Comparative genomics of two jute species and insight into fibre biogenesis

Md Shahidul Islam; Jennifer A. Saito; Emdadul Mannan Emdad; Borhan Ahmed; Mohammad Moinul Islam; Abdul Halim; Quazi Md Mosaddeque Hossen; Md Zakir Hossain; Rasel Ahmed; Md Sabbir Hossain; Shah Md Tamim Kabir; Md Sarwar Alam Khan; Md Mursalin Khan; Rajnee Hasan; Nasima Aktar; Ummay Honi; Rahin Islam; Md Mamunur Rashid; Xuehua Wan; Shaobin Hou; Taslima Haque; Muhammad Shafiul Azam; Mahdi Muhammad Moosa; Sabrina M. Elias; A. M.Mahedi Hasan; Niaz Mahmood; Md Shafiuddin; Saima Shahid; Nusrat Sharmeen Shommu; Sharmin Jahan; Saroj Roy; Amlan Chowdhury; Ashikul Islam Akhand; Golam Morshad Nisho; Khaled Salah Uddin; Taposhi Rabeya; S. M.Ekramul Hoque; Afsana Rahman Snigdha; Sarowar Mortoza; Syed Abdul Matin; Md Kamrul Islam; M. Z.H. Lashkar; Mahboob Zaman; Anton Yuryev; Md Kamal Uddin; Md Sharifur Rahman; Md Samiul Haque; Md Monjurul Alam; Haseena Khan; Maqsudul Alam

doi:10.1038/nplants.2016.223

Comparative genomics of two jute species and insight into fibre biogenesis

Md Shahidul Islam, Jennifer A. Saito, Emdadul Mannan Emdad, Borhan Ahmed, Mohammad Moinul Islam, Abdul Halim, Quazi Md Mosaddeque Hossen, Md Zakir Hossain, Rasel Ahmed, Md Sabbir Hossain, Shah Md Tamim Kabir, Md Sarwar Alam Khan, Md Mursalin Khan, Rajnee Hasan, Nasima Aktar, Ummay Honi, Rahin Islam, Md Mamunur Rashid, Xuehua Wan, Shaobin HouTaslima Haque, Muhammad Shafiul Azam, Mahdi Muhammad Moosa, Sabrina M. Elias, A. M.Mahedi Hasan, Niaz Mahmood, Md Shafiuddin, Saima Shahid, Nusrat Sharmeen Shommu, Sharmin Jahan, Saroj Roy, Amlan Chowdhury, Ashikul Islam Akhand, Golam Morshad Nisho, Khaled Salah Uddin, Taposhi Rabeya, S. M.Ekramul Hoque, Afsana Rahman Snigdha, Sarowar Mortoza, Syed Abdul Matin, Md Kamrul Islam, M. Z.H. Lashkar, Mahboob Zaman, Anton Yuryev, Md Kamal Uddin, Md Sharifur Rahman, Md Samiul Haque, Md Monjurul Alam, Haseena Khan, Maqsudul Alam

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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.

Original language	English
Article number	16223
Journal	Nature Plants
Volume	3
DOIs	https://doi.org/10.1038/nplants.2016.223
State	Published - Jan 30 2017

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Islam, M. S., Saito, J. A., Emdad, E. M., Ahmed, B., Islam, M. M., Halim, A., Hossen, Q. M. M., Hossain, M. Z., Ahmed, R., Hossain, M. S., Kabir, S. M. T., Khan, M. S. A., Khan, M. M., Hasan, R., Aktar, N., Honi, U., Islam, R., Rashid, M. M., Wan, X., ... Alam, M. (2017). Comparative genomics of two jute species and insight into fibre biogenesis. Nature Plants, 3, Article 16223. https://doi.org/10.1038/nplants.2016.223

@article{84bc6ee0ef8140a29e2f3a2f05e0b6d0,

title = "Comparative genomics of two jute species and insight into fibre biogenesis",

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.",

author = "Islam, {Md Shahidul} and Saito, {Jennifer A.} and Emdad, {Emdadul Mannan} and Borhan Ahmed and Islam, {Mohammad Moinul} and Abdul Halim and Hossen, {Quazi Md Mosaddeque} and Hossain, {Md Zakir} and Rasel Ahmed and Hossain, {Md Sabbir} and Kabir, {Shah Md Tamim} and Khan, {Md Sarwar Alam} and Khan, {Md Mursalin} and Rajnee Hasan and Nasima Aktar and Ummay Honi and Rahin Islam and Rashid, {Md Mamunur} and Xuehua Wan and Shaobin Hou and Taslima Haque and Azam, {Muhammad Shafiul} and Moosa, {Mahdi Muhammad} and Elias, {Sabrina M.} and Hasan, {A. M.Mahedi} and Niaz Mahmood and Md Shafiuddin and Saima Shahid and Shommu, {Nusrat Sharmeen} and Sharmin Jahan and Saroj Roy and Amlan Chowdhury and Akhand, {Ashikul Islam} and Nisho, {Golam Morshad} and Uddin, {Khaled Salah} and Taposhi Rabeya and Hoque, {S. M.Ekramul} and Snigdha, {Afsana Rahman} and Sarowar Mortoza and Matin, {Syed Abdul} and Islam, {Md Kamrul} and Lashkar, {M. Z.H.} and Mahboob Zaman and Anton Yuryev and Uddin, {Md Kamal} and Rahman, {Md Sharifur} and Haque, {Md Samiul} and Alam, {Md Monjurul} and Haseena Khan and Maqsudul Alam",

year = "2017",

month = jan,

day = "30",

doi = "10.1038/nplants.2016.223",

language = "Ingl{\'e}s",

volume = "3",

journal = "Nature Plants",

issn = "2055-026X",

publisher = "Palgrave Macmillan Ltd.",

}

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 2017, 'Comparative genomics of two jute species and insight into fibre biogenesis', Nature Plants, vol. 3, 16223. https://doi.org/10.1038/nplants.2016.223

TY - JOUR

T1 - Comparative genomics of two jute species and insight into fibre biogenesis

AU - Islam, Md Shahidul

AU - Saito, Jennifer A.

AU - Emdad, Emdadul Mannan

AU - Ahmed, Borhan

AU - Islam, Mohammad Moinul

AU - Halim, Abdul

AU - Hossen, Quazi Md Mosaddeque

AU - Hossain, Md Zakir

AU - Ahmed, Rasel

AU - Hossain, Md Sabbir

AU - Kabir, Shah Md Tamim

AU - Khan, Md Sarwar Alam

AU - Khan, Md Mursalin

AU - Hasan, Rajnee

AU - Aktar, Nasima

AU - Honi, Ummay

AU - Islam, Rahin

AU - Rashid, Md Mamunur

AU - Wan, Xuehua

AU - Hou, Shaobin

AU - Haque, Taslima

AU - Azam, Muhammad Shafiul

AU - Moosa, Mahdi Muhammad

AU - Elias, Sabrina M.

AU - Hasan, A. M.Mahedi

AU - Mahmood, Niaz

AU - Shafiuddin, Md

AU - Shahid, Saima

AU - Shommu, Nusrat Sharmeen

AU - Jahan, Sharmin

AU - Roy, Saroj

AU - Chowdhury, Amlan

AU - Akhand, Ashikul Islam

AU - Nisho, Golam Morshad

AU - Uddin, Khaled Salah

AU - Rabeya, Taposhi

AU - Hoque, S. M.Ekramul

AU - Snigdha, Afsana Rahman

AU - Mortoza, Sarowar

AU - Matin, Syed Abdul

AU - Islam, Md Kamrul

AU - Lashkar, M. Z.H.

AU - Zaman, Mahboob

AU - Yuryev, Anton

AU - Uddin, Md Kamal

AU - Rahman, Md Sharifur

AU - Haque, Md Samiul

AU - Alam, Md Monjurul

AU - Khan, Haseena

AU - Alam, Maqsudul

PY - 2017/1/30

Y1 - 2017/1/30

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85011268712&partnerID=8YFLogxK

U2 - 10.1038/nplants.2016.223

DO - 10.1038/nplants.2016.223

M3 - Artículo

C2 - 28134914

AN - SCOPUS:85011268712

SN - 2055-026X

VL - 3

JO - Nature Plants

JF - Nature Plants

M1 - 16223

ER -

Comparative genomics of two jute species and insight into fibre biogenesis

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