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DIFFERENTIAL GENE EXPRESSION IN THE SRIKANDI HYBRID Oreochromis niloticus x O. aureus EXPOSED TO ENVIRONMENTS OF HIGHLY DIFFERENT SALINITY BY RNA SEQUENCING

Imron* and Khairul Syahputra
 
Research Institute for Fish Breeding
Jl. Raya 2 Sukamandi Pantura, Patokbeusi, Subang 41263,
West Java, Indonesia
Corresponding author: imronnawawi@kkp.go.id

Tilapia Srikandi is an interspesific hybrid resulting from crossing between female O. niloticus and male O. Aureus. It has shown a wide salinity tolerance and performed outstanding culture performance in both freshwater and brackish water, and even in marine environments. While physiological mechanisms underlying this phenomena have been investigated, less studies have been devoted  toward understanding it in genomic level. This study was aimed to dissect the patterns of gene expression at genomic level in this taxon when they were exposed to environments with highly different salinity.

Muscle tissue of fish hybrids reared in fresh water and saline water, were sampled respectively.  Genomic RNA from these samples were extracted using RNA extraction protocols, followed by Reverse Transcriptase procedures to synthesize the cDNA, and library preparation to prepare for Next Generation Sequencing (NGS). The samples were then analysed in high throughput Illumina Miseq NGS system.  The resulting data were then analysed using a series of bioinformatics pipelines. In sequential order, the pipelines implemented were FastQC, Tophat, Cufflinks, Cuffmerge, and Cuffdiff. The FastQC was carried out to check for quality of sequences before proceeding to next steps. The Tophat was applied to map and align RNA-Seq reads to stickleback Gasteroteus acuelatus genomes and then analyzed the mapping results to identify splice junctions between exons. The Cufflinks was implemented to assemble RNA transcripts and estimate their abundance, followed by Cuffmerge which merged together assemblies resulted from Cufflinks. Finally, Cuffdiff was applied to find significant changes in transcript expression, splicing, as well as promoter use.

Results show that high quality sequence data were successfully generated as indicated by Q score between 30 to 40 (Figure 1). Further, majority of gene (98%) were similarly expressed in both freshwater and saline water environments. Two percent of genes that were differentially expressed consist of 25% over expressed in saline water while 75% over expressed in freshwater. Based on this study, we suggest that high salinity tolerance of Srikandi hybrid may be associated with the presence of the genes over expressed in saline environment.




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