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A consortium of researchers in Bangladesh has successfully decoded the jute plant draft genome sequencing. The consortium consisted of Dhaka University, Bangladesh Jute Research Institute and software company DataSoft Systems Bangladesh Ltd. in collaboration with Centre for Chemical Biology, University of Science Malaysia and University of Hawaii at Manoa, USA. On June 16, 2010, Bangladeshi Prime Minister Sheikh Hasina had disclosed in the parliament that Bangladeshi researchers had successfully done draft jute genome sequencing which will contribute to improving jute fibre. Bangladesh is the second country after Malaysia among the developing nations in this kind of achievement.
It all began in February 2008, when Maqsudul Alam approached Professor Ahmad Shamsul Islam, Coordinator of GNOBB (Global Network of Bangladeshi Biotechnologists) regarding the possibility of sequencing the jute genome. The Bangladeshi science community, which was already looking into the possibility of getting the jute genome sequenced, responded to this offer, which started the process. The whole process began with many long conference calls between Dr. Alam and plant molecular biologists, Professors Haseena Khan and Zeba Islam Seraj of the Department of Biochemistry and Molecular Biology, University of Dhaka. They established connection with University of Hawaii, USA and University of Science Malaysia for technical support and prepared a project proposal to collect fund from different institutions. At the beginning there were many assurance but the reality was different. In the primary stage Genome Research Center USA and University of Science Malaysia gave some technical help to collect research data about jute from all over the world. To analyze huge amount of data there arose a need for a super computer. There was still need of funding for field research. "Swapnajatra" team become frustrated by not getting proper support. It became difficult to keep engage the team members. In 2009, The Daily Prothom Alo published an article about the research that changed everything. Agriculture Minister Matia Chowdhury introduced Dr. Maqsudul Alam to prime minister Sheikh Hasina and assured about further support. Thus team "Swapnajatra" regained their confidence and continued their work.
Genomic DNA (gDNA) from Tossa Jute (Corchorus olitorius O-4) was used for high-throughput Next Generation Sequencing (NGS) platforms, including 454 GS FLX, Illumina/Solexa, and SOLiD. More than 50X coverage (over 100 billions of A, C, G, and Ts) of Jute genome-sequencing data were used for the draft assembly. Several open-source and commercial genome assembly and annotation pipelines were used to assemble and analyze the raw data. To validate the draft genome, transcriptome analysis was also carried out. For data analysis, different computational resources, ranging from a high-performance Cluster Server to Dell servers to Silicon Graphics SGI Altix-350 and 450, were used.
Department of Biochemistry and Molecular Biology, University of Dhaka
In the backdrop of such exchanges, Dr. Alam visited Bangladesh in March 2008. During his visit, he was invited by the Bangladesh Society for Biochemistry and Molecular Biology to give a talk on his work on blood supplement, and this set the stage for a number of talks and presentations, including one presentation, which ran for several hours at the Department of Biochemistry and Molecular Biology on the "nuts and bolts" of genome sequencing. The audience included many students and faculty from many departments of the biological science and also personnel from renowned computer software company DataSoft.
This dedicated audience helped to form the first working body, more than two years before the actual project began. This team was called the "Swapna Jaatra", or the "Dream Journey", a name suggested by a graduate student from Dhaka University participating in Dr. Alam's presentation. Also in this meeting, the core team was formed with two major components, biology and computing. Dr. Haseena Khan from the Department of Biochemistry and Molecular Biology, DU and Mr. Mahboob Zaman of DataSoft were made the two team leaders of the two components respectively.
Through this brief interaction with the biology graduates from the Department of Biochemistry and Molecular Biology, and also the Department of Genetic Engineering and Biotechnology of University of Dhaka, Dr. Maqsudul Alam got his first very positive impression of the intellectual capability of the young individuals. This impression was later translated in the excellent handling of the raw data, and this would make him to comment later that he has never come across such talented students.