Identification and functional analysis of the LEAFY gene in longan flower induction.

BACKGROUND: Flowering at the right time is a very important factor affecting the stable annual yield of longan. However, a lack of knowledge of the regulatory mechanism and key genes of longan flowering restricts healthy development of the longan industry. Therefore, identifying relevant genes and analysing their regulatory mechanism are essential for scientific research and longan industry development. RESULTS: DlLFY (Dimocarpus longan LEAFY) contains a 1167 bp open reading frame and encodes 388 amino acids. The amino acid sequence has a typical LFY/FLO family domain. DlLFY was expressed in all tissues tested, except for the leaf, pericarp, and pulp, with the highest expression occurring in flower buds. Expression of DlLFY was significantly upregulated at the early flower induction stage in "SX" ("Shixia"). The results of subcellular localization and transactivation analysis showed that DlLFY is a typical transcription factor acting as a transcriptional activator. Moreover, overexpression of DlLFY in Arabidopsis promoted early flowering and restrained growth, resulting in reduced plant height and rosette leaf number and area in transgenic plants. DNA affinity purification sequencing (DAP-Seq) analysis showed that 13 flower-related genes corresponding to five homologous genes of Arabidopsis may have binding sites and be putative target genes. Among these five flower-related genes, only AtTFL1 (terminal flower 1) was strongly inhibited in transgenic lines. CONCLUSION: Taken together, these results indicate that DlLFY plays a pivotal role in controlling longan flowering, possibly by interacting with TFL1.

Strigolactones Might Regulate Ovule Development after Fertilization in Xanthoceras sorbifolium.

Strigolactones (SLs) were recently defined as a novel class of plant hormones that act as key regulators of diverse developmental processes and environmental responses. Much research has focused on SL biosynthesis and signaling in roots and shoots, but little is known about whether SLs are produced in early developing seeds and about their roles in ovule development after fertilization. This study revealed that the fertilized ovules and early developing pericarp in Xanthoceras sorbifolium produced minute amounts of two strigolactones: 5-deoxystrigol and strigol. Their content decreased in the plants with the addition of exogenous phosphate (Pi) compared to those without the Pi treatment. The exogenous application of an SL analog (GR24) and a specific inhibitor of SL biosynthesis (TIS108) affected early seed development and fruit set. In the Xanthoceras genome, we identified 69 potential homologs of genes involved in SL biological synthesis and signaling. Using RNA-seq to characterize the expression of these genes in the fertilized ovules, 37 genes were found to express differently in the fertilized ovules that were aborting compared to the normally developing ovules. A transcriptome analysis also revealed that in normally developing ovules after fertilization, 12 potential invertase genes were actively expressed. Hexoses (glucose and fructose) accumulated at high concentrations in normally developing ovules during syncytial endosperm development. In contrast, a low ratio of hexose and sucrose levels was detected in aborting ovules with a high strigolactone content. XsD14 virus-induced gene silencing (VIGS) increased the hexose content in fertilized ovules and induced the proliferation of endosperm free nuclei, thereby promoting early seed development and fruit set. We propose that the crosstalk between sugar and strigolactone signals may be an important part of a system that accurately regulates the abortion of ovules after fertilization. This study is useful for understanding the mechanisms underlying ovule abortion, which will serve as a guide for genetic or chemical approaches to promote seed yield in Xanthoceras.

Recovery Effects of Nephelium lappaceum var. pallens (Hiern) Leenh. Extract on Testosterone-Induced Inhibition of Hair Growth in C57BL/6 Mice and Human Follicular Dermal Papilla Cells.

Although various hair health medicines have been developed and are used today, additional safe and effective natural hair growth therapies still need to be developed. Nephelium lappaceum var. pallens (Hiern) Leenh. extract (NLE) reportedly exhibits anticancer, antidiabetic, and antioxidant effects, which could be linked to androgenic processes; however, there are no reports of its effects on testosterone (TS)-inhibited hair growth. The present study investigated the effects of NLE on TS-induced inhibition of hair growth in C57BL/6 mice and human follicular dermal papilla cells. Oral administration of NLE restored hair growth that was suppressed following subcutaneous injection of TS more effectively than finasteride, a drug used for treating hair loss. Histological analysis demonstrated that oral NLE administration increased the number and diameter of hair follicles in the dorsal skin of C57BL/6 mice. In addition, western blot and immunofluorescence assays showed that the oral NLE administration restored TS-induced suppression of cyclin D1, proliferating cell nuclear antigen, and loricrin expression in the skin cells of the mice. Finally, TS suppression of cell proliferation in human follicular dermal papilla cells was significantly reversed by NLE pretreatment. The results suggest that NLE is a promising nutraceutical for hair growth because it promotes hair growth in androgenetic alopecia-like models.

Genome-Wide Identification and Expression Analysis of GATA Family Genes in Dimocarpus longan Lour.

GATA transcription factors, which are DNA-binding proteins with type IV zinc finger binding domains, have a role in transcriptional regulation in biological organisms. They have an indispensable role in the growth and development of plants, as well as in improvements in their ability to face various environmental stresses. To date, GATAs have been identified in many gene families, but the GATA gene in longan (Dimocarpus longan Lour) has not been studied in previous explorations. Various aspects of genes in the longan GATA family, including their identification and classification, the distribution of their positions on chromosomes, their exon/intron structures, a synteny analysis, their expression at different temperatures, concentration of PEG, early developmental stages of somatic embryos and their expression levels in different tissues, and concentrations of exogenous hormones, were investigated in this study. This study showed that the 22 DlGATAs could be divided into four subfamilies. There were 10 pairs of homologous GATA genes in the synteny analysis of DlGATA and AtGATA. Four segmental replication motifs and one pair of tandem duplication events were present among the DlGATA family members. The cis-acting elements located in promoter regions were also found to be enriched with light-responsive elements, which contained related hormone-responsive elements. In somatic embryos, DlGATA4 is upregulated for expression at the globular embryo (GE) stage. We also found that DlGATA expression was strongly up-regulated in roots and stems. The study demonstrated the expression of DlGATA under hormone (ABA and IAA) treatments in embryogenic callus of longan. Under ABA treatment, DlGATA4 was up-regulated and the other DlGATA genes did not respond significantly. Moreover, as demonstrated with qRT-PCR, the expression of DlGATA genes showed strong up-regulated expression levels under 100 µmol·L-1 concentration IAA treatment. This experiment further studied these and simulated their possible connections with a drought response mechanism, while correlating them with their expression under PEG treatment. Overall, this experiment explored the GATA genes and dug into their evolution, structure, function, and expression profile, thus providing more information for a more in-depth study of the characteristics of the GATA family of genes.

Lepiginosides A-D: three new triterpenoid saponins and a new farnesyl glycoside from the stembarks of Lepisanthes rubiginosa (roxb.) leenh.

Phytochemical investigation of methanolic extract of L. rubiginosa using modern chromatographic techniques has led to the isolation of three new triterpenoid saponins, lepiginosides A-C (1-3), a new farnesyl glycoside, lepiginoside D (4), together with lepisantheside B (5) and gleditsoside C (6). The characterization and structural elucidation of the isolated compounds were established by extensive spectroscopic data analysis and comparison with literature data. Moreover, the antibacterial activity against seven bacteria, but none is active.

Application of films developed with tilapia gelatin (Oreochromis niloticus), added with pitomba plant extract (Talisia esculenta) in Hawaii papaya.

In the present study, a film based on the gelatin skin of tilapia (Oreochromis niloticus) was developed, using surfactants and adding plant extract of pitomba seed (Talisia esculenta). The aim was to investigate the mechanical and barrier properties of the cover, as well as its effectiveness in conserving papayas against diseases caused by fungi. The film presented tensile strength of 38.78 MPa, elongation of 120.49%, and water vapor permeability of 5.90 g.mm.h-1.m2.kPa-1 when equally composed of SDS and Tween 80, in a percentage of 40% in relation to the total mass of the film. The films lasted 12 d in an environment with a relative humidity of 75% (25 ºC), longer than the shelf life of papaya (limited to 8 d). With applying the film with the extract, the incidence of diseases such as anthracnose, fusariosis, and stem rot caused by these microorganisms in papaya was reduced.

Cellulose fibers and ellagitannin-rich extractives from rambutan (Nephelium Lappaceum L.) peel by an eco-friendly approach.

This study assesses the viability of an accelerated solvent extraction technique employing environmentally friendly solvents to extract ellagitannins while producing cellulose-rich fibers from rambutan peel. Two sequential extraction protocols were investigated: 1) water followed by acetone/water (4:1, v:v), and 2) acetone followed by acetone/water (4:1, v:v), both performed at 50 °C. The first protocol had a higher extraction yield of 51 %, and the obtained extractives featured a higher total phenolic (531.4 ± 22.0 mg-GAE/g) and flavonoid (487.3 ± 16.9 mg-QE/g) than the second protocol (495.4 ± 32.8 mg-GAE/g and 310.6 ± 31.4 mg-QE/g, respectively). The remaining extractive-free fibers were processed by bleaching using either 2 wt% sodium hydroxide with 3 wt% hydrogen peroxide or 4-5 wt% peracetic acid. Considering bleaching efficiency, yield, and process sustainability, the single bleaching treatment with 5 wt% of peracetic acid was selected as the most promising approach to yield cellulose-rich fibers. The samples were analyzed by methanolysis to determine the amount and type of poly- and oligosaccharides and studied by 13C solid-state nuclear magnetic resonance spectroscopy and thermal gravimetric analysis. The products obtained from the peels demonstrate significant potential for use in various sectors, including food, nutraceuticals, cosmetics, and paper production.

Longan Polysaccharides with Covalent Selenylation Combat the Fumonisin B1-Induced Cell Toxicity and Barrier Disruption in Intestinal Epithelial (IEC-6) Cells.

In this study, the soluble, but non-digestible, longan (Dimocarpus longan Lour.) polysaccharides (LP) were extracted from dried longan fruits and then chemically selenylated to produce two selenylated products, namely SeLP1 and SeLP2, with different selenylation extents. The aim was to investigate their protective effects on rat intestinal epithelial (IEC-6) cells exposed to the food toxin fumonisin B1 (FB1). LP only contained total Se content of less than 0.01 g/kg, while SeLP1 and SeLP2 were measured with respective total Se content of up to 1.46 and 4.79 g/kg. The cell viability results showed that these two selenylated products were more efficient than LP in the IEC-6 cells in alleviating FB1-induced cell toxicity, suppressing lactate dehydrogenase (LDH) release, and decreasing the generation of intracellular reactive oxygen species (ROS). These two selenylated products were also more effective than LP in combating FB1-induced barrier disruption via increasing the transepithelial electric resistance (TEER), reducing the paracellular permeability, decreasing the mitochondrial membrane potential (MMP) loss, and maintaining cell barrier integrity by upregulating the tight-junction-related genes and proteins. FB1 caused cell oxidative stress and barrier dysfunction by activating the MAPK and mitochondrial apoptosis signaling pathways, while SeLP1 and SeLP2 could regulate the tMAPK- and apoptosis-related proteins to suppress the FB1-mediated activation of the two pathways. Overall, SeLP2 was observed to be more active than SeLP1 in the IEC-6 cells. In conclusion, the chemical selenylation of LP caused an activity enhancement to ameliorate the FB1-induced cell cytotoxicity and intestinal barrier disruption. Meanwhile, the increased selenylation of LP would endow the selenylated product SeLP2 with more activity.

Integrated Metabolomic and Transcriptomic Analyses Reveal the Potential Regulation of Flavonoids in the Production of Embryogenic Cultures during Early Somatic Embryogenesis of Longan (Dimocarpus longan Lour.).

Embryogenic cultures of longan (Dimocarpus longan Lour.) contain various metabolites with pharmacological properties that may function in the regulation of somatic embryogenesis (SE). In this study, based on widely targeted metabolomics, 501 metabolites were obtained from the embryogenic calli, incomplete compact proembryogenic cultures, and globular embryos during early SE of longan, among which 41 flavonoids were differentially accumulated during the SE. Using RNA sequencing, 36 flavonoid-biosynthesis-related genes and 43 MYB and 52 bHLH transcription factors were identified as differentially expressed genes. Furthermore, Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed that the flavonoid metabolism-related pathways were significantly enriched during the early SE. These results suggested that the changes in flavonoid levels in the embryogenic cultures of longan were mediated by MYBs and bHLHs via regulating flavonoid-biosynthesis-related genes, thus potentially regulating early SE. The identified metabolites in the embryogenic cultures of longan can be used to develop pharmaceutical ingredients.

Bioavailability and Antioxidant Activity of Rambutan (Nephelium lappaceum) Peel Polyphenols during in Vitro Simulated Gastrointestinal Digestion, Caco-2 Monolayer Cell Model Application, and Colonic Fermentation.

The bioavailability of rambutan peel polyphenols (RPPs) was studied via in vitro simulated digestion, a Caco-2 monolayer cell model, and colonic fermentation. Total phenolic content of RPPs decreased with the progress of the simulated digestion. A total of 38 phenolic compounds were identified during the digestion and colonic fermentation, of which 12 new metabolites were found during colonic fermentation. The possible biotransformation pathways were inferred. Geraniin was transformed into corilagin, ellagic acid, and gallic acid during the digestion and colonic fermentation. Ellagic acid could be further transformed into urolithin under the action of intestinal microbiota. The transformation of ellagitannins could be beneficial to transport on Caco-2 monolayer cell. The antioxidant capacity of RPPs increased with the progress of gastrointestinal digestion. Furthermore, RPPs could increase the yield of short-chain fatty acids, decrease the pH value, promote the growth of beneficial bacteria, and inhibit the growth of pathogenic Escherichia coli/Shigella during colonic fermentation.

Safety Assessment of Schleichera oleosa Lour. Leaves Extract: Acute and Subchronic Studies.

<b>Background and Objective:</b> <i>Schleichera oleosa</i> (Sapindaceae) has been reported to be useful in traditional medicine and it has some potential pharmacological activities, such as anticancer, antioxidant and antimicrobial activities. This study aimed to assess its safety to provide complete data required for the development of <i>S. oleosa</i> as herbal medicine. <b>Materials and Methods:</b> The safety assessment of the extract was carried out by testing acute and subchronic toxicity in mice (male and female) and rats (male and female), respectively. The doses used in the acute toxicity test were 1000, 2000, 3000, 4000 and 5000 mg kg¹ of body weight and those in the subchronic treatment were 100, 200 and 400 mg kg¹ of body weight. <b>Results:</b> In the acute toxicity test, the <i>S. oleosa</i> leaf extract at all doses indicated that the LD₅₀ value of the extract was higher than 5000 mg kg¹ b.wt., which suggested that this extract is practically non-toxic according to the toxicity criteria. Furthermore, the subchronic toxicity test found that the administration of the extract to male and female rats at a daily dose of 100 and 200 mg kg¹ b.wt., for 90 days did not cause any significant change in blood haematology, blood biochemistry and histopathological picture of liver, kidney, heart, lymph and lung. Despite there being a significant increase in white blood counts, long-term use of the <i>S. oleosa</i> leaf extract is relatively safe. <b>Conclusion:</b> The results provided evidence regarding the potential of <i>S. oleosa</i> leaves to be used as herbal medicine. However, further research needs to be done to verify that activity and its safety in long-term use.

Exploring the Antioxidant Potential of Talisia esculenta Using In Vitro and In Vivo Approaches.

Medicinal plants, such as Talisia esculenta, are rich in antioxidant biomolecules, which are used in the treatment and prevention of many diseases. The antioxidant potential of T. esculenta extracts obtained from leaves and fruit peels was investigated using biochemical and 3T3 cell line assays as well as in vivo assays using an organism model Tenebrio molitor. Four extracts were tested: hydroethanolic extracts from leaves (HF) and from fruit peels (HC), and infusion extracts from leaves (IF) and from fruit peels (IC). The biochemical assays demonstrated an antioxidant capacity verified by TAC, reducing power, DPPH, and copper chelating assays. None of the extracts exhibited cytotoxicity against 3T3 cells, instead offering a protection against CuSO4-induced oxidative stress. The antioxidant activity observed in the extracts, including their role as free radical scavengers, copper chelators, and stress protectors, was further confirmed by T. molitor assays. The CLAE-DAD analysis detected phenolic compounds, including gallic acid, rutin, and quercitrin, as the main constituents of the samples. This study highlights that leaf and fruit peels extracts of T. esculenta could be effective protectors against ROS and copper-induced stress in cellular and invertebrate models, and they should be considered as coadjutants in the treatment and prevention of diseases related to oxidative stress and for the development of natural nutraceutical products.

Genome-wide analysis of the heat shock transcription factor family reveals saline-alkali stress responses in Xanthoceras sorbifolium.

The heat shock transcription factor (HSF) family is involved in regulating growth, development, and abiotic stress. The characteristics and biological functions of HSF family member in X. sorbifolium, an important oil and ornamental plant, have never been reported. In this study, 21 XsHSF genes were identified from the genome of X. sorbifolium and named XsHSF1-XsHSF21 based on their chromosomal positions. Those genes were divided into three groups, A, B, and C, containing 12, one, and eight genes, respectively. Among them, 20 XsHSF genes are located on 11 chromosomes. Protein structure analysis suggested that XsHSF proteins were conserved, displaying typical DNA binding domains (DBD) and oligomerization domains (OD). Moreover, HSF proteins within the same group contain specific motifs, such as motif 5 in the HSFC group. All XsHSF genes have one intron in the CDS region, except XsHSF1 which has two introns. Promoter analysis revealed that in addition to defense and stress responsiveness elements, some promoters also contained a MYB binding site and elements involved in multiple hormones responsiveness and anaerobic induction. Duplication analysis revealed that XsHSF1 and XsHSF4 genes were segmentally duplicated while XsHSF2, XsHSF9, and XsHSF13 genes might have arisen from transposition. Expression pattern analysis of leaves and roots following salt-alkali treatment using qRT-PCR indicated that five XsHSF genes were upregulated and one XsHSF gene was downregulated in leaves upon NaCl treatment suggesting these genes may play important roles in salt response. Additionally, the expression levels of most XsHSFs were decreased in leaves and roots following alkali-induced stress, indicating that those XsHSFs may function as negative regulators in alkali tolerance. MicroRNA target site prediction indicated that 16 of the XsHSF genes may be regulated by multiple microRNAs, for example XsHSF2 might be regulated by miR156, miR394, miR395, miR408, miR7129, and miR854. And miR164 may effect the mRNA levels of XsHSF3 and XsHSF17, XsHSF9 gene may be regulated by miR172. The expression trends of miR172 and miR164 in leaves and roots on salt treatments were opposite to the expression trend of XsHSF9 and XsHSF3 genes, respectively. Promoter analysis showed that XsHSFs might be involved in light and hormone responses, plant development, as well as abiotic stress responses. Our results thus provide an overview of the HSF family in X. sorbifolium and lay a foundation for future functional studies to reveal its roles in saline-alkali response.

The morphoanatomy of Serjania erecta Radlk (Sapindaceae) provides evidence of biotrophic interactions by endophytic fungi within leaves.

Background: The leaves of Serjania erecta Radlk (Sapindaceae) are renowned in ethnobotany for their medicinal properties and are significant as a medicinal resource for traditional Brazilian communities. As necrotic spots are common on these leaves, indicating interaction with phytopathogenic fungi, it was hypothesized that biotrophic fungal species colonize the leaf tissues of S. erecta. Methods: To test this hypothesis, we employed standard techniques in plant anatomy, which enabled us to investigate the interaction of fungal structures with plant tissues and describe the morphoanatomical and histochemical characteristics of the epidermis and limbus of S. erecta. Results: The anatomical analysis showed the existence of leaf teeth on the leaf tips. Additionally, hyphae, conidiospores, and spores of Bipolaris/Curvularia species were detected on the adaxial epidermis. Moreover, melanized microsclerotia were found in glandular areas of the leaf teeth and the phloem, providing evidence of biotrophic behavior. The hypothesis that biotrophic phytopathogenic fungi interact with S. erecta leaf tissues was confirmed, despite the presence of many bioactive compounds (such as flavonoids, alkaloids, and essential oils), as evidenced by histochemical analyses. The presence of tector, glandular, and scabiform trichomes on the leaf teeth and epidermis was also revealed. This study presents, for the first time, the synthesis of essential oils and alkaloids in the leaves of S. erecta. Additionally, it investigates previously unexplained aspects of the anatomy and histochemistry of the species, as well as its interaction with resident microorganisms. Therefore, it is recommended that future research focus on extracting and characterizing the oils and alkaloids of S. erecta, as well as exploring other aspects related to its microbiome and its relationship.

Molecular phylogeny of Urvillea (Paullinieae, Sapindaceae) and its implications in stem vascular diversity.

BACKGROUND AND AIMS: The tribe Paullinieae has the highest diversity of vascular variants among the seed plants. The developmental diversity is better understood in the species-rich genera Paullinia and Serjania; however, the phylogeny and diversity of vascular variants in the smaller genera of Paullinieae remain understudied. Here we investigate the evolution of development of stem vasculatures in the small genus Urvillea. METHODS: We generate the first molecular phylogeny of Urvillea derived from 11 markers using a maximum likelihood and Bayesian approach. In combination with phylogenetic reconstruction, stochastic character mapping is used to assess evolutionary changes in stem ontogenies, determined from developmental anatomy of stems collected in the field or from herbarium and wood collections. KEY RESULTS: Urvillea is supported as a monophyletic group and sister to Serjania. There are five stem ontogenies in Urvillea, including typical growth and four different vascular variants. Most stem ontogenies initiate with lobed stems in primary growth. Lobed stems in secondary growth are ancestral in Urvillea, but this ontogeny was lost multiple times. A reversal to typical growth occurred in non-climbing species. Phloem wedges, fissured stems, and ectopic cambia each evolved once independently. Phloem wedges is an intermediate developmental stage in the formation of fissured stems, which is characterized by a continuous fragmentation of vascular tissues. Lobed stems may generate constriction zones and lobes may split or not. CONCLUSIONS: Urvillea is the third most diverse genus (after Serjania and Paullinia) with respect to the number of vascular variants within Paullinieae. One ontogeny (fissured stems) is exclusive to the genus. Differential cambial activity and ectopic cambia are the main ontogenetic processes generating stem diversity. The evolutionary history of vascular variants demonstrates the large developmental plasticity of the cambium in such a small genus and further demonstrates that complex anatomies have repeatedly evolved within Paullinieae lianas.

Effects of pretreatment methods on the physicochemical properties of dried longan (Dimocarpus longan Lour.) pulps.

Several pretreatment methods were used before hot air drying to determine the effects of pretreatment on the physicochemical properties of dried longan pulps to address issues of low efficiency and excessive browning of pulps in dried longan. The results showed that pretreatment methods such as sodium chloride steeping, hot blanching, and freeze-thawing reduced the moisture content in dried longan pulps and increased the hardness of dried longan pulps. Ultrasound, microwave, and hot blanching methods reduced the degree of browning of dried longan pulps. Freeze thawing led to a decrease in polysaccharide content in dried longan pulps. The use of ultrasound- and microwave-based pretreatment methods increased the contents of free phenolics and total phenolics and increased the oxygen radical absorbance capacity indices. Alkenes and alcohols constituted the primary volatile flavor substances in longan. It was inferred that it was favorable to use the hot blanching method before subjecting the samples to conditions of hot air drying as the moisture content and degree of browning could be reduced effectively. The results reported herein can potentially help manufacturers improve drying efficiency. The results provide a platform to produce high-quality products from dried longan pulps. PRACTICAL APPLICATION: Longan pulps should be subjected to conditions of the hot blanching method before subjecting the samples to conditions of hot air drying to reduce the moisture content and degree of browning. The results reported herein can help manufacturers improve the drying efficiency of pulps. The results can be exploited to produce high-quality products from dried longan pulps.

Optimization of Supercritical Fluid CO2 Extraction from Yellow Horn Seed and Its Anti-Fatigue and Antioxidant Activity.

A supercritical fluid carbon dioxide (SF-CO2) extraction method was used to obtain the optimum process for extracting yellow horn seed oil. The anti-fatigue and antioxidant properties of the extracted oil were investigated through animal experiments. The optimum process conditions for SF-CO2 extraction of the yellow horn oil were 40 MPa, 50 °C and 120 min, with an extraction yield of 31.61%. The high-dose group of yellow horn oil could significantly increase the weight-bearing swimming time, the hepatic glycogen (HG) content and decrease the lactic acid (LA) content and blood urea nitrogen (BUN) content (p < 0.05) in mice. Moreover, it improved the antioxidant ability by reducing the malondialdehyde (MDA) content (p < 0.01) and raising the glutathione reductase (GR) content and superoxide dismutase (SOD) content (p < 0.05) in mice. Yellow horn oil has the effects of being an anti-fatigue and antioxidant substance, which provides a basis for its further utilization and development.

Genome-wide high-throughput chromosome conformation capture analysis reveals hierarchical chromatin interactions during early somatic embryogenesis.

Somatic embryogenesis (SE), like zygotic embryo development, is a progressive process. Early SE is the beginning of a switch from a somatic to an embryogenic state and is an important stage for initiating chromatin reprogramming of SE. Previous studies suggest that changes in chromatin accessibility occur during early SE, although information on the 3D structure of chromatin is not yet available. Here, we present a chromosome-level genome assembly of longan (Dimocarpus longan) using PacBio combined with high-through chromosome conformation capture scaffolding, which resulted in a 446 Mb genome assembly anchored onto 15 scaffolds. During early SE, chromatin was concentrated and then decondensed, and a large number of long terminal repeat retrotransposons (LTR-RTs) were enriched in the local chromatin interaction region, suggesting LTR-RTs were involved in chromatin reorganization. Early SE was accompanied by the transformation from A to B compartments, and the interactions between B compartments were enhanced. Results from chromatin accessibility, monomethylation of histone H3 at lysine 4 (H3K4me1) modification, and transcription analyses further revealed a gene regulatory network for cell wall thickening during SE. Particularly, we found that the H3K4me1 differential peak binding motif showed abnormal activation of ethylene response factor transcription factors and participation in SE. The chromosome-level genomic and multiomics analyses revealed the 3D conformation of chromatin during early SE, providing insight into the molecular mechanisms underlying cell wall thickening and the potential regulatory networks of TFs during early SE in D. longan. These results provide additional clues for revealing the molecular mechanisms of plant SE.