Improved CTAB method for RNA extraction of thick waxy leaf tissues from sago palm (Metroxylon sagu Rottb.)

Background There is a growing interest in transcriptomics studies parallel to the advancement of transcriptome databases and bioinformatics, which provided the opportunity to study responses to growths, stimuli and stresses. There is an increase in demand for excellent RNA extraction techniques. Gen...

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Bibliographic Details
Published in:Chemical and biological technologies in agriculture 2022-09, Vol.9 (1), p.1-14, Article 63
Main Authors: Yan, Wei-Jie, Pendi, Fifi Hafizzah, Hussain, Hasnain
Format: Article
Language:English
Subjects:
Agricultural production
Agriculture
Assembly
Bioinformatics
Biomedical and Life Sciences
Dogs
Gene sequencing
Improved CTAB method
Leaves
Life Sciences
Methodology
Methods
Metroxylon sagu
Organic Chemistry
Plant Biochemistry
Plant Physiology
Plant tissues
Ribonucleic acid
RNA
RNA extraction
Sago
Soil Science & Conservation
Transcriptomes
Transcriptomics
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Summary:Background There is a growing interest in transcriptomics studies parallel to the advancement of transcriptome databases and bioinformatics, which provided the opportunity to study responses to growths, stimuli and stresses. There is an increase in demand for excellent RNA extraction techniques. General RNA extraction protocols can be used in RNA extraction, but the quality and quantity vary in different types of tissues from different organisms. Hence, a specific RNA extraction method for each organism’s tissue type is required to obtain the desired RNA quality and quantity. Results The improved CTAB RNA extraction method is superior to the PCI method and MRIP method for thick waxy leaves that were applied for mature sago palm ( Metroxylon sagu Rottb.) leaf tissue and produce total RNA extract with good purity (OD 260/280 ≥ 1.8, OD 260/230 ≥ 2.0) and integrity (RIN ~ 7). RNA sequencing was conducted with the extracted samples and showed good assembly results (Q20 ≥ 97, Q30 ≥ 91%, assembly mean length ≥ 700 bp). Conclusion The improved CTAB RNA extraction method enables rapid, cost-effective, and relatively simple RNA extraction from waxy, fibrous and high-in-polyphenol sago palm ( M. sagu Rottb.) leaf tissue with next-generation RNA sequencing recommended quality. Graphical Abstract
ISSN:2196-5641
2196-5641
DOI:10.1186/s40538-022-00329-9