Cloning and functional mechanism of the dwarf gene gba affecting stem elongation and cellulose biosynthesis in jute (Corchorus olitorius).

Plant height (PH) is an important factor affecting bast fiber yield in jute. Here, we report the mechanism of dwarfism in the 'Guangbaai' (gba) of jute. The mutant gba had shorter internode length and cell length compared to the standard cultivar 'TaiZi 4' (TZ4). Exogenous GA3 treatment indicated that gba is a GA-insensitive dwarf mutant. Quantitative trait locus (QTL) analysis of three PH-related traits via a high-density genetic linkage map according to re-seq showed that a total of 25 QTLs were identified, including 13 QTLs for PH, with phenotypic variation explained ranging from 2.42 to 74.16%. Notably, the functional mechanism of the candidate gene CoGID1a, the gibberellic acid receptor, of the major locus qPHIL5 was evaluated by transgenic analysis and virus-induced gene silencing. A dwarf phenotype-related single nucleotide mutation in CoGID1a was identified in gba, which was also unique to the dwarf phenotype of gba among 57 cultivars. Cogid1a was unable to interact with the growth-repressor DELLA even in the presence of highly accumulated gibberellins in gba. Differentially expressed genes between transcriptomes of gba and TZ4 after GA3 treatment indicated up-regulation of genes involved in gibberellin and cellulose synthesis in gba. Interestingly, it was found that up-regulation of CoMYB46, a key transcription factor in the secondary cell wall, by the highly accumulated gibberellins in gba promoted the expression of cellulose synthase genes CoCesA4 and CoCesA7. These findings provide valuable insights into fiber development affected by endogenous gibberellin accumulation in plants.

The sequential microbial breakdown of pectin is the principal incident during water retting of jute (Corchorus spp.) bast fibres.

The extraction of bast fibres such as jute from plant stems involves the removal of pectin, hemicellulose, and other noncellulosic materials through a complex microbial community. A consortium of pectinolytic bacterial strains has been developed and commercialized to reduce the retting time and enhance fibre quality. However, there are currently no studies on jute that describe the structural changes and sequential microbial colonization and pectin loss that occur during microbe-assisted water retting. This study investigated the stages of microbial colonization, microbial interactions, and sequential degradation of pectic substances from jute bark under controlled and conventional water retting. The primary occurrence during water retting of bast fibres is the bacterially induced sequential breakdown of pectin surrounding the fibre bundles. The study also revealed that the pectin content of the jute stem significantly decreases during the retting process. These findings provide a strong foundation for improving microbial strains for improved pectinolysis with immense industrial significance, leading to a sustainable jute-based "green" economy.

Multi-omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius).

Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi-omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome-wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole-3-acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.

Evolution and expression analysis of the caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene family in jute (Corchorus L.).

BACKGROUND: Jute is considered one of the most important crops for fiber production and multipurpose usages. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a crucial enzyme involved in lignin biosynthesis in plants. The potential functions of CCoAOMT in lignin biosynthesis of jute have been reported in several studies. However, little is known about the evolution of the CCoAOMT gene family, and either their expression level at different developing stages in different jute cultivars, as well as under abiotic stresses including salt and drought stress. RESULTS: In the present study, 66 CCoAOMT genes from 12 species including 12 and eight CCoAOMTs in Corchorus olitorius and C. capsularis were identified. Phylogenetic analysis revealed that CCoAOMTs could be divided into six groups, and gene expansion was observed in C. olitorius. Furthermore, gene expression analysis of developing jute fibers was conducted at different developmental stages (15, 30, 45, 60, and 90 days after sowing [DAS]) in six varieties (Jute-179 [J179], Lubinyuanguo [LB], and Qiongyueqing [QY] for C. capsularis; Funong No.5 [F5], Kuanyechangguo [KY], and Cvlv [CL] for C. olitorius). The results showed that CCoAOMT1 and CCoAOMT2 were the dominant genes in the CCoAOMT family. Of these two dominant CCoAOMTs, CCoAOMT2 showed a constitutive expression level during the entire growth stages, while CCoAOMT1 exhibited differential expression patterns. These two genes showed higher expression levels in C. olitorius than in C. capsularis. The correlation between lignin content and CCoAOMT gene expression levels indicated that this gene family influences the lignin content of jute. Using real-time quantitative reverse transcription PCR (qRT-PCR), a substantial up-regulation of CCoAOMTs was detected in stem tissues of jute 24 h after drought treatment, with an up to 17-fold increase in expression compared to that of untreated plants. CONCLUSIONS: This study provides a basis for comprehensive genomic studies of the entire CCoAOMT gene family in C. capsularis and C. olitorius. Comparative genomics analysis among the CCoAOMT gene families of 12 species revealed the close evolutionary relationship among Corchorus, Theobroma cacao and Gossypium raimondii. This study also shows that CCoAOMTs are not only involved in lignin biosynthesis, but also are associated with the abiotic stress response in jute, and suggests the potential use of these lignin-related genes to genetically improve the fiber quality of jute.

Evaluation of the anti-infective potential of the seed endophytic fungi of Corchorus olitorius through metabolomics and molecular docking approach.

BACKGROUND: Endophytic fungi are very rich sources of natural antibacterial and antifungal compounds. The main aim of this study is to isolate the fungal endophytes from the medicinal plant Corchorus olitorius seeds (F. Malvaceae), followed by antimicrobial screening against various bacterial and fungal strains. RESULTS: Seven endophytic fungal strains belonging to different three genera were isolated, including Penicillium, Fusarium, and Aspergillus. The seven isolated endophytic strains revealed selective noticeable activity against Escherichia coli (ATCC25922) with varied IC50s ranging from 1.19 to 10 µg /mL, in which Aspergillus sp. (Ar 6) exhibited the strongest potency against E. coli (ATCC 25,922) and candida albicans (ATCC 10,231) with IC50s 1.19 and 15 µg /mL, respectively. Therefore, the chemical profiling of Aspergillus sp. (Ar 6) crude extract was performed using LC-HR-ESI-MS and led to the dereplication of sixteen compounds of various classes (1-16). In-silico analysis of the dereplicated metabolites led to highlighting the compounds responsible for the antimicrobial activity of Aspergillus sp. extract. Moreover, molecular docking showed the potential targets of the metabolites; Astellatol (5), Aspergillipeptide A (10), and Emericellamide C (14) against E. coli and C. albicans. CONCLUSION: These results will expand the knowledge of endophytes and provide us with new approaches to face the global antibiotic resistance problem and the future production of undiscovered compounds different from the antibiotics classes.

Health risk assessment for uptake and accumulation of pharmaceuticals in jute mallow (Corchorus olitorius) irrigated with treated hospital wastewater.

The use of reclaimed water for crop irrigation presents a route through which pharmaceuticals enter the agro-environment, raising concerns about their potential inclusion into the food chain and associated health risks. The main objective of this study was to determine the accumulation of six pharmaceuticals (paracetamol, diclofenac and ibuprofen, ciprofloxacin, tetracycline, and sulfamethoxazole) in edible part of jute mallow (JM) (Corchorus olitorius) irrigated with treated hospital wastewater (THWW) and potential health risks associated with the consumption of the contaminated JM. In a greenhouse experiment, JM vegetable was grown in soils irrigated with groundwater and THWW. After 4 weeks of cultivation, the pharmaceutical concentrations in the soil and JM tissues were determined. The uptake and accumulation of the pharmaceuticals in the irrigated JM and the human health risks associated with their consumption were evaluated. Results showed that the THWW-irrigated and groundwater-irrigated soils accumulated all the studied pharmaceuticals except paracetamol and sulfamethoxazole, with the concentrations in the soil before and after irrigation ranging from 0.01 to 0.14 µg g-1 and 0.03 to 1.35 µg g-1, respectively. In JM leaves, the accumulation was in the order of tetracycline > ciprofloxacin > ibuprofen > diclofenac and tetracycline > ciprofloxacin > diclofenac > ibuprofen under THWW-irrigated and groundwater-irrigated treatments, respectively. Under both treatments, the uptake and accumulation of the studied pharmaceuticals were in the order of roots > stem > leaves. The health risk assessment indicated that the consumption of the studied pharmaceuticals through JM implies some risks to human health and the risks were in the order of tetracycline > diclofenac > ciprofloxacin > ibuprofen > paracetamol > sulfamethoxazole. This study has demonstrated that irrigation with reclaimed water is a major route of pharmaceuticals into the food chain and a key determinant of associated health risks.

Antimicrobial Bioactivity and GC-MS Analysis of Different Extracts of Corchorus olitorius L Leaves.

Results: Crude extracts of Corchorus olitorius L leaves and their TLC-separated components demonstrated bioactivity against Staphylococcus aureus (14 mm), Streptococcus pneumoniae (16 mm), and Escherichia coli (11 mm) but neither against Candida albicans nor Mycobacteria tuberculosis. However, the overall zones of inhibition were smaller compared to the positive control (≥18 mm). GC-MS analysis of the active components revealed the presence of methyl esters. Conclusion: Corchorus olitorius L is bioactive against both Gram-negative and Gram-positive bacteria but neither against fungi nor mycobacteria. The bioactivity is attributable to the presence of methyl esters. Since methyl esters already have proven bioactivity in some studies, they could be further studied and optimized for possible pharmaceutical use. Further, to provide a more comprehensive antimicrobial spectrum of Corchorus olitorius L in Uganda, purified active components could be investigated using a wider range of organisms.

Phytochemical Analysis, Acute Toxicity, as well as Antihyperglycemic and Antidiabetic Activities of Corchorus olitorius L. Leaf Extracts.

Backgroundand Aim. Diabetes mellitus is a metabolic disorder that has no known cure with continuous endeavors to find a therapy for the condition. According to some studies, traditional leafy vegetables could prevent and manage diabetes by modifying the carbohydrate and lipid metabolism. In this study, a phytochemical analysis, acute toxicity, as well as antihyperglycemic and antidiabetic activity testing of the methanolic, diethyl ether, and aqueous leaf extracts of Corchorus olitorius L. was performed. Materials and Methods. Methanolic, diethyl ether, and aqueous leaf extracts of Corchorus olitorius L. were prepared by serial extraction. Phytochemical analysis was performed following standard methods. 52 mice were separated into 13 groups (A-M) of 4 and received extracts' doses ranging from 1000 mg/kg to 5000 mg/kg for the acute toxicity testing. For the antihyperglycemic and antidiabetic activities testing, 48 rats were divided into 8 groups of 6 and received 500 mg/kg of each extract. 10 mg/kg of glibenclamide and distilled water were used as controls. Data were analyzed using Prism GraphPad version 8.0.2 (263). Results. Phytochemical analysis revealed the presence of alkaloids, reducing sugars, saponins, and terpenoids. There were no acute toxicity signs observed in this study. Corchorus olitorius L. extracts demonstrated moderate antihyperglycemic and antidiabetic activities. The methanolic extract exhibited the highest degree of antihyperglycemic activity. However, there was no statistically significant difference between the extracts and the negative control (p > 0.05), but with glibenclamide (p < 0.01). Conclusion. Corchorus olitorius L. is a safe and potential postprandial antidiabetic vegetable that could minimize the rise in blood glucose after a meal. We therefore recommend further investigations into the antidiabetic properties of the vegetable using purified extracts.

Ecofriendly Green Synthesis of Copper (II) Oxide Nanoparticles Using Corchorus olitorus Leaves (Molokhaia) Extract and Their Application for the Environmental Remediation of Direct Violet Dye via Advanced Oxidation Process.

In this research, copper (II) oxide nanoparticles were prepared by an ecofriendly green method using the extract of corchorus olitorus leaves (Molokhaia) as a surfactant, capping and anti-agglomeration agent. The ecofriendly green CuO NPs were characterized using different chemical and physical techniques and the results confirmed the formation of monoclinic tenorite CuO nanoparticles with an average particle size of 12 nm and BET surface area of 11.1 m2/g. The eco-friendly green CuO NPs were used in environmental remediation for the efficient catalytic degradation of direct violet dye via advanced oxidation process (AOP) in presence of H2O2. The impact of AOP environmental parameters affecting the degradation process was investigated. Moreover, the catalytic degradation of the direct violet dye using the ecofriendly green CuO NPs was studied kinetically and thermodynamically and the results showed that the catalytic degradation process agreed well with the pseudo-second-order kinetic model and the process was spontaneous and endothermic in nature. Finally, high catalytic degradation of the direct violet dye was observed when the eco-friendly prepared green CuO NPs were placed in real water samples.

The Potential of Corchorus olitorius Seeds Buccal Films for Treatment of Recurrent Minor Aphthous Ulcerations in Human Volunteers.

Aphthous ulcers are very common disorders among different age groups and are very noxious and painful. The incidence of aphthous ulcer recurrence is very high and it may even last for a maximum of 6 days and usually, patients cannot stand its pain. This study aims to prepare a buccoadhesive fast dissolving film containing Corchorus olitorius seed extract to treat recurrent minor aphthous ulceration (RMAU) in addition to clinical experiments on human volunteers. An excision wound model was used to assess the in vivo wound healing potential of Corchorus olitorius L. seed extract, with a focus on wound healing molecular targets such as TGF-, TNF-, and IL-1. In addition, metabolomic profiling using HR-LCMS for the crude extract of Corchorus olitorius seeds was explored. Moreover, molecular docking experiments were performed to elucidate the binding confirmation of the isolated compounds with three molecular targets (TNF-α, IL-1ß, and GSK3). Additionally, the in vitro antioxidant potential of C. olitorius seed extract using both H2O2 and superoxide radical scavenging activity was examined. Clinical experiments on human volunteers revealed the efficiency of the prepared C. olitorius seeds buccal fast dissolving film (CoBFDF) in relieving pain and wound healing of RMAU. Moreover, the wound healing results revealed that C. olitorius seed extract enhanced wound closure rates (p ≤ 0.001), elevated TGF-ß levels and significantly downregulated TNF-α and IL-1ß in comparison to the Mebo-treated group. The phenotypical results were supported by biochemical and histopathological findings, while metabolomic profiling using HR-LCMS for the crude extract of Corchorus olitorius seeds yielded a total of 21 compounds belonging to diverse chemical classes. Finally, this study highlights the potential of C. olitorius seed extract in wound repair uncovering the most probable mechanisms of action using in silico analysis.

Effect of Common Cooking and Drying Methods on Phytochemical and Antioxidant Properties of Corchorus olitorius Identified Using Liquid Chromatography-Mass Spectrometry (LC-MS).

In this study, Corchorus olitorius leaves were subjected to different thermal treatments (blanching, boiling, drying, frying, and steaming) and analyzed, total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity. Furthermore, Fourier transform infrared spectroscopy (FTIR) was used to identify functional groups, while metabolites were identified with LC-MC. The TPC and antioxidant activity of C. olitorius were significantly (p < 0.05) increased by cooking and drying. The steam-cooked sample had the highest TPC (18.89 mg GAE/g) and TFC (78.42 mg QE/g). With ABTS, FRAP, and DPPH assays, the steam-cooked sample exhibited the highest antioxidant activity of 119.58, 167.31, and 122.23 µM TE/g, respectively. LC-MS identified forty-two (42) metabolites in C. olitorius that included phenolic acid derivatives, flavonoid derivatives, and amino acid derivatives. Overall, steaming appears to be the best cooking method, with respect to the retention of phytochemical compounds and antioxidant activity.

Net ecosystem CO2 exchange from jute crop (Corchorus olitorius L.) and its environmental drivers in tropical Indo-Gangetic plain using open-path eddy covariance technique.

Present study is a maiden attempt to assess net ecosystem exchange (NEE) of carbon dioxide (CO2) flux from jute crop (Corchorus olitorius L.) in the Indo-Gangetic plain by using open-path eddy covariance (EC) technique. Diurnal variations of NEE were strongly influenced by growth stages of jute crop. Daytime peak NEE varied from - 5 µmol m-2 s-1 (in germination stage) to - 23 µmol m-2 s-1 (in fibre development stage). The ecosystem was net CO2 source during nighttime with an average NEE value of 5-8 µmol m-2 s-1. Combining both daytime and nighttime CO2 fluxes, jute ecosystem was found to be a net CO2 sink on a daily basis except the initial 9 days from date of sowing. Seasonal and growth stage-wise NEEs were computed, and the seasonal total NEE over the jute season was found to be - 268.5 gC m-2 (i.e. 10.3 t CO2 ha-1). In different jute growth stages, diurnal variations of NEE were strongly correlated (R2 > 0.9) with photosynthetic photon flux density (PPFD). Ecosystem level photosynthetic efficiency parameters were estimated at each growth stage of jute crop using the Michaelis-Menten equation. The maximum values of photosynthetic capacity (Pmax, 63.3 ± 1.15 µmol CO2 m-2 s-1) and apparent quantum yield (α, 0.072 ± 0.0045 µmol CO2 µmol photon-1) were observed during the active vegetative stage, and the fibre development stage, respectively. Results of the present study would significantly contribute to understanding of the carbon flux from the Indian agro-ecosystems, which otherwise are very sparse.

Reference genomes of the two cultivated jute species.

Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome-level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo-chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole-genome resequencing resulted in post-domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker-trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome-wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.

Present Status and Future Prospects of Jute in Nanotechnology: A Review.

Nanotechnology has transformed the world with its diverse applications, ranging from industrial developments to impacting our daily lives. It has multiple applications throughout financial sectors and enables the development of facilitating scientific endeavors with extensive commercial potentials. Nanomaterials, especially the ones which have shown biomedical and other health-related properties, have added new dimensions to the field of nanotechnology. Recently, the use of bioresources in nanotechnology has gained significant attention from the scientific community due to its 100 % eco-friendly features, availability, and low costs. In this context, jute offers a considerable potential. Globally, its plant produces the second most common natural cellulose fibers and a large amount of jute sticks as a byproduct. The main chemical compositions of jute fibers and sticks, which have a trace amount of ash content, are cellulose, hemicellulose, and lignin. This makes jute as an ideal source of pure nanocellulose, nano-lignin, and nanocarbon preparation. It has also been used as a source in the evolution of nanomaterials used in various applications. In addition, hemicellulose and lignin, which are extractable from jute fibers and sticks, could be utilized as a reductant/stabilizer for preparing other nanomaterials. This review highlights the status and prospects of jute in nanotechnology. Different research areas in which jute can be applied, such as in nanocellulose preparation, as scaffolds for other nanomaterials, catalysis, carbon preparation, life sciences, coatings, polymers, energy storage, drug delivery, fertilizer delivery, electrochemistry, reductant, and stabilizer for synthesizing other nanomaterials, petroleum industry, paper industry, polymeric nanocomposites, sensors, coatings, and electronics, have been summarized in detail. We hope that these prospects will serve as a precursor of jute-based nanotechnology research in the future.

Anticancer Effects of the Corchorus olitorius Aqueous Extract and Its Bioactive Compounds on Human Cancer Cell Lines.

Corchorus olitorius is a common, leafy vegetable locally known as "Saluyot" in the Philippines. Several studies have reported on its various pharmacological properties, such as antioxidant, anti-inflammatory, analgesic, and anticancer properties. However, little is known about its effects on angiogenesis. This study aimed to evaluate the anticancer properties, such as the antiproliferative, anti-angiogenic, and antitumor activities, of the C. olitorius aqueous extract (CO) and its bioactive compounds, chlorogenic acid (CGA) and isoquercetin (IQ), against human melanoma (A-375), gastric cancer (AGS), and pancreatic cancer (SUIT-2), using in vitro and in ovo biological assays. The detection and quantification of CGA and IQ in CO were achieved using LC-MS/MS analysis. The antiproliferative, anti-angiogenic, and antitumor activities of CO, CGA, and IQ against A-375, AGS, and SUIT-2 cancer cell lines were evaluated using MTT and CAM assays. CGA and IQ were confirmed to be present in CO. CO, CGA, and IQ significantly inhibited the proliferation of A-375, AGS, and SUIT-2 cancer cells in a dose-dependent manner after 48 h of treatment. Tumor angiogenesis (hemoglobin levels) of A-375 and AGS tumors was significantly inhibited by CO, CGA, IQ, and a CGA-IQ combination. The growth of implanted A-375 and AGS tumors was significantly reduced by CO, CGA, IQ, and a CGA-IQ combination, as measured in tumor weight. Our investigation provides new evidence to show that CO has promising anticancer effects on various types of human cancer cells. CO and its compounds are potential nutraceutical products that could be used for cancer treatment.

Assessing lodging damage of jute crop due to super cyclone Amphan using multi-temporal Sentinel-1 and Sentinel-2 data over parts of West Bengal, India.

The present study is a maiden attempt to assess jute crop lodging due to super cyclone Amphan (20 May 2020) by synergistic use of Sentinel-2 (optical) and Sentinel-1 (SAR) data over part of West Bengal, India. Pre-event Sentinel-2 data (9 April, 14 May) along with the ground information were used to map the jute crop of the affected districts with accuracy of 85%. The cross-polarized backscatter (σ0VH) of Sentinel-1 was found to be sensitive to the sudden change in the canopy structure due to lodging and partial flooding. [Formula: see text](σ0VH_22 May - σ0VH_16 May) indicating post-event damage was > 2.5 dB over the affected jute crop and [Formula: see text] (σ0VH_22 May - σ0VH_28 May) representing post-event recovery showed > 1.5 dB for recovered crop, depending on the crop vigor/height. Decision matrix was prepared combining [Formula: see text] and [Formula: see text] for NDVI-based crop vigor strata (low, medium, and high) to classify the area into affected, marginally affected and normal. Overall accuracy of the classified map was found to be 84.12% with kappa coefficient of 0.74. Nearly, 12.5% of the jute area, i.e., 38,119 ha was found to be either affected or marginally affected due to Amphan and distributed in the southern part of Murshidabad, north-eastern Nadia, northern 24 Paraganas (N), and middle region of Hooghli district. Geospatial map of block-wise affected jute area was prepared to facilitate informed decision making. The study demonstrated an operational methodology for assessing crop lodging due to natural calamities to support relief management and crop insurance.

Gene coexpression network analysis and tissue-specific profiling of gene expression in jute (Corchorus capsularis L.).

BACKGROUND: Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially cultivated species of jute. Gene expression is spatiotemporal and is influenced by many factors. Therefore, to understand the molecular mechanisms of tissue development, it is necessary to study tissue-specific gene expression and regulation. We used weighted gene coexpression network analysis, to predict the functional roles of gene coexpression modules and individual genes, including those underlying the development of different tissue types. Although several transcriptome studies have been conducted on C. capsularis, there have not yet been any systematic and comprehensive transcriptome analyses for this species. RESULTS: There was significant variation in gene expression between plant tissues. Comparative transcriptome analysis and weighted gene coexpression network analysis were performed for different C. capsularis tissues at different developmental stages. We identified numerous tissue-specific differentially expressed genes for each tissue, and 12 coexpression modules, comprising 126 to 4203 genes, associated with the development of various tissues. There was high consistency between the genes in modules related to tissues, and the candidate upregulated genes for each tissue. Further, a gene network including 21 genes directly regulated by transcription factor OMO55970.1 was discovered. Some of the genes, such as OMO55970.1, OMO51203.1, OMO50871.1, and OMO87663.1, directly involved in the development of stem bast tissue. CONCLUSION: We identified genes that were differentially expressed between tissues of the same developmental stage. Some genes were consistently up- or downregulated, depending on the developmental stage of each tissue. Further, we identified numerous coexpression modules and genes associated with the development of various tissues. These findings elucidate the molecular mechanisms underlying the development of each tissue, and will promote multipurpose molecular breeding in jute and other fiber crops.

Genome-wide identification, characterization and expression profiling of gibberellin metabolism genes in jute.

BACKGROUND: Gibberellin (GA) is one of the most essential phytohormones that modulate plant growth and development. Jute (Corchorus sp.) is the second most important source of bast fiber. Our result has shown that exogenous GA can positively regulate jute height and related characteristics which mean increasing endogenous GA production will help to get a jute variety with improved characteristics. However, genes involved in jute GA biosynthesis have not been analyzed precisely. RESULTS: Genome-wide analysis identified twenty-two candidate genes involved in jute GA biosynthesis pathway. Among them, four genes- CoCPS, CoKS, CoKO and CoKAO work in early steps. Seven CoGA20oxs, three CoGA3oxs, and eight GA2oxs genes work in the later steps. These genes were characterized through phylogenetic, motif, gene structure, and promoter region analysis along with chromosomal localization. Spatial gene expression analysis revealed that 11 GA oxidases were actively related to jute GA production and four of them were marked as key regulators based on their expression level. All the biosynthesis genes both early and later steps showed tissue specificity. GA oxidase genes were under feedback regulation whereas early steps genes were not subject to such regulation. CONCLUSION: Enriched knowledge about jute GA biosynthesis pathway and genes will help to increase endogenous GA production in jute by changing the expression level of key regulator genes. CoGA20ox7, CoGA3ox2, CoGA2ox3, and CoGA2ox5 may be the most important genes for GA production.

De novo assembly of transcriptome and genome-wide identification reveal GA3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis).

BACKGROUND: WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis. RESULTS: A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress. CONCLUSIONS: A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.

Genome-wide identification of fasciclin-like arabinogalactan proteins in jute and their expression pattern during fiber formation.

Fasciclin-like arabinogalactan proteins (FLAs), a class of arabinogalactan proteins (AGPs) are involved in plant growth and development via cell communication and adhesion. FLAs were also associated with fiber and wood formation in plants but no information is available about the roles of FLA proteins during fibre development of jute. Here, we performed molecular characterization, evolutionary relationship and expression profiling of FLAs proteins in jute (Corchorus olitorius). In total, nineteen CoFLA genes have been identified in jute genome, which were divided into four classes like FLAs of other species based on protein structure and similarity. All CoFLAs have N-terminal signal peptide and one or two FAS domain while two FLAs lack well defined AGP region and eight FLAs were devoid of C-terminal glycosylphosphatidylinositol (GPI) anchor. Expression analysis of different regions of jute stem suggested their involvement in different fiber development stages. Four genes CoFLA 11, 12, 20, and 23 were highly or predominately expressed in fiber containing bark tissues while the expression levels of six CoFLA genes 02, 03, 04, 06, 14 and 19 were comparatively higher in stick. Higher transcripts levels of CoFLA 12 and 20 in the middle bark tissues suggest their involvement in fiber elongation. In contrast, the CoFLA 11 and 23 were more expressed in bottom bark tissues suggesting their potential involvement in secondary cell wall synthesis. Our study can serve as solid foundation for further functional exploration of FLAs and in future breeding program of jute aiming fiber improvement.