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Comparative Genomics of Two Jute Species and Insight Into Fiber Biogenesis

Md Shahidul Islam
Department of BiochemistryBasic, Patuakhali Science and Technology University, PSTU and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Jennifer A. Saito
Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA

Emdadul Mannan Emdad
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Borhan Ahmed
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Mohammad Moinul Islam
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Abdul Halim
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Quazi Md Mosaddeque Hossen
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Md Zakir Hossain
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Rasel Ahmed
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Md Sabbir Hossain
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Shah Md Tamim Kabir
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Md Sarwar Alam Khan
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Md Mursalin Khan
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Rajnee Hasan
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Nasima Aktar
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Ummay Honi
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Rahin Islam
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Md Mamunur Rashid
Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Xuehua Wan
Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA.

Shaobin Hou
Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA.

Taslima Haque
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Muhammad Shafiul Azam
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Mahdi Muhammad Moosa
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Sabrina M. Elias
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

A. M. Mahedi Hasan
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Niaz Mahmood
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Md Shafiuddin
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Saima Shahid
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Nusrat Sharmeen Shommu
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Sharmin Jahan
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Saroj Roy
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Amlan Chowdhury
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Ashikul Islam Akhand
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Golam Morshad Nisho
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Khaled Salah Uddin
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Taposhi Rabeya
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

S. M. Ekramul Hoque
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Afsana Rahman Snigdha
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Sarowar Mortoza
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Syed Abdul Matin
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Md Kamrul Islam
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

M. Z. H. Lashkar
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Mahboob Zaman
DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh.

Anton Yuryev
Elsevier, Rockville, Maryland, Missouri 63043, USA

Md Kamal Uddin
Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Md Sharifur Rahman
Department of Telecommunications, Dhaka 1208, Bangladesh.

Md Samiul Haque
Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Md Monjurul Alam
Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.

Haseena Khan
Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh

Maqsudul Alam
Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA.

Abstract/ Executive Summary:

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.

Keywords: Genomics, Species, Fiber, Biogenesis, Jute

Location: In Bangladesh

Start Date:

End Date:

Program Area: Variety and Species

Commodity: Jute

Objectives:

To determine the Comparative genomics and insight into fiber biogenesis of two jute species.

Methodology:

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 platforms. 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). Superscaffolding 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. Gene annotation. 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 transcriptbased 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. Pathway reconstruction. Metabolic and regulatory pathways were reconstructed with Pathway Studio software based on the Resnet-Plant 4.0 database. Predicted jute ideologues 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. Statistical analyses. 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

Source of Information: Nature Plants · January 2017, VOLUME: 3, ARTICLE NUMBER: 16223

Article Link (Online Journal): https://www.researchgate.net/publication/313070986 (DOI: 10.1038/nplants.2016.223)

Funding Source:

Total Budget (Tk.) :

Achievement/Findings:

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. Among them, 329 C. olitorius and 344 C. capsularis genes were identified based on the analysis of homologous genes reportedly involved in plant fibre formation24 which facilitated us to propose a model for bast fibre biogenesis in jute. It was found that 174 (53%) C. olitorius and 216 (63%) C. capsularis genes were expressed significantly within the fibre cells and seedlings. Genes encoding the WOX4, APL and HAT22 transcription factors and the TDIF signalling peptide, which are involved in vascular cambium initiation and proliferation^25–28, were highly expressed in fibre cells, suggesting their importance in fibre differentiation.

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