IDENTIFICATION AND CHARACTERIZATION OF LNCRNA FROM MULTIPLE TRANSCRIPTOMIC DATA FROM DATABASE OF BANANA PLANT (MUSA SPP.)
Long non-coding RNA (lncRNA) is one of RNAs which is trasncribed by genome DNA. It has neither Open Reading Frame (ORF), nor the potential to be encoded into protein, starting with 200 bp in length. Research about lncRNA started to develop after the discovery regarding their role as gene regulatory...
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| Format: | Final Project |
| Language: | Indonesia |
| Online Access: | https://digilib.itb.ac.id/gdl/view/42149 |
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| Institution: | Institut Teknologi Bandung |
| Language: | Indonesia |
| Summary: | Long non-coding RNA (lncRNA) is one of RNAs which is trasncribed by genome DNA. It has neither Open Reading Frame (ORF), nor the potential to be encoded into protein, starting with 200 bp in length. Research about lncRNA started to develop after the discovery regarding their role as gene regulatory mechanism which had impacts on disease response, flower development to fruit ripening in strawberry and tomato plants. Unfortunately, Characterization of lncRNA in genomic scale was yet to be done in fruit-producing plants, especially banana, one of the most produced crop in Indonesia. lncRNA characterization then became essential in regulating gene expression in banana, potentially increasing banana production yield. Identification and characterization of lncRNA were the objective of this research. Transcriptomics data in banana plants were collected from multiple databases. Cavendish (SRR924324), Berangan (SRR2132798), Yunnan (SRR6894782), Dajiao (SRR516083), and Klutuk banana transcriptomics data were retrieved from EMBL-EBI and NCBI databases and analyzed with bioinformatics workflow with specific parameters. Identified lncRNAs were processed with psRNATarget program to predict their interaction tendency with miRNAs. The results showed that each cultivar had different amount of lncRNAs, where Cavendish had the highest amount (3509 transcripts) and Berangan had the lowest (1761 transcripts). Characterization result indicated that lncRNA distribution within chromosome was not uniform, but concentrated in specific chromosome. Low lncRNA transcripts conservation were observed between all cultivars. Moreover, The result showed that most lncRNA had below 1000 bp in size (? 75% of all transcripts found). Prediction of lncRNA interaction showed that two of the lncRNA analyzed had specitivity in inhibition interaction with miRNA, which was miR397 in Cavendish transcript and miR444 in Klutuk transcript.
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