accD , clpP , ndhK , rbcL , rpl20 , rpl22 , rpl23 , rpoC1 , rps15 , and rps4 ) which exhibited potential positive selective signatures. Five hypervariable genic regions ( rps15 , ycf1 , rpoA , ndhF , and rpl22 ) and five hypervariable intergenic regions ( trnH-GUG - psbA , rpl32 - trnL-UAG , psbZ - trnG-GCC , trnK-UUU - rps 16 and ndhF - rpl32 ) were identified. Overall, phylogenomic analysis based on 123 Ficus chloroplast genomes showed promise for studying the evolutionary relationships in Ficus , despite cyto-nuclear discordance. Furthermore, based on the phylogenetic performance of the F . sarmentosa complex and F . auriculata complex, the chloroplast genome also exhibited a promising phylogenetic resolution in closely related species.

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant-insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale cophylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on an average, wasps had sequences from 77% of 6 genes (5.6 kb), figs had sequences from 60% of 5 genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based cophylogenetic analyses further support the codiversification hypothesis. Biogeographic analyses indicate that the present-day distribution of fig and pollinator lineages is consistent with a Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term codiversification.

Background Jasmonate-ZIM domain (JAZ) repressors negatively regulate signal transduction of jasmonates, which regulate plant development and immunity. However, no comprehensive analysis of the JAZ gene family members has been done in the common fig ( Ficus carica L.) during fruit development and hormonal treatment. Results In this study, 10 non-redundant fig JAZ family genes (FcJAZs ) distributed on 7 chromosomes were identified in the fig genome. Phylogenetic and structural analysis showed that FcJAZ genes can be grouped into 5 classes. All the classes contained relatively complete TIFY and Jas domains. Yeast two hybrid (Y2H) results showed that all FcJAZs proteins may interact with the identified transcription factor, FcMYC2. Tissue-specific expression analysis showed that FcJAZs were highly expressed in the female flowers and roots. Expression patterns of FcJAZs during the fruit development were analyzed by RNA-Seq and qRT-PCR. The findings showed that, most FcJAZs were significantly downregulated from stage 3 to 5 in the female flower, whereas downregulation of these genes was observed in the fruit peel from stage 4 to 5. Weighted-gene co-expression network analysis (WGCNA) showed the expression pattern of FcJAZs was correlated with hormone signal transduction and plant-pathogen interaction. Putative cis -elements analysis of FcJAZs and expression patterns of FcJAZs which respond to hormone treatments revealed that FcJAZs may regulate fig fruit development by modulating the effect of ethylene or gibberellin. Conclusions This study provides a comprehensive analysis of the FcJAZ family members and provides information on FcJAZs contributions and their role in regulating the common fig fruit development.

Summary The mechanism regulating fruit textural changes has not been fully elucidated. Transcription factor FcERF100 showed rapid transcription repression during drastic texture loss in fig (Ficus carica L.) fruit ripening. Transient overexpression of FcERF100 delayed fig fruit softening and significantly decreased the transcript abundance of a key cell wall‐modifying pectate lyase gene, FcPL7. Yeast one‐hybrid (Y1H) assay, chromatin immunoprecipitation‐qPCR, electrophoretic mobility shift assay (EMSA), and dual‐luciferase reporter assay revealed that FcERF100 represses FcPL7 transcription by direct promoter binding via GCC‐box and DRE/CRT elements. Stable transgenic fig lines further verified FcERF100's inhibitory effect on FcPL7 expression. We detected FcERF28 as an upstream element of FcERF100 by Y1H and EMSA, revealing its binding to, and activation of FcERF100 by dual‐luciferase assay. Taken together, the FcERF28–FcERF100 transcriptional cascade serves as a synergistic flow‐limiting valve for FcPL7 abundance. We then identified a NAC transcription factor, FcNOR, using FcERF100 as the bait by yeast two‐hybrid screening. FcNOR silencing retarded fig fruit softening, with decreased FcPL7 transcript and pectate lyase activity. FcNOR interacted with FcERF100 to form a protein complex, attenuating FcERF100's transcriptional repression of FcPL7. Moreover, FcNOR bound directly to the promoter of FcERF100 and inhibited its transcription. In addition, ethylene treatment upregulated FcNOR and FcPL7 expression and downregulated FcERF28 and FcERF100 expression. Our findings reveal a novel FcERF100‐centered regulatory complex and resolve how the complex achieves the necessary cell wall modification during an early stage of fruit growth and implements drastic softening at fruit ripening by modulating component proportions.

Background Radix Fici Hirtae, the dry root of Ficus hirta , is a famous ethnomedicine and food that has been widely used by Yao and Zhuang nationalities in southern China for its potent antitumor, antifungal, and hepatoprotective effects. Recently, owing to over-exploitation and habitat destruction, F. hirta has been pushed to the brink of depletion. In addition, cultivation and breeding have resulted in severe intermixing and degeneration over the past 20 years. However, little is known about the genetic background and medicinal quality of F. hirta across populations, which restricts its protection and utilization. In this study, we conducted an evaluation of the chloroplast DNA (cpDNA) genetic diversity and population structure of F. hirta in southern China, and further evaluated its medicinal quality based on HPLC fingerprinting and the content determination of the active components. Results F. hirta presented high overall genetic diversity ( H d = 0.792) for cpDNA but low genetic diversity ( H d = 0.000 ~ 0.467) within populations. All seventeen populations were genetically assigned into two groups, most of which were not geographically clustered together. Mantel test revealed no significant isolation by distance pattern for F. hirta ( P  = 0.233), which might be related to its habitat fragmentation. High population differentiation ( F ST  = 0.912) was detected in F. hirta , and AMOVA revealed that 91.17% of cpDNA variation occurred between populations. HPLC fingerprint analysis indicated that most F. hirta samples derived from 14 geographic origins had highly similar components (similarity = 0.828 ~ 0.975). Fourteen origins of F. hirta were clustered into three groups by HCA, PCA and OPLS-DA. Psoralen and bergapten were the differentiated quality markers among the groups. The medicinal quality of the populations NN, SD and HZ within southwestern group was much greater than that of the ND and GZ populations within southeastern group, which is consistent with the comprehensive quality scores for each origin ( Y  = 1.78 ~-0.82). The medicinal quality formation of F. hirta was highly correlated with geographical environment but not with cpDNA genetic variation. Conclusions F. hirta presented high overall genetic diversity and population differentiation, but without significant isolation by distance, which might relate to its habitat fragmentation. Different geographic origins’ Radix Fici Hirtae were chemically clustered into three groups, which were mainly differentiated by psoralen and bergapten. The medicinal quality of Radix Fici Hirtae exhibited a southwest to southeast variation pattern across southern China, and its quality formation was influenced mostly by geographical environments. Our results provide references for the conservation, core collection construction and improvement of F. hirta .

The Ficus genus, having radiated from the tropics and subtropics to the temperate zone worldwide, is the largest genus among woody plants, comprising over 800 species. Evolution of the Ficus species results in genetic diversity, global radiation and geographical differentiations, suggesting adaption to diverse environments and coping with stresses. Apart from familiar physiological changes, such as stomatal closure and alteration in plant hormone levels, the Ficus species exhibit a unique mechanism in response to abiotic stress, such as regulation of leaf temperature and retention of drought memory. The stress-resistance genes harbored by Ficus result in effective responses to abiotic stress. Understanding the stress-resistance mechanisms in Ficus provides insights into the genetic breeding toward stress-tolerant crop cultivars. Following upon these issues, we comprehensively reviewed recent progress concerning the Ficus genes and relevant mechanisms that play important roles in the abiotic stress responses. These highlight prospectively important application potentials of the stress-resistance genes in Ficus.

The dried fig cv. Sabz of Iran, distinguishes out among the several fig cultivars for its unique characteristics and excellent properties. The aims to this study were 1) Carefully monitoring the resulting phenotypic changes in growth patterns, leaf morphology, shoot traits, root characteristics, and other relevant traits after irradiated with different gamma rays; 2) Investigating the LD 25 , 50 , 75 and GR 25 , 50 , 75 values at different gamma radiation doses for chose optimum dose. According to our results, the LD 50 was 70 Gy, while the LD 25 and LD 75 were approximately 48 and 95 Gy, respectively. Data analysis revealed that higher doses, ranging from 50 to 90 Gy, led to a reduction in leaf area for fig hardwood cuttings compared to those exposed to lower doses of gamma irradiation (10, 20, 30, and 40 Gy). In fig cuttings, the plant height gradually decreased in line with increasing irradiation doses up to 60 Gy. Among the root traits, root number was particularly influenced by higher radiation doses. On other hand, when fig cuttings were exposed to a 40 Gy radiation dosage, the average root count dropped by 50%. However, when fig cuttings were subjected to a 90 Gy radiation dose, the average root count surged by 90.7% in comparison to the control treatment. Additionally, the GR 50 values were 63 Gy for internode length, 67 Gy for leaf area and 56 Gy for plant height and aerial biomass. However, the GR 50 values for root number, root volume, and root biomass were 46 Gy, 57 Gy, and 51 Gy, respectively. An analysis based on the GR 25 , GR 50 , and GR 75 values indicated that plant height, aerial biomass and root biomass exhibited greater sensitivity to radioactivity in comparison to other plant portions of the fig. According to the biological responses in the ‘Sabz’ fig, 60 Gy of gamma radiation is a suitable dose for initial mutagenesis studies.