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.

Background Although it is becoming evident that individual’s immune system has a decisive influence on SARS-CoV-2 disease progression, pathogenesis is largely unknown. In this study, we aimed to profile the host transcriptome of COVID-19 patients from nasopharyngeal samples along with virus genomic features isolated from respective host, and a comparative analyses of differential host responses in various SARS-CoV-2 infection systems. Results Unique and rare missense mutations in 3C-like protease observed in all of our reported isolates. Functional enrichment analyses exhibited that the host induced responses are mediated by innate immunity, interferon, and cytokine stimulation. Surprisingly, induction of apoptosis, phagosome, antigen presentation, hypoxia response was lacking within these patients. Upregulation of immune and cytokine signaling genes such as CCL4, TNFA, IL6, IL1A, CCL2, CXCL2, IFN, and CCR1 were observed in lungs. Lungs lacked the overexpression of ACE2 as suspected, however, high ACE2 but low DPP4 expression was observed in nasopharyngeal cells. Interestingly, directly or indirectly, viral proteins specially non-structural protein mediated overexpression of integrins such as ITGAV, ITGA6, ITGB7, ITGB3, ITGA2B, ITGA5, ITGA6, ITGA9, ITGA4, ITGAE, and ITGA8 in lungs compared to nasopharyngeal samples suggesting the possible way of enhanced invasion. Furthermore, we found comparatively highly expressed transcription factors such as CBP, CEBP, NFAT, ATF3, GATA6, HDAC2, TCF12 which have pivotal roles in lung injury. Conclusions Even though this study incorporates a limited number of cases, our data will provide valuable insights in developing potential studies to elucidate the differential host responses on the viral pathogenesis in COVID-19, and incorporation of further data will enrich the search of an effective therapeutics.

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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.Jute, second most important natural fibre after cotton, is cultivated in East Asia and some parts of Latin America 1-3 . Jute is a bast or phloem fibre in the bark of stems, cemented together by pectin and gummy substances 4 . Commercial extraction of jute fibre is water based microbiological retting where jute bundles are submerged into slow running river water and subjected to decomposition of pectin, hemicelluloses, and other mucilaginous substances 2,5 . In this process, pectin is depolymerized by pectinases, primarily comprising four enzymes: Polygalacturonase (PG), Pectin Lyase (PNL), Pectate lyase and Pectin esterase. However, PG 6 , and PNL 7 are primary retting enzymes. In addition, xylanase makes jute fibre softer by selective removal of non-fibrous hemicelluloses without affecting strength of cellulosic fibre. Pectinolytic microorganisms having xylanase activity devoid of cellulase activity is an additional beneficial aspect to improve fibre quality 8 . The quality of fibre is largely determined by the efficiency of retting process 1,2,9,10 and various factors are responsible for proper retting as well as improved fibre quality. Most promising water based microbiological retting process mostly involves bacteria along with various fungi, protozoa, algae and diatoms 10-13 . Main aerobic retting bacteria belong to genus Bacillus viz., B. subtilis, B. polymyxa, B. mesentericus, B.pumilus, B. cereus, B. megaterium and B. macerans, initiate retting 14-18 along with large numbers of gram-negative genera such as Erwinia and Pseudomonas 9,19 . At the later stage of retting some anaerobic bacteria from genus Clostridium -Clostridium acetobutylicum, Clostridium stercorarium, Clostridium tertium come to carry on the retting process 20 . As microorganisms are the ma...

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.

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The demand for products made by jute fiber is increasing day-by-day for its biodegradable nature regarding environmental concerns. To gain this opportunity correctly, the development of high yielding and improved fiber quality jute variety is essential for ensuring diversified use of jute fiber. The major developed jute varieties, so far, are the outcome of conventional breeding which is a very time consuming process. Improvement of fiber quality and yield through genetic modification approach is highly desired. However, very little is known about the molecular mechanism behind fiber cell formation in jute. Here, we attempted to do the whole transcriptome sequencing of fiber cell RNA to reveal the molecular mechanisms were happening in the premises of jute fiber cells. We performed RNA isolation from jute fiber cells followed by whole transcriptome sequencing. De novo assembly of sequencing reads resulted in 21,294 contigs representing the transcriptome size of 4.07 Mbp. Gene ontology analysis assigned 14144 genes (52.21%) for biological process, 8399 genes (31%) involved in molecular function and 4549 genes (16.79%) for cellular component. Total 66 fiber related genes were found from reference based annotation where 9 genes involved in fiber cell initiation and elongation and the rest 57 for secondary cell wall development. We presented the overall view of the jute fiber cell transcriptome in this study. These findings help for understanding the molecular basis of fiber formation in jute plant.

As the COVID-19 pandemic progresses, fatality and cases of new infections are also increasing at an alarming rate. SARS-CoV-2 follows a highly variable course and it is becoming more evident that individual’s immune system has a decisive influence on the progression of the disease. However, the detailed underlying molecular mechanisms of the SARS-CoV-2 mediate disease pathogenesis are largely unknown. Only a few host transcriptional responses in COVID-19 have been reported so far from the Western world, but no such data has been generated from the South-Asian region yet to correlate the conjectured lower fatality around this part of the globe. In this context, we aimed to perform the transcriptomic profiling of the COVID-19 patients from Bangladesh along with the reporting of the SARS-CoV-2 isolates from these patients. Moreover, we performed a comparative analysis to demonstrate how differently the various SARS-CoV-2 infection systems are responding to the viral pathogen. We detected a unique missense mutation at 10329 position of ORF1ab gene, annotated to 3C like proteinase, which is found in 75% of our analyzed isolates; but is very rare globally. Upon the functional enrichment analyses of differentially modulated genes, we detected a similar host induced response reported earlier; this response was mainly mediated by the innate immune system, interferon stimulation, and upregulated cytokine expression etc. in the Bangladeshi patients. Surprisingly, we did not perceive the induction of apoptotic signaling, phagosome formation, antigen presentation and production, hypoxia response within these nasopharyngeal samples. Furthermore, while comparing with the other SARS-CoV-2 infection systems, we spotted that lung cells trigger the more versatile immune and cytokine signaling which was several folds higher compared to our reported nasopharyngeal samples. We also observed that lung cells did not express ACE2 in a very high amount as suspected, however, the nasopharyngeal cells are found overexpressing ACE2. But the amount of DPP4 expression within the nasal samples was significantly lower compared to the other cell types. Surprisingly, we observed that lung cells express a very high amount of integrins compared to the nasopharyngeal samples, which might suggest the putative reasons for an increased amount of viral infections in the lungs. From the network analysis, we got clues on the probable viral modulation for the overexpression of these integrins. Our data will provide valuable insights in developing potential studies to elucidate the roles of ethnicity effect on the viral pathogenesis, and incorporation of further data will enrich the search of an effective therapeutics.