J. Biosci. Agric. Res. | Volume 26, Issue 02, 2204-2210 | https://doi.org/10.18801/jbar.260220.269
Article type: Research article | Received: 15.10.2020; Revised: 30.11.2020; First published online: 10 December 2020.
Article type: Research article | Received: 15.10.2020; Revised: 30.11.2020; First published online: 10 December 2020.
Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell
Rasel Ahmed 1, Md. Sabbir Hossain 1, Shah Md. Tamim Kabir 1, Borhan Ahmed 1, Rajnee Hasan 1, Mohammad Saiful Alam Sarker 1, Md. Zablul Tareq 2, Emdadul Mannan Emdad 1 and Md. Shahidul Islam 1
1 Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
2 Jute Agriculture Experimental Station, Bangladesh Jute Research Institute, Jagir, Manikganj, Bangladesh.
✉ Corresponding author: [email protected] (Ahmed, R.).
1 Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
2 Jute Agriculture Experimental Station, Bangladesh Jute Research Institute, Jagir, Manikganj, Bangladesh.
✉ Corresponding author: [email protected] (Ahmed, R.).
Abstract
The demand for products made by jute fiber is increasing day-by-day for its biodegradable nature regarding environmental concerns. To gain this opportunity correctly, the development of high yielding and improved fiber quality jute variety is essential for ensuring diversified use of jute fiber. The major developed jute varieties, so far, are the outcome of conventional breeding which is a very time consuming process. Improvement of fiber quality and yield through genetic modification approach is highly desired. However, very little is known about the molecular mechanism behind fiber cell formation in jute. Here, we attempted to do the whole transcriptome sequencing of fiber cell RNA to reveal the molecular mechanisms were happening in the premises of jute fiber cells. We performed RNA isolation from jute fiber cells followed by whole transcriptome sequencing. De novo assembly of sequencing reads resulted in 21,294 contigs representing the transcriptome size of 4.07 Mbp. Gene ontology analysis assigned 14144 genes (52.21%) for biological process, 8399 genes (31%) involved in molecular function and 4549 genes (16.79%) for cellular component. Total 66 fiber related genes were found from reference based annotation where 9 genes involved in fiber cell initiation and elongation and the rest 57 for secondary cell wall development. We presented the overall view of the jute fiber cell transcriptome in this study. These findings help for understanding the molecular basis of fiber formation in jute plant.
Key Words: Jute, Fiber cell, Transcriptome, Sequencing and De novo assembly
The demand for products made by jute fiber is increasing day-by-day for its biodegradable nature regarding environmental concerns. To gain this opportunity correctly, the development of high yielding and improved fiber quality jute variety is essential for ensuring diversified use of jute fiber. The major developed jute varieties, so far, are the outcome of conventional breeding which is a very time consuming process. Improvement of fiber quality and yield through genetic modification approach is highly desired. However, very little is known about the molecular mechanism behind fiber cell formation in jute. Here, we attempted to do the whole transcriptome sequencing of fiber cell RNA to reveal the molecular mechanisms were happening in the premises of jute fiber cells. We performed RNA isolation from jute fiber cells followed by whole transcriptome sequencing. De novo assembly of sequencing reads resulted in 21,294 contigs representing the transcriptome size of 4.07 Mbp. Gene ontology analysis assigned 14144 genes (52.21%) for biological process, 8399 genes (31%) involved in molecular function and 4549 genes (16.79%) for cellular component. Total 66 fiber related genes were found from reference based annotation where 9 genes involved in fiber cell initiation and elongation and the rest 57 for secondary cell wall development. We presented the overall view of the jute fiber cell transcriptome in this study. These findings help for understanding the molecular basis of fiber formation in jute plant.
Key Words: Jute, Fiber cell, Transcriptome, Sequencing and De novo assembly
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Article Citations:
MLA
Ahmed, R.et al. "Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell". Journal of Bioscience and Agriculture Research, 26(02), (2020):2204-2210.
APA
Ahmed, R., Hossain, M. S., Kabir, S. M. T., Ahmed, B., Hasan, R., Sarker, M. S. A., Tareq, M. Z., Emdad, E. M. and Islam, M. S. (2020). Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell.Journal of Bioscience and Agriculture Research, 26(02), 2204-2210.
Chicago
Ahmed, R., Hossain, M. S., Kabir, S. M. T., Ahmed, B., Hasan, R., Sarker, M. S. A., Tareq, M. Z., Emdad, E. M. and Islam, M. S. "Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell". Journal of Bioscience and Agriculture Research, 26(02), (2020): 2204-2210.
Harvard
Ahmed, R., Hossain, M. S., Kabir, S. M. T., Ahmed, B., Hasan, R., Sarker, M. S. A., Tareq, M. Z., Emdad, E. M. and Islam, M. S. 2020. Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell. Journal of Bioscience and Agriculture Research, 26(02), pp. 2204-2210.
Vancouver
Ahmed R, Hossain MS, Kabir SMT, Ahmed B, Hasan R, Sarker MSA, Tareq MZ, Emdad EM and Islam MS. Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell. Journal of Bioscience and Agriculture Research, 2020 December 26(02): 2204-2210.
Ahmed, R.et al. "Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell". Journal of Bioscience and Agriculture Research, 26(02), (2020):2204-2210.
APA
Ahmed, R., Hossain, M. S., Kabir, S. M. T., Ahmed, B., Hasan, R., Sarker, M. S. A., Tareq, M. Z., Emdad, E. M. and Islam, M. S. (2020). Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell.Journal of Bioscience and Agriculture Research, 26(02), 2204-2210.
Chicago
Ahmed, R., Hossain, M. S., Kabir, S. M. T., Ahmed, B., Hasan, R., Sarker, M. S. A., Tareq, M. Z., Emdad, E. M. and Islam, M. S. "Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell". Journal of Bioscience and Agriculture Research, 26(02), (2020): 2204-2210.
Harvard
Ahmed, R., Hossain, M. S., Kabir, S. M. T., Ahmed, B., Hasan, R., Sarker, M. S. A., Tareq, M. Z., Emdad, E. M. and Islam, M. S. 2020. Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell. Journal of Bioscience and Agriculture Research, 26(02), pp. 2204-2210.
Vancouver
Ahmed R, Hossain MS, Kabir SMT, Ahmed B, Hasan R, Sarker MSA, Tareq MZ, Emdad EM and Islam MS. Whole transcriptome sequencing and analysis of jute (Corchorus olitorius) fiber cell. Journal of Bioscience and Agriculture Research, 2020 December 26(02): 2204-2210.
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