Sains Malaysiana 46(8)(2017): 1231–1240

http://dx.doi.org/10.17576/jsm-2017-4608-08

RNA Extractions of Mangosteen (Garcinia mangostana L.) Pericarps for Sequencing

(Pengekstrakan RNA Perikarpa Manggis (Garcinia mangostanaL.) untuk Penjujukan)

 

AZHANI ABDUL-RAHMAN, NAJAH IZZATI SULEMAN, WAN ADIBAH ZAKARIA, HOE-HAN, GOH NORMAH MOHD NOOR & WAN MOHD AIZAT*

 

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

Received: 3 June 2016/Accepted: 7 February 2017

 

ABSTRACT

This study employed several RNA extraction methods for mangosteen pericarps prior to RNA sequencing. The sequencing platform heavily relies on a high quality RNA yield. However, pericarp tissues contain a lot of phenolic compounds that results in low RNA quality. Hence, we studied several RNA extraction methods to obtain the most suitable method for the best RNA quality from the pericarps of mangosteen. Five different methods including Lopez and Gomez, modified hexadecyltrimethyl ammonium bromide (CTAB) method, several commercial kits from TranszolUP, Favorgen and Qiagen RNeasy were compared. By optimising the CTAB method, it was found to be the best method to obtain pure RNA (high A260/A280 ratio) with the highest yields (up to approximately 600-800 ng/μL concentration). The QC control of these samples using bioanalyzer validated their suitability for the downstream RNA sequencing. This report details the method for extracting high quality and high yield RNA samples from fruit that are rich in polyphenolic compounds such as mangosteen.

 

Keywords: Mangosteen; pericarp; RNA extractions; RNA-seq

 

ABSTRAK

Platform penjujukan bergantung sepenuhnya kepada hasil RNA yang berkualiti tinggi. Walau bagaimanapun, tisu kulit manggis mengandungi banyak sebatian fenol yang menyebabkan kualiti RNA menjadi rendah. Oleh itu, penyelidikan ini mengkaji beberapa kaedah pengekstrakan RNA untuk mendapatkan kaedah yang paling sesuai bagi penghasilan RNA yang berkualiti tinggi daripada perikarpa manggis. Lima kaedah yang berbeza termasuk kaedah Lopez dan Gomez, kaedah yang diubah suai daripada heksadesiltrimetil ammonium bromida (CTAB), beberapa kit komersial daripada TranszolUP, Favorgen dan Qiagen Rneasy telah dibandingkan. Dengan mengoptimumkan kaedah CTAB, ia telah didapati menjadi kaedah terbaik untuk mendapatkan RNA tulen (A260/A280 nisbah tinggi) dengan kadar hasil tertinggi (kepekatan sehingga kira-kira 600-800 ng/μL). Kawalan QC sampel ini menggunakan bioanalisis untuk disahkan kesesuaiannya bagi analisis hiliran penjujukan RNA. Laporan ini memperincikan kaedah untuk mengekstrak hasil RNA yang banyak dan berkualiti tinggi daripada buah-buahan yang kaya dengan sebatian polifenol seperti manggis.

 

Kata kunci: Manggis; pengekstrakan RNA; perikarpa; RNA-seq

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*Corresponding author; email: wma@ukm.edu.my