Long non-coding RNA as environmental regulator in a non-model fish

The majority of the transcribed genome does not have coding potential but is composed of non-coding transcripts that are involved in transcriptional and post-transcriptional regulation of protein-coding genes. Regulation of gene expression is important in determining the response of organisms to changes in the environment, and therefore their persistence as population or species under global change. However, lncRNAs are scarcely studied especially in non-model organisms due to the lack of a reliable pipeline for their accurate identification and annotation. Here, we present a pipeline which uses a combination of alignment-dependent and independent methods for the identification of conserved and species-specific lncRNAs from RNA-Seq data. Validation of this pipeline was performed using existing RNA-Seq data from Acanthochromis polyacanthus brain tissue, identifying a total of 4,728 lncRNAs across the whole genome, the majority of which (3,272) are intergenic. To investigate the possible implications of these lncRNAs, we estimated the expression changes of lncRNAs and neighbouring coding genes in response to ocean acidification. We found that intergenic lncRNAs might adjust the expression of neighbouring coding genes related to pH regulation, neural signal transduction and ion transport, which are known to be important in the response to ocean acidification in fish. Overall, this pipeline enables the use of existing RNA sequencing technology to reveal additional underlying molecular mechanisms involved in the response to environmental changes in non-model species by integrating the study of lncRNAs with gene expression. ### Competing Interest Statement The authors have declared no competing interest.