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.

Characterization, prebiotic and immune-enhancing activities of rhamnogalacturonan-I-rich polysaccharide fraction from molokhia leaves.

Plant-derived polysaccharides possess potential health benefits that improve intestinal health and the immune system. Molokhia leaves have a large amount of mucilage polysaccharide; in the present study, crude polysaccharide extract was prepared from molokhia leaves. The molecular weight of molokhia leaf polysaccharide fraction (MPF) was estimated to be 51.2 × 103 Da. Polysaccharide was methylated and the structure of MPF was mainly composed of rhamnogalacturonan-I structure with side chains, such as galactans and linear glucan (starch), as shown by GC-MS analysis. To study the biofunctional effects of MPF, its prebiotic and intestinal immune-enhancing activities were assayed in vitro. MPF exhibited good prebiotic activity, as shown by its high prebiotic scores, and increased contents of total short-chain fatty acids on five probiotic strains. In addition, MPF showed immune-enhancing activity on Peyer's patches, as revealed by the high bone marrow cell proliferating activity and production of immunoglobulin A and cytokines. These results demonstrate that MPF may be a potential beneficial prebiotic and intestinal immune-enhancer, which may have wide implications in the food industry.

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.

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, 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.

Pectinolytic Bacterial Consortia Reduce Jute Retting Period and Improve Fibre Quality.

Jute fibre is the second most important fibre next to cotton. It is obtained from the bark of plant through microbial retting process. Here we report optimized microbial retting protocol that can lower retting period and produce high fibre quality. A total of 451 bacterial colonies have been isolated from five jute retting water samples in Bangladesh. Higher pectinolytic bacterial isolates were predominant in the later stage of jute retting. Out of these, 168 isolates have been screened by both semi-quantitative and quantitative pectinase, xylanase and cellulase enzyme assay. Among them, 144 isolates have been selected on the basis of extra cellular enzyme activity of these three enzymes. 16 s ribosomal gene sequencing analysis identified 2 phyla- Firmicutis (80.55%) and Proteobacteria (19.45%). To check the synergistic and antagonistic effect 10 selected isolates were tested in 167 different combinations. Three best combinations were identified that lowered retting period from 18-21 days to 10 days producing high quality fibre in both laboratory and field trial. This improved retting technology can be adopted in industrial scale for the production of quality jute fibre in a controlled condition in reduced water quantity without polluting the environment.

Influence of phosphorus on copper phytoextraction via modulating cellular organelles in two jute (Corchorus capsularis L.) varieties grown in a copper mining soil of Hubei Province, China.

Soil in mining areas is typically highly contaminated with heavy metals and lack essential nutrients for plants. Phosphorus reduces oxidative stress, improves plant growth, composition, and cellular structure, as well as facilitates the phytoremediation potential of fibrous crop plant species. In this study, we investigated two jute (Corchorus capsularis) varieties HongTieGuXuan and GuBaChangJia cultivated in copper (Cu)-contaminated soil (2221 mg kg-1), under different applications of phosphorus (0, 30, 60, and 120 kg ha-1) at both anatomical and physiological levels. At the same Cu concentration, the tolerance index of HongTieGuXuan was higher than that of GuBaChangJia, indicating that HongTieGuXuan may be more tolerant to Cu stress. Although the normal concentration of P (60 kg ha-1) in the soil improved plant growth, biomass, chlorophyll content, fibre yield and quality, and gaseous exchange attributes. However, high concentration of P (120 kg ha-1) was toxic to both jute varieties affected morphological and physiological attributes of the plants under same level of Cu. Moreover, Cu toxicity increased the oxidative stress in the leaves of both jute varieties was overcome by the activities of antioxidant enzymes. Furthermore, the high concentration of Cu altered the ultrastructure of chloroplasts, plastoglobuli, mitochondria, and many other cellular organelles in both jute varieties. Thus, phytoextraction of Cu by both jute varieties increased with the increase in P application in the Cu-contaminated soil. This suggests that P application enhanced the phytoremediation potential jute plants and can be cultivated as fibrous crop in Cu-contaminated sites.

Morpho-physiological traits, gaseous exchange attributes, and phytoremediation potential of jute (Corchorus capsularis L.) grown in different concentrations of copper-contaminated soil.

Jute (Corchorus capsularis L.) is the most commonly used natural fiber as reinforcement in green composites and, due to its huge biomass, deep rooting system, and metal tolerance in stressed environments, it is an excellent candidate for the phytoremediation of different heavy metals. Therefore, the present study was carried out to examine the growth, antioxidant capacity, gaseous exchange attributes, and phytoremediation potential of C. capsularis grown at different concentrations of Cu (0, 100, 200, 300, and 400 mg kg-1) in a glass house environment. The results illustrate that C. capsularis can tolerate Cu concentrations of up to 300 mg kg-1 without significant decreases in growth or biomass, but further increases in Cu concentration (i.e., 400 mg kg-1) lead to significant reductions in plant growth and biomass. The photosynthetic pigments and gaseous exchange attributes in the leaves of C. capsularis decreased as the Cu concentration in the soil increased. Furthermore, high concentrations of Cu in the soil caused lipid peroxidation by increasing the malondialdehyde content in the leaves. This implies that elevated Cu levels cause oxidative damage in C. capsularis. Antioxidants, such as superoxidase dismutase and peroxidase, come into play to scavenge the reactive oxygen species which are generated as a result of oxidative stress. In the present study, the concentrations of Cu in different parts of the plant (the roots, leaves, stem core, and fibers) were also investigated at four different stages of the life cycle of C. capsularis, i.e., 30, 60, 90, and 120 days after sowing (DAS). The results of this investigation reveal that, in the earlier stages of the growth, Cu was highly accumulated in the belowground parts of the plant while little was transported to the aboveground parts. Contrastingly, at a fully mature stage of the growth (120 DAS), it was observed that the majority of Cu was transported to the aboveground parts of the plant and very little accumulated in the belowground parts. The results also show a progressive increase in Cu uptake in response to increasing Cu concentrations in the soil, suggesting that C. capsularis is a potential bio-resource for the phytoremediation of Cu in Cu-contaminated soil.

Impact of conventional retting of jute (Corchorus spp.) on the environmental quality of water: a case study.

Production of quality jute fibre primarily depends on the retting process of jute. However, the quality of retting water is of great concern because of the scarcity of available water bodies for retting. A study conducted on physico-chemical and microbiological changes in retting water (pre- and post-retting) from four intensively jute-growing districts namely Nadia, North 24 Parganas, Hooghly and South Dinajpur of West Bengal, India, during jute retting. The post-retting water samples recorded lower pH (6.22 to 7.08) and higher EC (electrical conductivity) (0.509 to 0.850 ds/m) compared with pre-retting water samples (pH 6.63 to 7.44; EC 0.197 to 0.330 ds/m) collected from all the four districts under study. The biological oxygen demand (BOD) and chemical oxygen demand (COD) increased several folds in the post-retting water samples indicating very high microbial growth and activities and depleted oxygen level compared with pre-retting water. The Ca + Mg (calcium + magnesium) content in pre-retting water was high (24.15 to 36.60 ppm) which raised further (61.30 to 103.67 ppm) in post-retting water, while the bicarbonate content also increased and ranged between 2.72 and 6.81 me/l in post-retting water compared with its status in pre-retting water (1.30 to 3.15 me/l). The post-retting water was found to be a rich source of nutrients like nitrogen (N), phosphorus (P), iron (Fe), manganese (Mn), zinc (Zn) and copper (Cu) which increased substantially because of jute retting as compared with their status in pre-retting water. The population of pectinolytic, xylanolytic, cellulolytic and ligninolytic bacterial cfu (colony forming unit) increased by 1.5 times in post-retting water as compared with pre-retting water, because these specific bacterial population were involved in the degradation of pectin, xylan, cellulose and lignin during retting of jute. Thus, post-retting water can be judiciously used as a potent source of primary, secondary and micronutrients for succeeding crops besides having higher BOD and COD as a result of higher microbial growth related to jute retting.

Effects of peat on plant growth and lead and zinc phytostabilization from lead-zinc mine tailing in southern China: Screening plant species resisting and accumulating metals.

In order to investigate the toxicity-resistance of eighteen Chinese native plants in lead (Pb)-zinc (Zn) mine tailings, we categorized their resistance to Pb and Zn, and tested their potential for phytoremediation effectiveness of Pb and Zn. Fourteen woody plant species belonging to 12 families, and 4 herbaceous species belonging to 4 families, were grown in pots with mixtures of 100% tailing +0% peat (CK), 90% tailing +10% peat (A1), and 80% tailing + 20% peat (A2), respectively. Plant height and biomass, chlorophyll content, and Pb and Zn contents of non-rhizosphere spoil mixtures and plant tissues were measured. Fifteen of the plants grew in all three spoil mixtures. Both A1 and A2 had higher plant height and biomass increment and chlorophyll contents than CK. The content of Pb and Zn in plant shoots and roots was CK > A1 > A2. The value of BCF less than 0.1, compared to 1, was a more precise classification basis for plants excluding metals. Screening for Pb and Zn resistant plants and their bioremediation potential produced the following candidate species: Sapium sebiferum, Salix matsudana, Hibiscus cannabinus, Corchorus capsularis, Ricinus communis, and Populus nigra. These species were highly Pb and Zn tolerant species, with notable growth characteristics and capacities to bioaccumulate Pb and Zn from the mine tailings. Compared to CK, the removal of Pb and Zn from non-rhizosphere spoil increased by an average of 9.64% and 9.6%, respectively in A1, but decreased in A2. The results indicated candidate species and 10% peat addition in the tailing were significant in phytoremediation of Pb and Zn regarding environmental safety.

Transcriptome profiling uncovers ß-galactosidases of diverse domain classes influencing hypocotyl development in jute (Corchorus capsularis L.).

Enzyme ß-galactosidase (EC 3.2.1.23) is known to influence vascular differentiation during early vegetative growth of plants, but its role in hypocotyl development is not yet fully understood. We generated the hypocotyl transcriptome data of a hypocotyl-defect jute (Corchorus capsularis L.) mutant (52,393 unigenes) and its wild-type (WT) cv. JRC-212 (44,720 unigenes) by paired-end RNA-seq and identified 11 isoforms of ß-galactosidase, using a combination of sequence annotation, domain identification and structural-homology modeling. Phylogenetic analysis classified the jute ß-galactosidases into six subfamilies of glycoside hydrolase-35 family, which are closely related to homologs from Malvaceous species. We also report here the expression of a ß-galactosidase of glycoside hydrolase-2 family that was earlier considered to be absent in higher plants. Comparative analysis of domain structure allowed us to propose a domain-centric evolution of the five classes of plant ß-galactosidases. Further, we observed 1.8-12.2-fold higher expression of nine ß-galactosidase isoforms in the mutant hypocotyl, which was characterized by slower growth, undulated shape and deformed cell wall. In vitro and in vivo ß-galactosidase activities were also higher in the mutant hypocotyl. Phenotypic analysis supported a significant (P ≤ 0.01) positive correlation between enzyme activity and undulated hypocotyl. Taken together, our study identifies the complete set of ß-galactosidases expressed in the jute hypocotyl, and provides compelling evidence that they may be involved in cell wall degradation during hypocotyl development.

A Novel Method for the Pentosan Analysis Present in Jute Biomass and Its Conversion into Sugar Monomers Using Acidic Ionic Liquid.

Recently, ionic liquids (ILs) are used for biomass valorization into valuable chemicals because of their remarkable properties such as thermal stability, lower vapor pressure, non-flammability, higher heat capacity, and tunable solubility and acidity. Here, we demonstrate a method for the synthesis of C5 sugars (xylose and arabinose) from the pentosan present in jute biomass in a one-pot process by utilizing a catalytic amount of Brønsted acidic 1-methyl-3-(3-sulfopropyl)-imidazolium hydrogen sulfate IL. The acidic IL is synthesized in the lab and characterized using NMR spectroscopic techniques for understanding its purity. The various properties of BAIL are measured such as acid strength, thermal and hydrothermal stability, which showed that the catalyst is stable at a higher temperature (250 °C) and possesses very high acid strength (Ho 1.57). The acidic IL converts over 90% of pentosan into sugars and furfural. Hence, the presenting method in this study can also be employed for the evaluation of pentosan concentration in other kinds of lignocellulosic biomass.

Heavy metal accumulation by Corchorus olitorius L. irrigated with wastewater.

Many agricultural soils in Egypt irrigated with untreated wastewater. Herein, we investigated the effect of untreated industrial wastewater irrigation on the soil and fodder plant Corchorus olittorius (Jew mallow). It also aimed to assess its effect on the growth measurements as well as analyses of soils, irrigation waters, and plants for heavy metal and nutrient concentrations. Significant differences between irrigation waters and soil irrigated with fresh and wastewater were recognized. Wastewater irrigation leads to remarkable reduction in the growth parameters and reduced its vegetative biomass. The concentration of Pb, Cd, Cr, Cu, Fe, and Zn were high significant and above phytotoxic concentrations in leaves (edible part) and roots of wastewater-irrigated plant. The present study indicated that Jew mallow plant tends to phytostabilize (Cd, Ni, and Mn) in its root and had the ability to translocate (Pb, Cu, Cr, Fe, and Zn) to its leaves. Higher concentrations of Cd, Cu, Cr, Pb, Fe, Mn, Ni, and Zn in the roots than leaves indicate that the roots are hyper-accumulators for Pb, Cr, Cu, Fe, and Zn more than the leaves. The research study recommended that there is a need to protect the soil from contamination through regular monitoring and not to cultivate Jew mallow in wastewater-irrigated soil and that it had a high capacity to accumulate heavy metals in its edible part and causes several harmful health effects for consumers.

Development of an InDel polymorphism database for jute via comparative transcriptome analysis.

Jute (Corchorus spp.) is one of the most commercially important bast fiber crops in the world. However, molecular markers and high-density genetic maps are still lacking on jute compared with other crops. Insertion/deletion (InDel) markers, one of the most abundant sources of DNA/RNA variations in plant genomes, can easily be distinguished among different accessions using high-throughput sequencing. Using three transcriptome datasets, we identified and developed InDel markers. Altogether, 51 172 InDel sites in 18 800 unigenes were discovered, and the number of InDel loci per unigene varied from 1 to 31. Further, we found 94 InDel types, varying from 1 to 159 bp; the most common were single-nucleotide (23 028), binucleotide (9824), and trinucleotide (9182). In total, 49 563 InDels in 18 445 transcripts were discovered in the comparison between TC and YG, followed by 48 934 InDels in 18 408 transcripts between NY and YG, and 3570 InDels in 2701 unigenes between NY and TC. Additionally, there were 1273 InDel sites in 1129 unigenes with polymorphisms between any two of the three accessions. Twenty-nine (58%) primer pairs represented polymorphisms when compared to the jute accessions, and PIC varied from 0.340 to 0.680, with an average of 0.491.

Morphological, Histobiochemical and Molecular Characterisation of Low Lignin Phloem Fibre (llpf) Mutant of Dark Jute (Corchorus olitorius L.).

Lignin is a versatile plant metabolite challenging high-end industrial applications of several plant products including jute. Application of developmental mutant in regulation of lignification in jute may open up door for much awaited jute based diversified products. In the present study, a novel dark jute (Corchorus olitorius L.) mutant with low lignin (7.23%) in phloem fibre being compared to wild-type JRO 204 (13.7%) was identified and characterised. Unique morphological features including undulated stem, petiole and leaf vein distinguished the mutant in gamma ray irradiated mutant population. Histological and biochemical analysis revealed reduced lignification of phloem fibre cells of the plant. RT-PCR analysis demonstrated temporal transcriptional regulation of CCoAMT1 gene in the mutant. The mutant was found an extremely useful model to study phloem fibre developmental biology in the crop besides acting as a donor genetic stock for low lignin containing jute fibre in dark jute improvement programme.

Modification of Monolignol Biosynthetic Pathway in Jute: Different Gene, Different Consequence.

Lignin, a cross-linked macromolecule of hydrophobic aromatic structure, provides additional rigidity to a plant cell wall. Although it is an integral part of the plant cell, presence of lignin considerably reduces the quality of the fiber of fiber-yielding plants. Decreasing lignin in such plants holds significant commercial and environmental potential. This study aimed at reducing the lignin content in jute-a fiber crop, by introducing hpRNA-based vectors for downregulation of two monolignoid biosynthetic genes- cinnamate 4-hydroxylase (C4H) and caffeic acid O-methyltransferase (COMT). Transgenic generations, analyzed through Southern, RT-PCR and northern assays showed downregulation of the selected genes. Transgenic lines exhibited reduced level of gene expression with ~ 16-25% reduction in acid insoluble lignin for the whole stem and ~13-14% reduction in fiber lignin content compared to the control lines. Among the two transgenic plant types one exhibited an increase in cellulose content and concomitant improvement of glucose release. Composition of the lignin building blocks was found to alter and this alteration resulted in a pattern, different from other plants where the same genes were manipulated. It is expected that successful COMT-hpRNA and C4H-hpRNA transgenesis in jute will have far-reaching commercial implications leading to product diversification and value addition.

Comparative genomics of two jute species and insight into fibre biogenesis.

Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production1. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species2 in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.).

BACKGROUND: Jute fiber, extracted from stem bast, is called golden fiber. It is essential for fiber improvement to discover the genes associated with jute development at the vegetative growth stage. However, only 858 EST sequences of jute were deposited in the GenBank database. Obviously, the public available data is far from sufficient to understand the molecular mechanism of the fiber biosynthesis. It is imperative to conduct transcriptomic sequence for jute, which can be used for the discovery of a number of new genes, especially genes involved in cellulose biosynthesis. RESULTS: A total of 79,754,600 clean reads (7.98 Gb) were generated using Illumina paired-end sequencing. De novo assembly yielded 48,914 unigenes with an average length of 903 bp. By sequence similarity searching for known proteins, 27,962 (57.16 %) unigenes were annotated for their function. Out of these annotated unigenes, 21,856 and 11,190 unigenes were assigned to gene ontology (GO) and euKaryotic Ortholog Groups (KOG), respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 14,216 unigenes were mapped to 268 KEGG pathways. Moreover, 5 Susy, 3 UGPase, 9 CesA, 18 CSL, 2 Kor (Korrigan), and 12 Cobra unigenes involving in cellulose biosynthesis were identified. Among these unigenes, the unigenes of comp11264_c0 (SuSy), comp24568_c0 (UGPase), comp11363_c0 (CesA), comp11363_c1 (CesA), comp24217_c0 (CesA), and comp23531_c0 (CesA), displayed relatively high expression level in stem bast using FPKM and RT-qPCR, indicating that they may have potential value of dissecting mechanism on cellulose biosynthesis in jute. In addition, a total of 12,518 putative gene-associate SNPs were called from these assembled uingenes. CONCLUSION: We characterized the transcriptome of jute, discovered a broad survey of unigenes associated with vegetative growth and development, developed large-scale SNPs, and analyzed the expression patterns of genes involved in cellulose biosynthesis for bast fiber. All these provides a valuable genomics resource, which will accelerate the understanding of the mechanism of fiber development in jute.

Artificial miRNA-mediated down-regulation of two monolignoid biosynthetic genes (C3H and F5H) cause reduction in lignin content in jute.

Artificial microRNAs (amiRNA) provide a new feature in the gene silencing era. Concomitantly, reducing the amount of lignin in fiber-yielding plants such as jute holds significant commercial and environmental potential, since this amount is inversely proportional to the quality of the fiber. The present study aimed at reducing the lignin content in jute, by introducing amiRNA based vectors for down-regulation of two monolignoid biosynthetic genes of jute, coumarate 3-hydroxylase (C3H) and ferulate 5-hydroxylase (F5H). The transgenic lines of F5H-amiRNA and C3H-amiRNA showed a reduced level of gene expression, which resulted in about 25% reduction in acid insoluble lignin content for whole stem and 12-15% reduction in fiber lignin as compared to the non-transgenic plants. The results indicate successful F5H-amiRNA and C3H-amiRNA transgenesis for lignin reduction in jute. This is likely to have far-reaching commercial implications and economic acceleration for jute producing countries.