Four types of ncRNA (Non-coding RNA), including tRNA, snRNA, miRNA, and rRNA were predicted. We used tRNAscan-SE (v1.3.1) to predict tRNA in our genome with default parameters. The genome was aligned against Rfam (v12.0) database (Nawrocki E P et al., 2015) and based on mapping results we used infernal (v1.1.1) (Nawrocki E P & Eddy S R, 2013) to infer snRNA and miRNA. We aligned vertebrate rRNA database against Mekong tiger perch genome to predict rRNA.
The CpG islands (CGIs), which are clusters of CpGs in CG-rich regions, were identified on genome wide using CpGIScan52 with the parameters “–length 500–gcc 55–oe 0.65”.
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