African Journal of
Biotechnology

  • Abbreviation: Afr. J. Biotechnol.
  • Language: English
  • ISSN: 1684-5315
  • DOI: 10.5897/AJB
  • Start Year: 2002
  • Published Articles: 12254

Full Length Research Paper

Modified protocol for RNA isolation from different parts of field-grown jute plant suitable for NGS data generation and quantitative real-time RT-PCR

Rasel Ahmed
  • Rasel Ahmed
  • Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
  • Google Scholar
Md. Sabbir Hossain
  • Md. Sabbir Hossain
  • Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
  • Google Scholar
Md. Samiul Haque
  • Md. Samiul Haque
  • Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
  • Google Scholar
Md. Monjurul Alam
  • Md. Monjurul Alam
  • Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
  • Google Scholar
Md. Shahidul Islam
  • Md. Shahidul Islam
  • Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute, Dhaka, Bangladesh.
  • Google Scholar


  •  Received: 31 March 2019
  •  Accepted: 17 June 2019
  •  Published: 31 July 2019

References

Chomczynski P, Sacchi N (1987). Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analytical Biochemistry 162:156-159.
Crossref

 

Choudhary SB, Kumar M, Chowdhury I, Singh RK, Pandey SP, Sharma HK, Karmakar PG (2016). An efficient and cost effective method of RNA extraction from mucilage, phenol and secondary metabolite rich bark tissue of tossa jute (C. olitorius L.) actively developing phloem fiber. 3 Biotech 6:100.
Crossref

 
 

Doyle JJ, Doyle JL (1987). A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19:11-15.

 
 

Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A (2010). Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology 28:503-510.
Crossref

 
 

Hu CG, Honda C, Kita M, Zhang Z, Tsuda T, Moriguchi T (2002). A simple protocol for RNA isolation from fruit trees containing high levels of polysaccharides and polyphenol compounds. Plant Molecular Biology Report 20:69a-69g.
Crossref

 
 

Islam MS, Saito JA, Emdad EM, Ahmed B, Islam MM, Halim A, Hossen QMM, Hossain MZ, Ahmed R, Hossain MS, Kabir SM, Khan MS, Khan MM, Hasan R, Aktar N, Honi U, Islam R, Rashid MM, Wan X1, Hou S, Haque T, Azam MS, Moosa MM, Elias SM, Hasan AM, Mahmood N, Shafiuddin M, Shahid S, Shommu NS, Jahan S, Roy S, Chowdhury A, Akhand AI, Nisho GM, Uddin KS, Rabeya T, Hoque SM, Snigdha AR, Mortoza S, Matin SA, Islam MK, Lashkar MZ, 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 3:16223.
Crossref

 
 

Khan F, Islam A, Sathasivan AK (2004). Rapid method for high quality RNA isolation from jute: Corchorus capsularis L. and Corchorus olitorius L. Plant Tissue Culture & Biotechnology 14:63-68.

 
 

Khanuja SPS, Shasany AK, Darokar MP, Kumar S (1999). Rapid isolation of DNA from dry and fresh samples of plants producing large amounts of secondary metabolites and essential oils. Plant Molecular Biology Report 17:74.
Crossref

 
 

Kumar GRK, Eswaran N, Johnson TS (2011). Isolation of high-quality RNA from various tissues of Jatropha curcas for downstream applications. Analytical Biochemistry 413:63-65.
Crossref

 
 

Liu J, Lee W, Jiang Z, Chen Z, Jhunjhunwala S, Haverty PM, Gnad F, Guan Y, Gilbert HN, Stinson J, Klijn C, Guillory J, Bhatt D, Vartanian S, Walter K, Chan J, Holcomb T, Dijkgraaf P, Johnson S, Koeman J, Minna JD, Gazdar AF, Stern HM, Hoeflich KP, Wu TD, Settleman J, de Sauvage FJ, Gentleman RC, Neve RM, Stokoe D, Modrusan Z, Seshagiri S, Shames DS, Zhang Z (2012). Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Research 22:2315-2327.
Crossref

 
 

Mac Rae E (2007). Extraction of plant RNA. In 'Methods in molecular biology, Protocols for nucleic acid analysis by nonradioactive probes'. (Eds Hilario E, Mackay J, 2nd ed.) (New Jersey: Humana Press) 353:15-24.

 
 

Mahmood N, Ahmed R, Azam MS, Khan H (2011). A simple and swift method for isolating high quality RNA from jute (Corchorus spp.). Plant Tissue Culture & Biotechnology 21:207‐211.
Crossref

 
 

Pandey RN, Adams RP, Flournoy LE (1996). Inhibition of random amplified polymorphic DNAs (RAPDs) by plant polysaccharides. Plant Molecular Biology Report 14:17-22.
Crossref

 
 

Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK (2010). Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464:768-772.
Crossref

 
 

Rai V, Ghosh SJ, Dey N (2010). Isolation of total RNA from hard bamboo tissue rich in polyphenols and polysaccharides for gene expression studies. Electronic Journal of Biotechnology 13:5.
Crossref

 
 

Rio DC, Ares M Jr, Hannon GJ, Nilsen TW (2010). Purification of RNA by SDS Solubilization and Phenol Extraction. Cold Spring Harbor Protocols. doi: 10.1101/pdb.prot5438
Crossref

 
 

Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M (2011). AlleleSeq: analysis of allele-specific expression and binding in a network framework. Molecular Systems Biology 7:522.
Crossref

 
 

Samanta P, Sadhukhan S, Das S, Joshi A, Sen SK, Basu A (2011). Isolation of RNA from field-grown jute (Corchorus capsularis) plant in different developmental stages for effective downstream molecular analysis. Molecular Biotechnology 49:109-115.
Crossref

 
 

Sharma AD, Gill PK, Singh P (2003). RNA isolation from plant tissues rich in polysaccharides. Analytical Biochemistry 314:319-321.
Crossref

 
 

Stephen AM, phillips GO, williams PA (2006). Food polysaccharides and their applications. 2nd ed. (Boca Raton: CRC Press).

 
 

van Dam JEG, Bos HL ( 2004). The environmental impact of hard fibres and jute in non-textiles industrial application. Consultation of natural fibres. ESC-Fibres consultation No. 04/4. Short version of comprehensive review on the environmental impact of the natural fibres in industrial applications. Agrotechnology and Food Innovations (A & F), Wageningen UR, Wageningen, The Netherlands.

 
 

Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB (2008). Alternative isoform regulation in human tissue transcriptomes. Nature 456:470-476.
Crossref

 
 

Wang X, Wu Z, Zhang X (2010). Isoform Abundance Inference Provides a More Accurate Estimation of Gene Expression Levels in RNA-Seq. Journal of Bioinformatics and Computational Biology 8:177-192.
Crossref

 
 

Yamazaki E, kurita O, Matsumura Y (2009). High viscosity of hydrocolloid from leaves of Corchorus olitorius L. Food Hydrocolloids 23:655-660.
Crossref

 
 

Yang G, Zhou R, Tang T, Shi S (2008). Simple and Efficient Isolation of High-Quality Total RNA from Hibiscus tiliaceus, a Mangrove Associate and Its Relatives. Preparative Biochemistry and Biotechnology 38:257-264.
Crossref

 
 

Yockteng R, Almeida AMR, Yee S, Andre T, Hill C, Specht CD (2013). A Method for Extracting High-Quality RNA from Diverse Plants for Next-Generation Sequencing and Gene Expression Analyses. Applications in Plant Sciences 1:1300070.
Crossref