• Konstantinidis, Ioannis; Sætrom, Pål & Fernandes, Jorge Manuel de Oliveira (2023). Genome-wide hydroxymethylation profiles in liver of female Nile tilapia with distinct growth performance. Scientific Data. ISSN 2052-4463. 10(1), p. 1–8. doi: 10.1038/s41597-023-01996-5. Full text in Research Archive Show summary

  The mechanisms underlying the fast genome evolution that occurs during animal domestication are poorly understood. Here, we present a genome-wide epigenetic dataset that quantifies DNA hydroxymethylation at single nucleotide resolution among full-sib Nile tilapia (Oreochromis niloticus) with distinct growth performance. In total, we obtained 355 million, 75 bp reads from 5 large- and 5 small-sized fish on an Illumina NextSeq500 platform. We identified several growth-related genes to be differentially hydroxymethylated, especially within gene bodies and promoters. Previously, we proposed that DNA hydroxymethylation greatly affects the earliest responses to adaptation and potentially drives genome evolution through its targeted enrichment and elevated nucleotide transversion rates. This dataset can be analysed in various contexts (e.g., epigenetics, evolution and growth) and compared to other epigenomic datasets in the future, namely DNA methylation and histone modifications. With forthcoming advancements in genome research, this hydroxymethylation dataset will also contribute to better understand the epigenetic regulation of key genomic features, such as cis-regulatory and transposable elements.

• Nedoluzhko, Artem; Siriyappagouder, Prabhugouda; Sharko, Fedor; Galindo-Villegas, Jorge; Raeymaekers, Joost A. M. & Joshi, Rajesh [Show all 8 contributors for this article] (2023). The novel circular RNA CircMef2c is positively associated with muscle growth in Nile tilapia. Genomics. ISSN 0888-7543. 115(3), p. 1–14. doi: 10.1016/j.ygeno.2023.110598. Full text in Research Archive Show summary

  Muscle growth in teleosts is a complex biological process orchestrated by numerous protein-coding genes and non-coding RNAs. A few recent studies suggest that circRNAs are involved in teleost myogenesis, but the molecular networks involved remain poorly understood. In this study, an integrative omics approach was used to determine myogenic circRNAs in Nile tilapia by quantifying and comparing the expression profile of mRNAs, miRNAs, and circRNAs in fast muscle from full-sib fish with distinct growth rates. There were 1947 mRNAs, 9 miRNAs, and 4 circRNAs differentially expressed between fast- and slow-growing individuals. These miRNAs can regulate myogenic genes and have binding sites for the novel circRNA circMef2c. Our data indicate that circMef2c may interact with three miRNAs and 65 differentially expressed mRNAs to form multiple competing endogenous RNA networks that regulate growth, thus providing novel insights into the role of circRNAs in the regulation of muscle growth in teleosts.

• Konstantinidis, Ioannis; Sætrom, Pål; Brieuc, Marine Servane Ono; Jakobsen, Kjetill Sigurd; Liedtke, Hannes & Pohlmann, Caroline [Show all 8 contributors for this article] (2023). DNA hydroxymethylation differences underlie phenotypic divergence of somatic growth in Nile tilapia reared in common garden. Epigenetics. ISSN 1559-2294. 18(1). doi: 10.1080/15592294.2023.2282323. Full text in Research Archive Show summary

  Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study indicates that epimarkers may be applied in selective breeding programmes for superior phenotypes.

• Sharko, Fedor; Rbbani, Md Golam; Siriyappagouder, Prabhugouda; Raeymaekers, Joost A. M.; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira [Show all 7 contributors for this article] (2023). CircPrime: a web-based platform for design of specific circular RNA primers. BMC Bioinformatics. ISSN 1471-2105. 24(1). doi: 10.1186/s12859-023-05331-y. Full text in Research Archive Show summary

  Background Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing technologies and bioinformatic tools development. At the same time, polymerase chain reaction (PCR) cross-validation for circRNAs predicted by bioinformatic tools remains an essential part of any circRNA study before publication. Results Here, we present the CircPrime web-based platform, providing a user-friendly solution for DNA primer design and thermocycling conditions for circRNA identification with routine PCR methods. Conclusions User-friendly CircPrime web platform (http://circprime.elgene.net/) works with outputs of the most popular bioinformatic predictors of circRNAs to design specific circular RNA primers. CircPrime works with circRNA coordinates and any reference genome from the National Center for Biotechnology Information database).

• Solís, Francisco Javier Toledo; Fernandes, Jorge Manuel de Oliveira; Sarropoulou, Elena & Fernandez, Ignacio (2022). Non-coding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks. In Fernandez, Ignacio & Fernandes, Jorge Manuel de Oliveira (Ed.), Cellular and Molecular Approaches in Fish Biology. Academic Press. ISSN 978-0-12-822273-7. p. 105–160. doi: 10.1016/B978-0-12-822273-7.00012-4. Show summary

  Non-coding RNAs (ncRNAs) play a central role in the complex and tightly regulated processes sustaining life, from gene transcription to post-transcriptional regulation, including DNA methylation. Among the different ncRNAs, microRNAs (miRNAs) are the most extensively studied and characterized. Here, we will briefly describe their biogenesis and mechanisms of action. A broad range of methodological approaches have been applied to identify, quantify and functionally characterize miRNAs in different biological processes. Among them, high-throughput sequencing as well as the development of computational tools to predict the mRNA targets have been the most powerful approaches to determine in which biological processes miRNAs are involved and to infer the molecular pathways specifically regulated. The implementation of these methodologies in studies with different fish species have provided the first evidence of miRNAs controlling fish development, reproduction, immunocompetence, adaptation to environmental conditions and fish nutrition. Additionally, miRNAs are also potentially responsible for fish diversity. The development of different in vitro and in vivo biotechnological tools allowed researchers to go in depth and achieving their functional characterization. While an overview of all the available methodologies is here provided at a glance, the main steps of a general small RNA sequencing (RNA-Seq) protocol will be dissected as one of the most extensively used methodologies to identify and quantify miRNAs. Finally, the most recent progress on the use of these methodologies for biomarker discovery and future perspectives on the field of miRNAs will be discussed. Certainly, while knowledge gained during the last two decades increased our understanding of how miRNAs exert a key role in fish development and physiology, future efforts are needed to translate it in the use of miRNAs as more ethical and integrative biomarkers of fish physiological status and/or innovative therapies to solve important industrial bottlenecks in fish farming.

• Toledo-Solís, Francisco Javier; Fernandes, Jorge Manuel de Oliveira; Sarropoulou, Elena & Monzón, Ignacio Fernandez (2022). Noncoding RNAs in fish physiology and development: miRNAs as a cornerstone in gene networks. In Fernandez, Ignacio & Fernandes, Jorge Manuel de Oliveira (Ed.), Cellular and Molecular Approaches in Fish Biology. Academic Press. ISSN 978-0-12-822273-7. p. 105–159.
• Geraerts, Mare; Vangestel, Carl; Artois, Tom; Fernandes, Jorge Manuel de Oliveira; Jorissen, Michiel & Manda, Auguste [Show all 16 contributors for this article] (2022). Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources. Molecular Ecology. ISSN 0962-1083. 31(12), p. 3304–3322. doi: 10.1111/mec.16479.
• Jafari, Omid; Ebrahimi, Mansour; Hedayati, Ali-Akbar Hedayati; Zeinalabedini, Mehrshad; Poorbagher, Hadi & Nasrolahpourmoghadam, Maryam [Show all 7 contributors for this article] (2022). Integration of Morphometrics and Machine Learning Enables Accurate Distinction between Wild and Farmed Common Carp. Life. ISSN 2075-1729. 12(7). doi: 10.3390/life12070957. Full text in Research Archive
• Podgorniak, Tomasz; Dhanasiri, Anusha; Chen, Xianquan; Ren, Xu; Kuan, Pei-Fen & Fernandes, Jorge Manuel de Oliveira (2022). Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype. Epigenetics. ISSN 1559-2294. 17(10), p. 1281–1298. doi: 10.1080/15592294.2021.2017554. Show summary

  Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits.

• Abdelhafiz, Yousri Abdelmutalab Ahmed; Fernandes, Jorge Manuel de Oliveira; Larger, Simone; Albanese, Davide; Donati, Claudio & Jafari, Omid [Show all 8 contributors for this article] (2021). Breeding Strategy Shapes the Composition of Bacterial Communities in Female Nile Tilapia Reared in a Recirculating Aquaculture System. Frontiers in Microbiology. ISSN 1664-302X. 12, p. 1–16. doi: 10.3389/fmicb.2021.709611. Full text in Research Archive Show summary

  In industrial animal production, breeding strategies are essential to produce offspring of better quality and vitality. It is also known that host microbiome has a bearing on its health. Here, we report for the first time the influence of crossbreeding strategy, inbreeding or outbreeding, on the buccal and intestinal bacterial communities in female Nile tilapia (Oreochromis niloticus). Crossbreeding was performed within a family and between different fish families to obtain the inbred and outbred study groups, respectively. The genetic relationship and structure analysis revealed significant genetic differentiation between the inbred and outbred groups. We also employed a 16S rRNA gene sequencing technique to understand the significant differences between the diversities of the bacterial communities of the inbred and outbred groups. The core microbiota composition in the mouth and the intestine was not affected by the crossbreeding strategy but their abundance varied between the two groups. Furthermore, opportunistic bacteria were abundant in the buccal cavity and intestine of the outbred group, whereas beneficial bacteria were abundant in the intestine of the inbred group. The present study indicates that crossbreeding can influence the abundance of beneficial bacteria, core microbiome and the inter-individual variation in the microbiome.

• Rbbani, Md Golam; Nedoluzhko, Artem; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira (2021). Function of Circular RNAs in Fish and Their Potential Application as Biomarkers. International Journal of Molecular Sciences. ISSN 1661-6596. 22(13), p. 1–19. doi: 10.3390/ijms22137119. Full text in Research Archive Show summary

  Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.

• Konstantinidis, Ioannis; Anastasiadi, Dafni; Sætrom, Pål; Nedoluzhko, Artem; Mjelle, Robin & Podgorniak, Tomasz [Show all 8 contributors for this article] (2021). Epigenetic mapping of the somatotropic axis in Nile tilapia reveals differential DNA hydroxymethylation marks associated with growth. Genomics. ISSN 0888-7543. 113(5), p. 2953–2964. doi: 10.1016/j.ygeno.2021.06.037. Full text in Research Archive Show summary

  In vertebrates, the somatotropic axis comprising the pituitary gland, liver and muscle plays a major role in myogenesis. Its output in terms of muscle growth is highly affected by nutritional and environmental cues, and thus likely epigenetically regulated. Hydroxymethylation is emerging as a DNA modification that modulates gene expression but a holistic characterization of the hydroxymethylome of the somatotropic axis has not been investigated to date. Using reduced representation 5-hydroxymethylcytosine profiling we demonstrate tissue-specific localization of 5-hydroxymethylcytosines at single nucleotide resolution. Their abundance within gene bodies and promoters of several growth-related genes supports their pertinent role in gene regulation. We propose that cytosine hydroxymethylation may contribute to the phenotypic plasticity of growth through epigenetic regulation of the somatotropic axis.

• Nedoluzhko, Artem; Mjelle, Robin; Renström, Maria; Skjærven, Kaja H.; Piferrer, Francesc & Fernandes, Jorge Manuel de Oliveira (2021). The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation. Genomics. ISSN 0888-7543. 113(5), p. 3050–3057. doi: 10.1016/j.ygeno.2021.07.007. Full text in Research Archive Show summary

  DNA methylation is one of the main epigenetic mechanisms that regulate gene expression in a manner that depends on the genomic context and varies considerably across taxa. This DNA modification was first found in nuclear genomes of eukaryote several decades ago and it has also been described in mitochondrial DNA. It has recently been shown that mitochondrial DNA is extensively methylated in mammals and other vertebrates. Our current knowledge of mitochondrial DNA methylation in fish is very limited, especially in non-model teleosts. In this study, using whole-genome bisulfite sequencing, we determined methylation patterns within non-CpG (CH) and CpG (CG) contexts in the mitochondrial genome of Nile tilapia, a non-model teleost of high economic importance. Our results demonstrate the presence of mitochondrial DNA methylation in this species predominantly within a non-CpG context, similarly to mammals. We found a strand-specific distribution of methylation, in which highly methylated cytosines were located on the minus strand. The D-loop region had the highest mean methylation level among all mitochondrial loci. Our data provide new insights into the potential role of epigenetic mechanisms in regulating metabolic flexibility of mitochondria in fish, with implications in various biological processes, such as growth and development.

• Abdelhafiz, Yousri Abdelmutalab Ahmed; Fernandes, Jorge Manuel de Oliveira; Stefani, Erika; Albanese, Davide; Donati, Claudio & Kiron , Viswanath (2021). Power Play of Commensal Bacteria in the Buccal Cavity of Female Nile Tilapia. Frontiers in Microbiology. ISSN 1664-302X. 12. doi: 10.3389/fmicb.2021.773351. Full text in Research Archive Show summary

  Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.

• Lopez-Canovas, Amanda; Cabas, Isabel; Chaves-Pozo, Elena; Ros-Chumillas, Maria; Navarro-Segura, Laura & Lopez-Gomez, Antonio [Show all 9 contributors for this article] (2020). Nanoencapsulated Clove Oil Applied as an Anesthetic at Slaughtering Decreases Stress, Extends the Freshness and Lengthens Shelf Life of Cultured Fish. Foods. ISSN 2304-8158. 9(12), p. 2–20. doi: 10.3390/foods9121750. Full text in Research Archive Show summary

  In the aquaculture industry, fish are stunned using a wide range of methods, but all of them trigger stress responses and affect the fish flesh quality. Chilled water is considered one of the most efficient methods, but even this is not a stress-free experience for the fish. Anesthetics included in the ice slurry or in water could decrease this stress and delay the loss of flesh quality. In this work, we analyze the effect of clove oil (CO) nanoencapsulated in β-cyclodextrins (β-CD) (CO + β-CD), incorporated in the stunning bath, on the stress response and the organoleptic attributes of fresh marine and freshwater fish from four economically important fish species: Atlantic salmon, European seabass, Nile tilapia, and Rainbow trout. CO + β-CD reduces the time required to induce anesthesia, independently of water salinity, habitat or water temperature. The plasmatic glucose and cortisol levels decreased in all four species, although the concentrations of CO varied between species. Moreover, plasmatic lactate level differed between the marine and freshwater fish. The use of CO + β-CD extended the shelf life of fish from all the species studied (by 3–7 days). In conclusion, using CO encapsulated in β-CD for anesthetizing fish can be regarded as an improved fish-stunning technique that reduces the anesthesia-induction time, decreases the stress response, and extends the shelf life of fresh fish.

• Konstantinidis, Ioannis; Sætrom, Pål; Mjelle, Robin; Nedoluzhko, Artem; Robledo, Diego & Fernandes, Jorge Manuel de Oliveira (2020). Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Epigenetics. ISSN 1559-2294. 15(10), p. 1052–1067. doi: 10.1080/15592294.2020.1748914. Full text in Research Archive Show summary

  The historically recent domestication of fishes has been essential to meet the protein demands of a growing human population. Selection for traits of interest during domestication is a complex process whose epigenetic basis is poorly understood. Cytosine hydroxymethylation is increasingly recognized as an important DNA modification involved in epigenetic regulation. In the present study, we investigated if hydroxymethylation plays a role in fish domestication and demonstrated for the first time at a genome-wide level and single nucleotide resolution that the muscle hydroxymethylome changes after a single generation of Nile tilapia (Oreochromis niloticus, Linnaeus) domestication. The overall decrease in hydroxymethylcytosine levels was accompanied by the downregulation of 2015 genes in fish reared in captivity compared to their wild progenitors. In contrast, several myogenic and metabolic genes that can affect growth potential were upregulated. There were 126 differentially hydroxymethylated cytosines between groups, which were not due to genetic variation; they were associated with genes involved in immune-, growthand neuronal-related pathways. Taken together, our data unveil a new role for DNA hydroxymethylation in epigenetic regulation of fish domestication with impact in aquaculture and implications in artificial selection, environmental adaptation and genome evolution.

• Nedoluzhko, Artem; Slobodova, Natalia; Sharko, Fedor S.; Shalgimbayeva, Gulmira; Tsygankova, Svetlana V. & Boulygina, Eugenia S. [Show all 13 contributors for this article] (2020). A new strain group of common carp: The genetic differences and admixture events between Cyprinus carpio breeds. Ecology and Evolution. ISSN 2045-7758. 10(12), p. 5431–5439. doi: 10.1002/ece3.6286. Full text in Research Archive Show summary

  Common carp (Cyprinus carpio ) has an outstanding economic importance in freshwater aquaculture due to its high adaptive capacity to both food and environment. In fact, it is the third most farmed fish species worldwide according to the Food and Agriculture Organization. More than four million tons of common carp are produced annually in aquaculture, and more than a hundred thousand tons are caught from the wild. Historically, the common carp was also the first fish species to be domesticated in ancient China, and now, there is a huge variety of domestic carp strains worldwide. In the present study, we used double digestion restriction site‐associated DNA sequencing to genotype several European common carp strains and showed that they are divided into two distinct groups. One of them includes central European common carp strains as well as Ponto–Caspian wild common carp populations, whereas the other group contains several common carp strains that originated in the Soviet Union, mostly as cold‐resistant strains. We believe that breeding with wild Amur carp and subsequent selection of the hybrids for resistance to adverse environmental conditions was the attribute of the second group. We assessed the contribution of wild Amur carp inheritance to the common carp strains and discovered discriminating genes, which differed in allele frequencies between groups. Taken together, our results improve our current understanding of the genetic variability of common carp, namely the structure of natural and artificial carp populations, and the contribution of wild carp traits to domestic strains.

• Nedoluzhko, Artem; Sharko, Fedor S.; Rbbani, Md Golam; Teslyuk, Anton; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2020). CircParser: a novel streamlined pipeline for circular RNA structure and host gene prediction in non-model organisms. PeerJ. ISSN 2167-8359. 8. doi: 10.7717/peerj.8757. Full text in Research Archive Show summary

  Circular RNAs (circRNAs) are long noncoding RNAs that play a significant role in various biological processes, including embryonic development and stress responses. These regulatory molecules can modulate microRNA activity and are involved in different molecular pathways as indirect regulators of gene expression. Thousands of circRNAs have been described in diverse taxa due to the recent advances in high throughput sequencing technologies, which led to a huge variety of total RNA sequencing being publicly available. A number of circRNA de novo and host gene prediction tools are available to date, but their ability to accurately predict circRNA host genes is limited in the case of low-quality genome assemblies or annotations. Here, we present CircParser, a simple and fast Unix/Linux pipeline that uses the outputs from the most common circular RNAs in silico prediction tools (CIRI, CIRI2, CircExplorer2, find_circ, and circFinder) to annotate circular RNAs, assigning presumptive host genes from local or public databases such as National Center for Biotechnology Information (NCBI). Also, this pipeline can discriminate circular RNAs based on their structural components (exonic, intronic, exon-intronic or intergenic) using a genome annotation file.

• Podgorniak, Tomasz Krzysztof; Brockmann, Sven; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (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. ISSN 1559-2294. 14(8), p. 818–836. doi: 10.1080/15592294.2019.1618164. Full text in Research Archive Show summary

  Growth is a complex trait whose variability within a population cannot be explained solely by genetic variation. Epigenetic regulation is often suggested as an important factor shaping the phenotype, but its association with growth can be highly context- and species-dependent. Nevertheless, the mechanisms involved in epigenetic regulation of growth in fish are poorly understood. We have used reduced representation bisulphite sequencing to determine the genome-wide CpG methylation patterns in male and female Nile tilapia of different sizes but at the same early stage of domestication. The average CpG methylation level in the reduced genome representation was 63% across groups but many sites displayed group-specific methylation patterns. The number of differentially methylated (DM) CpGs was much higher when the interaction between sex and weight was included rather than when these factors were considered separately. There were 1128 DM CpGs between large and small females and 970 DM CpGs between large and small males. We have found many growth-related genes associated with DM CpGs, namely map3k5 and akt3 in females and gadd45g and ppargc1a in males. Only 5% of CpG locations associated with growth were common to both sexes. In particular, the autophagy-related gene atg14 displayed a high association of methylation with growth exclusively in males. The sexually dimorphic association between atg14 methylation and growth may uncover novel metabolic mechanisms at play during mouth brooding in Nile tilapia females. Taken together, our data suggest that epigenetic regulation of growth in Nile tilapia involves different gene networks in males and females.

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• Fernandez, Ignacio & Fernandes, Jorge Manuel de Oliveira (2022). Cellular and Molecular Approaches in Fish Biology. Academic Press. ISBN 978-0-12-822273-7. 438 p.
• Fernandes, Jorge Manuel de Oliveira; Sarropoulou, Elena; Kiron , Viswanath; Power, Deborah M. & Liu, John (2018). GIA2018: 5th International Symposium on Genomics in Aquaculture : Book of Abstracts. CCWP Events Lda. ISBN 978-989-99099-3-9. 62 p.

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• Rbbani, Md Golam; Nedoluzhko, Artem; Sharko, Fedor; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2021). Differences in the circular RNA transcriptome between wild and captive-bred Nile tilapia.
• Rbbani, Md Golam; Nedoluzhko, Artem; Siriyappagouder, Prabhugouda; Raeymaekers, Joost A. M.; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira (2021). Exploration of circRNA , miRNA and mRNA expression to identify their role in growth regulation in Nile tilapia.
• Konstantinidis, Ioannis; Sætrom, Pål; Liedtke, Hannes; Pohlmann, Caroline; Tsoulia, Thomais & Fernandes, Jorge Manuel de Oliveira (2021). Differences in liver DNA hydroxymethylation reflect the growth phenotype.
• Nedoluzhko, Artem; Rbbani, Md Golam; Sharko, Fedor; Siriyappagouder, Prabhugouda; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira (2021). Circular RNA workflow analysis and its application in aquaculture.
• Fernandes, Jorge Manuel de Oliveira (2021). Trends and limitations of epigenetic biomarkers.
• Fernandes, Jorge Manuel de Oliveira (2021). Unveiling the massive epigenome changes that occur during Nile tilapia domestication.
• Rbbani, Md Golam; Nedoluzhko, Artem; Siriyappagouder, Prabhugouda; Raeymaekers, Joost A. M.; Galindo-Villegas, Jorge & Fernandes, Jorge Manuel de Oliveira (2021). circRNA, miRNA and mRNA muscle transcriptomes indicate their role in growth regulation in Nile tilapia.
• Nedoluzhko, Artem; Sharko, Fedor; Rbbani, Md Golam; Teslyuk, Anton; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2021). Circular RNA host gene prediction in Nile tilapia using the novel circParser pipeline.
• Konstantinidis, Ioannis; Sætrom, Pål; Brieuc, Marine Servane Ono; Jakobsen, Kjetill Sigurd; Liedtke, Hannes & Pohlmann, Caroline [Show all 8 contributors for this article] (2021). DNA hydroxymethylation is linked to higher growth rate in Nile tilapia.
• Nedoluzhko, Artem; Mjelle, Robin; Renström, Maria; Skjærven, Kaja Helvik; Piferrer, Francesc & Fernandes, Jorge Manuel de Oliveira (2021). The mitochondrial 5-methylcytosine profile in Nile tilapia (Oreochromis niloticus).
• Nedoluzhko, Artem; Sharko, Fedor S.; Rabbani, Md Golam; Teslyuk, Anton; Konstantinidis, Ioannis & Fernandes, Jorge Manuel de Oliveira (2020). Circular RNA host gene and orthologue prediction using the self-designed CircParser pipeline.
• Nedoluzhko, Artem; Dandara Da Silva Berrutti, Paula; Guimarães, Igo Gomes; Konstantinidis, Ioannis; Babiak, Igor & Fernandes, Jorge Manuel de Oliveira (2020). Hydroxymethylation changes during early embryonic development in zebrafish.
• Fernandes, Jorge Manuel de Oliveira & Renström, Maria (2020). Mitochondrial DNA methylation in Nile tilapia Oreochromis niloticus.
• Fernandes, Jorge Manuel de Oliveira (2020). Epigenetics in aquaculture.
• Fernandes, Jorge Manuel de Oliveira (2019). Hooking the bigger fish through epigenetics. EU Research.
• Fernandes, Jorge Manuel de Oliveira (2019). Developmental plasticity of growth in teleosts.
• Fernandes, Jorge Manuel de Oliveira; Konstantinidis, Ioannis; Nedoluzhko, Artem & Mjelle, Robin (2019). Muscle transcriptome changes within one generation of Nile tilapia domestication.
• Konstantinidis, Ioannis; Sætrom, Pål & Fernandes, Jorge Manuel de Oliveira (2019). Tissue-specific hydroxymethylome profiles of Nile tilapia Oreochromis niloticus at single nucleotide resolution.
• Fernandes, Jorge Manuel de Oliveira; Konstantinidis, Ioannis; Pohlmann, Caroline; Tsoulia, Thomais & Liedtke, Hannes (2019). Differences in liver hydroxymethylomes of Nile tilapia with distinct growth rates.
• Wardale, Alex; Podgorniak, Tomasz Krzysztof; Renström, Maria; Babiak, Igor & Fernandes, Jorge Manuel de Oliveira (2018). Circulating micrornas as potential biomarkers of growth in Nile tilapia (Oreochromis niloticus). Show summary

  Aquaculture has become the fastest growing food-producing sector in the world. In particular, the increase in production of Nile tilapia (Oreochromis niloticus) has been of great significance in driving global demand and consumption, especially in developing countries. Therefore, establishing molecular biomarkers related to growth is of high relevance to the aquaculture industry. MicroRNAs (miRNAs) are small (~22 nt) non-coding RNAs involved primarily in post-transcriptional gene regulation and are implicated in a wide variety of physiological processes. Extracellular miRNAs that circulate in blood are particularly interesting as non-invasive biomarkers. In this study, Illumina compatible small RNA libraries were sequenced using the NextSeq 500 next-generation sequencer. We profiled blood serum miRNAs in fish of the same age, but different sizes. Four miRNAs were differentially expressed with size. Their predicted targets included the serum response factor (SRF) and myocyte enhancer factor 2a transcript (MEF2A). Down-regulation of the proteins encoded by these genes could result in reduced myoblast proliferation and increased skeletal muscle differentiation in large fish, respectively. These differentially expressed circulating miRNAs could potentially be used as biomarkers of growth. Acknowledgements: This project 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).

• Konstantinidis, Ioannis; Sætrom, Pål & Fernandes, Jorge Manuel de Oliveira (2018). Fast muscle hydroxymethylation patterns in wild and captive Nile tilapia (Oreochromis niloticus) provide insights into fish domestication. Show summary

  Introduction: Many studies in fish domestication have detected significant gene expression changes across generations. However, these changes cannot be explained entirely neither with the occurrence of mutations nor with changes in allele frequencies (Christie et al.,2016). DNA hydroxymethylation (5hmC) is one of the epigenetic modifications that can alter gene expression without causing any changes in the DNA sequence. It can serve both as an intermediate step in the demethylation process and as a stable epigenetic modification. The sustainable future of the aquaculture industry is relying more than ever on the domestication of fish species. Thus, a closer look into the epigenetic machinery of several cultivated fish species could provide significant insight into addressing these findings. Luyer et al.,(2017) provided recent evidence that hatchery conditions affect the epigenetic landscape, which has impact on the fitness of the species in question. However, methylation (5mC) analysis such as RRBS and WGBS cannot discriminate distinct epigenetic mechanisms such as 5mC and 5hmC. In this study, we compare for the first time the 5hmC profiles of wild Nile tilapia (Oreochromis niloticus) females and their female offspring reared in captivity. Our goal is to map the hydroxymethylome of these individuals, detect stable 5hmC loci and find inherited patterns and significant differences within the first stage of their domestication. Materials and Methods: Fast muscle from wild female Nile tilapia was sampled from river Nile, Luxor, Egypt. Their eggs were kept in egg rockers until 3-5 days post-hatching and then transferred to Mørkvedbukta research station in Bodø, Norway. After 5 months, fast muscle samples were taken from the first generation in captivity. Global 5hmC levels were calculated by liquid chromatography/mass spectrometry (LC/MS) analysis while the hydroxymethylation mapping at a single nucleotide level was determined by the reduced representation hydroxymethylation profiling (RRHP, Zymo Research). The sequencing was performed on an Illumina HiSeq 4000 platform at the Norwegian Sequencing Center. In order to identify differentially hydroxymethylated regions we have used R, the limma package and the software Circos for data visualization. Results and Discussion: The present study provides the first insight of 5hmC profiling during the first stage of domestication in fish. Our findings indicate significant differences between the wild and the first generation of reared Nile tilapia at both global 5hmC and single nucleotide levels (adj.p <0.05). In general, 5hmC levels are 14.9% higher in the wild individuals according to LC/MS results (p=0.04). Analysis of the differentially hydroxymethylated regions is leading us towards the understanding of how this epigenetic modification affects gene expression and how it may be involved in phenotypic changes observed during fish domestication. 20 Acknowledgements: I would like to thank the staff members of the research station Mørkvedbukta as well as the EPIFISH team for providing help with fish husbandry and sampling. This study is part of the EPIFISH project, which has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 683210) with additional support from the Research Council of Norway under the Toppforsk programme (grant agreement no 250548/F20). References M. R. Christie, M. L. Marine, S. E. Fox, R. A. French and M. S. Blouin 2016. A single generation of domestication heritably alters the expression of hundreds of genes. Nature Communications 7:10676. J. Luyer, M. Laporte, T.D. Beacham, K.H. Kaukinen, R.E. Withler,J.S. Leong, E.B. Rondeau, B.F. Koop and L. Bernatchez 2017. Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon. Proceedings of the National Academy of Sciences of the United States of America 114 (49): 12964-12969.

• Podgorniak, Tomasz Krzysztof; Brockmann, Sven & Fernandes, Jorge Manuel de Oliveira (2018). Growth-related epigenetic crossroads in fast muscle of Nile tilapia sharing a similar genetic background. Show summary

  Fish growth rate is one of the crucial factors for a sustainable and profitable aquaculture. Thus, many studies in applied research focused on growth improvement strategies, starting from selective breeding favoring specific gene candidates to optimization of rearing conditions. While artificial selection is based on a priori known genetic differences between slow and fast-growing phenotypes, little is still known on epigenetic mechanisms underlying growth rate differences. In order to get insights into epigenetic mechanisms regulating growth phenotype in tilapia, we used reduced representation bisulfite sequencing (RRBS) to compare the fast muscle methylomes of slow and fast growing fish coming from the same mother. Our hypothesis is that they could explain differences in phenotype patterns even when the parental background is similar. In this study, we compared the methylome of 24 fish (12 large- and 12 small-sized individuals, evenly distributed sex). We found that CpG methylation is related to body weight, but often in a sex-dependent manner. For example, the location of hypermethylated sites in large females were different from hypermethylated sites in large males. Only few CpG sites shared the same methylation patterns between the sexes. Surprisingly, several highly significant differentially methylated cytosines related to fast growth showed the opposite patterns between sexes. Enrichment analysis performed on each set of genes revealed the diversity of biological processes involved in growth regulation and suggests sex-specific pathways. Based on gene ontology terms, we found several connections between cytosine methylation, histone methylation and transcription factors suggesting that epigenetic regulation of growth in Nile tilapia takes place at different levels. Acknowledgements: This project 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).

• Ekvall, Hans; Konstantinidis, Ioannis; Podgorniak, Tomasz Krzysztof & Fernandes, Jorge Manuel de Oliveira (2018). DNA hydroxy- and methylation profiles of the Nile tilapia pituitary link hypermethylation and hyperhydroxymethylation to faster growth. Show summary

  Nile tilapia (Oreochromis niloticus) are amongst the most widely grown species in aquaculture and along with other tilapia species are the second most cultured fish worldwide. Its popularity arises from many positive production traits, of which growth rate is one of the most important. The pituitary gland is positioned at the center of several endocrine axes of hormonal pathways that affect behaviour, metabolism, stress response, and somatic growth. In particular, the hypothalamic–pituitary–somatotropic axis has a major influence in growth rates of fish. Candidate gene methylation studies of the tilapia pituitary have shown 5-methylcytosine (5mC) to be associated with the regulation of nearby gene expression and in sexually dimorphic growth in Nile tilapia. An extensive methylome profile of the tilapia pituitary could therefore reveal more growth associated methylation patterns. In this study, reduced representation profiling (RRHP) was used to identify differences in both 5mC and 5-hydroxymethylcytosine (5hmC) patterns between full siblings with both low and high growth rates and further compared to unrelated fast-growing tilapia. The results suggest that the significantly different loci in both DNA modification profiles tend to overlap. Furthermore, hypermethylation and hyperhydroxymethylation in fast growing fish drive most of the significant differences compared to slow growing fish. Several pituitary methylation marks associated with growth and nearby genes potentially involved in endocrine pathways were identified. In conclusion, the differentially methylated loci in the pituitary epigenome point to candidate epigenetic markers of growth. Acknowledgements: This project 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).

• Fernandes, Jorge Manuel de Oliveira; Konstantinidis, Ioannis & Podgorniak, Tomasz Krzysztof (2018). Growth-associated DNA methylation and hydroxymethylation marks in Nile tilapia muscle. Show summary

  Fish domestication is a rather complex process that results from a combination of random genetic drift, artificial selection for specific traits and adaptive selection to captivity conditions. The number of domesticated fish species of commercial importance is still limited but several breeding programmes have been established to selectively improve relevant traits, such as growth. In Nile tilapia (Oreochromis niloticus), growth performance has been dramatically increased through selective breeding to achieve an increase in weight of 10-15% per generation over more than 6 generations. The aquaculture industry has recently acknowledged the potential of epigenomic programming as a means of improving growth but little is known about the mechanisms underlying epigenetic regulation of muscle growth in fish. Cytosine methylation (5mC) and hydroxymethylation (5hmC) are the two main DNA modifications that play a key role in epigenetic regulation of gene expression in animals. The aim of this study was to compare the muscle methylomes and hydroxymethylomes between fast- and slow-growing full-sib Nile tilapia. Associations between 5mC/ 5hmC and growth performance revealed that epigenetic regulation of growth affects several genes and biological processes in a sex-specific manner. In female Nile tilapia, hyperhydroxymethylation of one gene of the ERM family was associated with improved growth. Moreover, methylation levels at 63 CpG positions were significantly different between small and large fish regardless of their gender. These CpGs were mostly intergenic but some were linked to genes involved in biological processes related to histone methylation and binding. If validated, such growth epimarkers could be used in future breeding programmes integrating epigenomic selection. Acknowledgement: This project 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). Keywords: Epigenetics; Domestication; Selective Breeding; Nile tilapia; Growth

• Fernandes, Jorge Manuel de Oliveira; Wardale, Alex; Podgorniak, Tomasz Krzysztof & Babiak, Igor (2018). Growth-associated circulating miRNAs in Nile tilapia Oreochromis niloticus. Show summary

  MicroRNAs (miRNAs) are small non-coding RNAs that negatively regulate their target mRNAs by binding to 3′ untranslated regions, thus resulting in translational inhibition or transcript degradation. They are involved in most biological processes, including muscle development and growth. Extracellular miRNAs found in blood are potential biomarkers of growth but to date they are poorly characterized in fish. As one of the main production traits in aquaculture, growth is often targeted in selective breeding programmes of commercial fish species. The aim of this study was to determine the miRNA transcriptomes in blood serum of small (x̅=87 g) and large (x̅=332 g) Nile tilapia (Oreochromis niloticus) females of the same age and reared under identical conditions. Next-generation sequencing using the Illumina platform revealed a total of 371 different miRNA transcripts in the blood serum of Nile tilapia. The most abundant miRNAs belonged to the let-7 family, which is known to regulate cell proliferation and immunity. There were clear differences in miRNA transcriptomes between small and large fish (Fig. 1). Two and four miRNA genes had significantly higher and lower transcript levels in large fish compared to their small counterparts, respectively (|fold change|>1.5, adjusted p-value<0.05). The differentially expressed miRNAs play important roles in muscle development in Nile tilapia and their putative targets include genes involved in myoblast proliferation and regulation of muscle growth (e.g., insulin-like growth factor 1). Hence, these circulating miRNAs are promising candidate biomarkers of growth that could contribute to sustainability of Nile tilapia farming. Acknowledgement: This project 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).

• Konstantinidis, Ioannis; Fernandes, Jorge Manuel de Oliveria & Sætrom, Pål (2017). The first hydroxymethylation map of fast muscle in Nile tilapia (Oreochromis niloticus).
• Podgorniak, Tomasz Krzysztof; Brockmann, Sven & Fernandes, Jorge Manuel de Oliveria (2017). Growth and the DNA methylation landscape in pituitary and fast muscle of Nile tilapia (Oreochromis niloticus).
• Fernandes, Jorge Manuel de Oliveria; Podgorniak, Tomasz Krzysztof & Brockmann, Sven (2017). A reduced representation of the DNA methylome in fast muscle of Nile tilapia Oreochromis niloticus.
• Fernandes, Jorge Manuel de Oliveria (2017). The emerging field of epigenetics in aquaculture.
• Fernandes, Jorge Manuel de Oliveria; Podgorniak, Tomasz Krzysztof & El-Zaeem, Samy (2016). Expression changes of miRNAs involved in epigenetic regulation are associated with domestication in Nile tilapia (Oreochromis niloticus).
• Fernandes, Jorge Manuel de Oliveira (2016). EPIFISH: Innovative Epigenetic Markers for Fish Domestication.
• Iqbal, Ramsha; Fernandes, Jorge Manuel de Oliveira; Bjørnevik, Marit & Galindo-Villegas, Jorge (2023). Changes of fast muscle cellularity in male and female Nile tilapia (Oreochromis niloticus) over three generations of domestication. Nord universitet. Show summary

  The demand for food consumption is increasing as the population of the world is growing. Aquaculture industries are playing a crucial role to maximize the production and quality of fish. Domestication has been extensively used in animals to modify phenotypes such as growth. Nile tilapia (O. niloticus) is one of the most consumed fish globally. The study aimed to examine the skeletal muscle cellularity in three generations (F1, F2, and F3) of Nile tilapia under domestication. The F0 offspring were bred in captivity and the F1 generation was obtained successfully. After three months of F1 generation in captivity, selected and control groups (including male and female) were divided on the basis of their weight. Selected fish had a weight at least 10 % higher than the average weight of all fish. The other generations F2 and F3 also followed the same procedure to divide into selected and control groups. Selected and control groups were kept in separate tanks. Fast muscle was sampled from fish across all three captivity generations (F1, F2 and F3), albeit at different ages. In each generation, we picked randomly 40 fish (20 males and 20 females) from each selected and control group. Biometric data such as body weight, total length and standard length were recorded for each fish. In addition, histological samples were prepared to examine the growth and development of fast muscle at each generation. In each generation, all male groups had larger fast muscle fibre diameter, weight and length than female groups. The study shows that the selected male groups from each generation contained the highest mean values for weight and length than control male groups. There were significant differences (P<0.05) in weight and length between control and selected male groups in F1 and F3 but not in F2. Control and selected females from F3 showed significant differences in growth. The higher number of larger muscle fibres observed in selected groups suggests that hypertrophy is one of the mechanisms involved in improved growth during domestication.

• Fernandes, Jorge Manuel de Oliveira & Konstantinidis, Ioannis (2020). DNA hydroxymethylation and improved growth of Nile tilapia (Oreochromis niloticus) during domestication. Nord universitet. Full text in Research Archive Show summary

  The worldwide demand for fish consumption is highly dependent on aquaculture production because commercial fishing reached its maximum exploitation since the 90’s. However, continued expansion of the aquaculture industry in a sustainable manner is dependent on several factors, including domestication of new species and establishment of selective breeding programmes. Domestication of new fish species is a rather complex and long process but the deployment of new molecular tools could improve and accelerate it through the holistic characterization of fish genomes. This thesis is based on the hypothesis that epigenetic mechanisms underlie genome-wide adaptation under captivity, since genetic mutations and allele shifts alone cannot explain the rapid transcriptomic changes of fish undergoing domestication. In a series of experiments, we investigated the role of DNA hydroxymethylation during the early stages of fish domestication, and its potential involvement in regulating somatic growth. At first, we discovered that the DNA hydroxymethylome in fast muscle changes rapidly within a single generation of domestication. As a result of our 5-hydroxymethylcytosine (5hmC) profiling at single nucleotide resolution, we were able to identify that 5hmCs are largely enriched within gene bodies, which supports the notion that they are functionally relevant epigenetic modifications. The annotation of differentially hydroxymethylated genes between wild and first-generation of fish under captivity revealed that the changes occurred primarily within genes involved in immunity, growth and neuronal activity. By comparing gene expression profiles in muscle between wild and first generation of Nile tilapia in captivity, we showed that immune-related genes were upregulated in the wild fish, while genes involved in metabolism and muscle-specific functions were downregulated. These findings revealed that the first generation of fish undergoing domestication is strongly influenced by the environmental conditions under captivity, namely the lack of pathogens and the optimal conditions of water temperature, oxygen, pH and diet. Thus, we provided for the first time a link between environmentally-mediated DNA hydroxymethylation and gene regulation in fish undergoing domestication. To further explore the connection between DNA hydroxymethylation and somatic growth, we compared the liver hydroxymethylomes of slow- and fast-growing full siblings and examined the 5hmC abundance in three major tissues that compose the somatotropic axis. Interestingly, we identified several differentially hydroxymethylated genes between slowand fast-growers. These genes were involved in signaling pathways related to cell growth, survival and proliferation such as the PI3K-Akt, the Ras- and Rho- protein signal transduction pathways. By comparing the DNA hydroxymethylomes among the muscle, liver and pituitary, we identified several differentially hydroxymethylated growth factors, receptors and enhancers with major implications in growth, metabolism and skeletal muscle development. Taken together, this thesis provides for the first time a direct link between DNA hydroxymethylation and fish domestication and associates epigenetic marks at single nucleotide resolution to somatic growth using cutting-edge molecular tools. When validated, these epigenetic markers can potentially improve current breeding strategies in aquaculture by providing a holistic approach for broodstock selection.

• Fernandes, Jorge Manuel de Oliveira & Wardale, Alex (2019). Circulating miRNAs as potential non-invasive biomarkers of growth in Nile tilapia (Oreochromis niloticus). Nord universitet. Show summary

  Our reliance on aquaculture for food security has significantly increased with an underestimated 9 billion people by 2050. In particular, the increase in production of Nile tilapia (Oreochromis niloticus) has been of great significance in driving global demand and consumption, especially in developing countries. Recent advances in sequencing technology have allowed us to identify molecular biomarkers, ultimately increasing production in various food producing sectors. In this study, blood serum samples were collected from Nile tilapia females of different sizes, reared under identical conditions, with the aim of identifying potential non-invasive biomarkers of growth. Next generation sequencing using the Illumina platform revealed 8 differentially expressed microRNAs between slow and fast-growing fish. In fast-growing fish, miR-122 and miR-24a were found upregulated (fold change 4.2 and 1.8, respectively), while downregulated miRNAs included miR-133b (fold change -5.4), miR-206 (fold change -3.4), miR-133a (fold change -3.3), miR-130b (fold change -2.4), miR-196a (fold change -2.1) and miR-10a (fold change -1.8). Of these, miR-122, miR-24a, miR-133, miR-206 were found to have important roles in muscle development and growth. Previous studies have revealed the crucial role of miR-206 in Nile tilapia growth, as well as its suitability and robustness as a serum biomarker in other organisms. The validation of these miRNAs and their putative targets could potentially lead to their use in tilapia selective breeding programmes, ultimately resulting in reduced losses and increased profit in the aquaculture industry.

• Ekvall, Hans Erland & Fernandes, Jorge Manuel de Oliveira (2018). Growth associated DNA methylation and hydroxymethylation profiles of the Nile tilapia (Oreochromis niloticus) pituitary uncover potential epigenetic markers. Nord universitet. Show summary

  The Nile tilapia (Oreochromis niloticus) is the world’s most widely farmed aquaculture species. The rate at which these fish grow is of central importance to farmers and sustainable production. Growth is a complex trait and playing a key role in growth are the hormones of the endocrine system in particular the pituitary gland. An ever‐increasing understanding of epigenetics (‘heritable’ changes to gene function apart from changes in underlying DNA sequence) suggest that there could be an important role for epigenetic marks to play in determining differences in growth. Therefore, connecting epigenetic mark differences, like DNA modifications, to fish of different growth rates could reveal parts of the epigenome that potentially influence growth. To that aim, this study uses a method that interrogates the ‘CCGG’ DNA sequence motif along the entire tilapia pituitary genome for such differences, in two DNA modifications, 5‐methylcytosine (5mC) and 5‐hydroxymethylcytosine (5hmC). The outcome reveals 266 (5mC/5hmC) and 178 (5hmC) of these significantly differential loci, maps them to genomic features and to genes potentially under their influence. These loci represent candidate growth markers in tilapia and potentially contribute to the understanding of how pituitary epigenetics can lead to growth.

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