IDENTIFICATION AND CHARACTERIZATION OF LONG NON-CODING RNA IN BANANA INFECTED BY BLOOD DISEASE BACTERIUM (BDB)

• Main Author: MUSTIKA DEWI - Nim: 10613071, REALITA
• Format: Final Project
• Language: Indonesia
• Online Access: https://digilib.itb.ac.id/gdl/view/23865
• Institution: Institut Teknologi Bandung

<p align="justify">Long non-coding RNA (lncRNA) is transcription product with the length of more than 200 bp and does not code any polypeptide. In former researches lncRNA is known to play a role in various biological process such as disease resistance, stress tolerance, and development in certain plants and animals. However the amount, structural characteristic, and expression of lncRNA in banana are not well studied. This research aims to identify, characterises and describe the expression of lncRNA in banana species which are resistant and susceptible to BDB infection. Musa balbisiana was used as susceptible species while Musa acuminata was used as resistant species. We infected both species with BDB in the stem and incubated for a week. The stems were then cut off and we isolated the whole RNA using modified Cordeiro et al. (2008) method. The total RNA were then sequenced using Ilumina New Generation Sequencing and analysed using TopHat and Cufflinks package. We used lncRNA finder package to eliminate the sequence that does not match the lncRNA characteristic. To find the specific lncRNA that is involved in BDB resistance, we used IntaRNA which predicts the lncRNA and short RNA interaction. CatRAPID was also used to predict the lncRNA interaction protein with ACO and ACS family protein. There are 1675 and 1921 transcripts in M. balbisiana and M. acuminata that is identified as high-confidence lncRNA (hc-lncRNA) respectively. We compared the expression level of hc-lncRNA in control and infected banana sample using Cuffdiff package. There are 3% lncRNA in M. balbisiana and 31.2% and M. acuminate, which shown significantly different expression level based on Jensen-Shannon distance with Benjamini-Hochberg correction. This result support the hypothesis that there are expression modulation in banana that been infected by blood disease. Based on IntaRNA analysis there are more than 17 lncRNA in each species which have high possibilities to interact with miRNA164 that play a role in disease resistance. Interaction prediction between lncRNA with ACO and ACS family protein using catRAPID showed that some lncRNAs have negative interaction with ACO and ACS family protein. The results indicate that lncRNA might have involved in the response for BDB infection along with another RNA or protein.<p align="justify"> <br /> <br />