Efficient isolation of high quality RNA from tropical palms for RNA-seq analysis

Xiao, Yong, Yang, Yaodong, Cao, Hongxing, Fan, Haikuo, Ma, Zilong, Lei, Xintao, Mason, Annaliese S., Xia, Zhihui and Huang, Xi (2012) Efficient isolation of high quality RNA from tropical palms for RNA-seq analysis. Plant Omics, 5 6: 584-589.

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Author Xiao, Yong
Yang, Yaodong
Cao, Hongxing
Fan, Haikuo
Ma, Zilong
Lei, Xintao
Mason, Annaliese S.
Xia, Zhihui
Huang, Xi
Title Efficient isolation of high quality RNA from tropical palms for RNA-seq analysis
Journal name Plant Omics   Check publisher's open access policy
ISSN 1836-0661
1836-3644
Publication date 2012-11-01
Year available 2012
Sub-type Article (original research)
Open Access Status File (Publisher version)
Volume 5
Issue 6
Start page 584
End page 589
Total pages 6
Place of publication Lismore, NSW Australia
Publisher Southern Cross Journals
Language eng
Formatted abstract
Currently, RNA-seq as a high throughput technology is being widely applied to various species to elucidate the complexity of the transcriptome and to discover large number of novel genes. However, the technology has had poor success in elucidating the transcriptome of tropical palms, as it is difficult to isolate high quality RNA from tropical palm tissues due to their high polysaccharide and polyphenol content. Here, we developed an RNA-isolation protocol for tropical palms, the MRIP method (Methods for RNA Isolation from Palms). The integrity of the RNA molecules extracted using this protocol was determined to be of high quality by means of gel electrophoresis and Agilent 2100 Bioanalyzer microfluidic electrophoresis chip examination with a RIN (RNA Integrity Number) value of more than 9, indicating that the mRNAs were of good integrity. Subsequently the isolated RNA was used for transcription analysis without further purification. With Illumina sequencing, we obtained 54.9 million short reads and then conducted de novo assembly to gain 57,304 unigenes with an average length of 752 base pairs. Moreover, the RNA isolated with this protocol was also successfully used for real-time RT-PCR. These results suggested that the RNA isolated was suitable for Illumina RNA sequencing and quantitative real-time RT-PCR. Furthermore, this method was also successful in isolating total RNA from the leaves of various Palmaceae species.
Keyword RNA isolation
RNA sequence
Cocos nucifera
Palmaceace
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: School of Agriculture and Food Sciences
Official 2013 Collection
 
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