DIFFERENCES IN THE CIRCULAR RNA TRANSCRIPTOME BETWEEN WILD AND CAPTIVE-BRED NILE TILAPIA

Introduction

 Domestication  of  organisms  started  as  early  as  in the  Neolithic period (c.14 000 years ago) . Historically, f ish  domestication began almost 1000 years later than man y other species, such as cattle, dogs, pigs, and horses . Domestication  is a complex and long process in which organisms are subject to human control in many aspects, including feeding and breeding, thus changing their phenotype compare to their wild ancestors.  Accumulating shreds of evidence suggest that  domestication plays crucial roles in modulating behaviour ,  size, colouration, morphology, and physiology in teleosts (Balon  et al. 2004). These modifications are often linked to changes in genetic structure through mutations and allele fixation . Investigations into more recently domesticated species reveal that phenotypic change is relatively fast, and expression of hundreds of gene can be altered in a single generation. Epigenetic modifications ,  potentially heritable modifications of  the  chemical structure of  the  genome without affecting the nucleotide sequence, are important in  the shaping phenotypic differences during  the domestication process.  The role of m ethylation, hydroxymethylation in domestication of fish has been described in artificial selection, environmental adaptation, and genome evolution (Podgorniak et al. 2019; Konstantinidis et al. 2020). In addition, non- coding RNAs  can also influence phenotypic diversity and fitness  by regulating  transcription mechanisms and give rise to the emergence of domestication traits. Circular RNAs  (circRNAs)  are a class of  endogenous non-codin g RNAs  that  have attracted interest in transcriptional regulation. They act as miRNA sponges and  play  a  regulatory role  in normal physiology as well as in pathological conditions. Despite the  importance  of circRNAs in several biological processes , their role in  fish  domestication remains largely unknown. In the present study , we  compared  wild and first-generation Nile tilapia (Oreochromis niloticus) reared in captivity  to determine the potential role of circRNAs in domestication.

Materials and methods

 The RNA-seq  dataset for the wild and domesticated group (twelve samples) were obtained from ribosomal RNA depleted RNA-seq libraries published by Konstantinidis et al. (2021) under accession number GSE135811 in Gene Expression Omnibus. After filtering low-quality reads and adapters, sequences  were mapped into the Nile tilapia reference genome (ASM185804v2). CircRNA prediction was performed for each RNA dataset with the circRNA in silico prediction tools CIRI2. Differential expression of circRNAs between the groups was assessed using circMeta (Chen L. et al., 2020) and the host genes of circRNAs were predicted using circParser (Artem et al., 2020).

Results

A total of 7,862 circRNAs were identified  from a muscle RNA-seq dataset (n=6) using the CIRI2 algorithm. Among them, 26 circRNAs  were  present in both  wild fish and their  progeny undergoing domestication (Fig. 1).  Further analysis revealed  39 differentially  expressed (DE) circRNAs .  Several DE circRNAs originate from host genes  known to be involved in domestication, such as MHC class I  and glutamate receptor-interacting protein 2. Furthermore, a number of  DE circRNAs orthologues were found to be conserved between  many fish species. Taken together, our findings reveal a potential role  for circRNAs in fish domestication .

Acknowledgements

 This study has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme [grant agreement no 683210] and from the Research Council of Norway under the Toppforsk programme [grant agreement no 250548/F20].

References

Balon, E.K., 2004. About the oldest domesticates among fishes. Journal of fish Biology, 65, pp.1-27.

 Chen, L., Wang, F., Bruggeman, E.C., Li, C. and Yao, B. (2020). circMeta: a unified computational framework for genomic feature annotation and differential expression analysis of circular RNAs. Bioinformatics, 36(2), pp.539-545.

 Konstantinidis, I., Sætrom, P., Mjelle, R., Nedoluzhko, A.V., Robledo, D. and Fernandes, J.M. (2020). Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Epigenetics, 15(10), pp.1052-1067.

 Nedoluzhko, A., Sharko, F., Rbbani, M.G., Teslyuk, A., Konstantinidis, I. and Fernandes, J.M. (2020). CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. PeerJ, 8, p.e8757.

Podgorniak, T., Brockmann, S., Konstantinidis, I. and Fernandes, J.M., 2019. Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication. Epigenetics, 14(8), pp.818-836.