Research Paper Jute
Genome sequencing and assembly
The genomes of C. olitorius var. O-4 and C. capsularis var. CVL-1 were sequenced using the WGS approach on the 454 platform. A total of 13.04 Gb of sequence data was generated for the C. olitorius genome, consisting of 5.65 Gb of shotgun sequences, 2.56 Gb of 3 kb paired-end sequences, 2.47 Gb of 8 kb paired-end sequences and 2.36 Gb of 20 kb paired-end sequences. For the C. capsularis genome, 13.69 Gb of sequence data was generated, consisting of 7.87 Gb of shotgun sequences, 2.04 Gb of 3 kb paired-end sequences, 2.26 Gb of 8 kb paired-end sequences and 1.51 Gb of 20 kb paired-end sequences (Supplementary Table 1).
We used the CABOG tool sffToCA to identify mated reads and remove duplicate mate pairs. The remaining read sequence data were converted to the fastq format, trimmed to a length of 65 bases and used in the assembly. The CABOG v7.0 pipelines were then run with default parameters using a kmer parameter of 22, which was selected after testing a range of kmer settings.
We used whole-genome optical mapping technology to improve and validate the assemblies (Supplementary Table 3). A total of 360,906 and 260,615 single-molecule restriction maps longer than 250 kb each, with an average size of 356.37 and 356.99 kb, were generated using the KpnI restriction enzyme for C. olitorius and C. capsularis, respectively (Supplementary Table 4). Super-scaffolding with optical map data was performed using Genome-Builder software (OpGen). Super-scaffolds and scaffolds were anchored to seven linkage groups using a combination of traditional markers and whole-genome mapping data using ALLMAPS software.
The accuracy and completeness of the assemblies were assessed by aligning isotigs that were generated from transcriptome sequencing onto the WGS scaffolds using BLAT (Supplementary Table 9). We also checked the relative completeness of the assemblies by performing core gene annotation using the CEGMA v2.5 pipelines (Supplementary Table 10).
Repetitive elements were identified and masked by RepeatModeler v1.0.7 and RepeatMasker Open-3.0 with default parameters. Gene prediction was performed using a combination of homology, de novo and transcript-based approaches (Supplementary Fig. 4). The predicted genes were analysed for functional domains and homologies by using InterProScan and Basic Local Alignment Search Tool (BLAST) against the NCBI non-redundant database, TrEMBL and SwissProt with Protein BLAST (BLASTP) (e < 1 × 10−5) and Blast2GO v3.3 with default parameters.
Genome comparison and evolution
Comparative analysis was performed to identify orthologous gene families among the genomes of C. olitorius, C. capsularis, Arabidopsis thaliana, Theobroma cacao, Gossypium raimondii, Glycine max, Populus trichocarpa, Ricinus communis, Fragaria vesca, Linum usitatissimum, Medicago truncatula, Vitis vinifera, Solanum lycopersicum, Solanum tuberosum and Oryza sativa. All predicted protein sequences of these plants (Supplementary Table 20) were searched against each other using BLASTP (e < 1 × 10−5) and clustered into orthologous groups using MCL-10-201 (inflation parameter, 1.5). Clusters containing single-copy orthologues were identified with exact one member per species. Phylogenetic relationships were determined from these single-copy orthologues using the maximum likelihood method.
Paralogous genes in C. olitorius and C. capsularis were detected by all-against-all protein sequence similarity searches using BLASTP. The synonymous substitution rate (Ks) was calculated for each gene pair. Paralogous genes were determined to be tandem duplicates if they were located within five genes from each other. Orthologous genes between C. olitorius and C. capsularis were identified using the reciprocal best hit method and the Ks values were calculated for each pair. Intra- and intergenomic regions of synteny were identified and visualized by SyMAP v4.0.
Metabolic and regulatory pathways were reconstructed with Pathway Studio software based on the Resnet-Plant 4.0 database. Predicted jute interologues and pathways were imported into a new Pathway Studio database for manual pathway reconstruction and genome analysis.
Fibre cell transcriptome sequencing and analysis
The transcriptomes of isolated fibre cells and whole seedlings were sequenced with an Illumina HiSeq 2,500 at HudsonAlpha Institute for Biotechnology, Huntsville, Alabama (Supplementary Tables 28 and 29). Expression patterns were compared by aligning the RNA-seq reads against the C. olitorius and C. capsularis genome sequences and quantifying the transcript abundances using the Cufflinks v2.2.1 package, which was visualized by R libraries. KEGG Orthology Based Annotation System (KOBAS) was used to identify the pathways in the C. olitorius and the C. capsularis genome using the model organism A. thaliana. KEGG (Release 74.0) and Biocyc v19.0 pathways were utilized to run R package piano v1.8.0 for Gene set analysis (GSA). Pathways in the distinct direction were selected for subsequent analysis based on adjusted P < 0.05. The differential gene expression from the in silico analysis were validated by RT–qPCR with randomly selected several fibre biosynthesis pathway genes. All primers used in this study are provided in Supplementary Table 42.
Two-tailed chi-squared tests were used to compare the distributions of GO subcategories between C. olitorius and C. capsularis (Fig. 3). For each GO subcategory, a 2 × 2 contingency table was constructed by recording the existence of the number of genes in a subcategory for each species and ranking the statistical significance of the differences.
Detailed methods and their associated references are in the Supplementary Information.
The WGS projects have been deposited at NCBI GenBank under BioProject ID PRJNA215141 and accession no. AWUE00000000 for C. olitorius and BioProject ID PRJNA215142 and accession no. AWWV00000000 for C. capsularis. The genomic and transcriptomic raw data have been deposited in the NCBI Sequence Read Archive (SRA) under SRP049494 and SRP053213 for C. olitorius and C. capsularis, respectively.
Cyanoethylation of jute fibers in the form of nonwoven fabric was studied, and these chemically modified fibers were used to make jute–polyester composites. The dynamic mechanical thermal properties of unsaturated polyester resin (cured) and composites of unmodified and chemically modified jute–polyester were studied by using a dynamic mechanical analyzer over a wide temperature range. The data suggest that the storage modulus and thermal transition temperature of the composites increased enormously due to cyanoethylation of fiber. An increase of the storage modulus of composites, prepared from chemically modified fiber, indicates its higher stiffness as compared to a composite prepared from unmodified fiber. It is also observed that incorporation of jute fiber (both unmodified and modified) with the unsaturated resin reduced the tan δ peak height remarkably. Composites prepared from cyanoethylated jute show better creep resistance at comparatively lower temperatures. On the contrary, a reversed phenomenon is observed at higher temperatures (120°C and above). Scanning electron micrographs of tensile fracture surfaces of unmodified and modified jute–polyester composites clearly demonstrate better fiber–matrix bonding in the case of the latter. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 1505–1513, 1999