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Islam MS, Saito JA, Emdad EM, Ahmed B, Islam MM, Halim A, Hossen QMM, Hossain MZ, Ahmed R, Hossain MS, Kabir SMT, Khan MSA, Khan MM, Hasan R, Aktar N, Honi U, Islam R, Rashid MM, Wan X, Hou S, Haque T, Azam MS, Moosa MM, Elias SM, Hasan AMM, Mahmood N, Shafiuddin M, Shahid S, Shommu NS, Jahan S, Roy S, Chowdhury A, Akhand AI, Nisho GM, Uddin KS, Rabeya T, Hoque SME, Snigdha AR, Mortoza S, Matin SA, Islam MK, Lashkar MZH, Zaman M, Yuryev A, Uddin MK, Rahman MS, Haque MS, Alam MM, Khan H, Alam M. Comparative genomics of two jute species and insight into fibre biogenesis. Nat Plants 2017; 3:16223. [PMID: 28134914 DOI: 10.1038/nplants.2016.223] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 12/21/2016] [Indexed: 02/08/2023]
Abstract
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.
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Affiliation(s)
- Md Shahidul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Jennifer A Saito
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,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
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Mohammad Moinul Islam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Abdul Halim
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Quazi Md Mosaddeque Hossen
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Zakir Hossain
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,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
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA
| | - Shaobin Hou
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,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
| | | | | | - 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
| | | | - Sharmin Jahan
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Saroj Roy
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Amlan Chowdhury
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Ashikul Islam Akhand
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Golam Morshad Nisho
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Khaled Salah Uddin
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Taposhi Rabeya
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - S M Ekramul Hoque
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Afsana Rahman Snigdha
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Sarowar Mortoza
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Syed Abdul Matin
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Md Kamrul Islam
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - M Z H Lashkar
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Mahboob Zaman
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,DataSoft Systems Bangladesh Limited, Dhaka 1207, Bangladesh
| | - Anton Yuryev
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Elsevier, Rockville, Maryland, Missouri 63043, USA
| | - Md Kamal Uddin
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Sharifur Rahman
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Department of Telecommunications, Dhaka 1208, Bangladesh
| | - Md Samiul Haque
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Md Monjurul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh
| | - Haseena Khan
- Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Maqsudul Alam
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Jute Genome Project, Bangladesh Jute Research Institute, Dhaka 1207, Bangladesh.,Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii 96822, USA
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