Biology subjects

Manousi, D.

Publications and source records attributed to Manousi, D..

7 recordsLinked to original sources

bioRxiv2025

Large-scale eQTL analyses in Atlantic salmon reveal persistent dosage compensation 100 million years after genome duplication.

Whole-genome duplication (WGD) through autopolyploidization has played a role in genome evolution across eukaryotes. A major consequence of WGD is the rewiring of gene regulatory networks, partly driven by selection on dosage balance. In multicellular organisms, evidence for dosage balance selection has relied on comparative patterns of duplicate gene retention and expression, with few studies directly examining regulatory architecture after WGD. Here, we analysed a large-scale eQTL dataset from Atlantic salmon (Salmo salar), which experienced a WGD 100 million years ago. We found that trans-regulatory connections were enriched between duplicated regions, indicating long-term conservation of ancestral interchromosomal regulatory interactions. Overall, 230 duplicated genes (5%) shared eQTLs, suggesting conserved regulatory control. Moreover, 16 gene pairs showed compensatory expression effects mediated by a common regulator, consistent with predictions of the dosage balance hypothesis. These gene pairs were significantly enriched in recently rediploidized regions. Our results indicate long-term maintenance of dosage balance after WGD. TeaserGenetic regulation in Atlantic salmon shows that duplicated genes can remain dosage-balanced across 100 million years of evolution.

evolutionary biology↗

bioRxiv2025

A major locus on chromosome 14 impacts developmental variation of Atlantic salmon smoltification

BackgroundSmoltification in anadromous Atlantic salmon is a complex developmental process involving physiological and cellular changes that enable freshwater fish to adapt to seawater. Central to this transformation is the functional transformation of the gill to manage osmoregulatory demands. While environmental cues like photoperiod are known to influence smolt development, the genetic architecture underlying smolt development -- particularly related to gill physiology -- remains poorly understood. ResultsA large-scale eQTL analysis across 3,000 Atlantic salmon subjected to three photoperiod regimes, identified over 45,000 significant SNP-gene expression associations in gill tissue. Notably, we discovered a 0.5 Mbp large trans-eQTL hotspot on chromosome 14. This hub-locus was associated with expression of more than 2,000 genes across the genome which were significantly enriched for gill cell type specific markers. In addition we found that the hub-locus was associated with somatic growth. Our findings support a "local tissue effect" model, where cis-regulatory or protein sequence variants within the hub-locus modulate cell proliferation and differentiation of gill cell types. ConclusionThis work advances our understanding of the genetic basis of smoltification in Atlantic salmon and provides a foundation for future studies using single-cell approaches to resolve cell-type specific mechanisms underlying genetic variation in smolt development.

genetics↗

bioRxiv2025

Gene gain and loss drive the diversification of gig immune genes in teleosts: structural and regulatory insights from Atlantic salmon

Interferon-stimulated genes (ISGs) are key players in vertebrate antiviral immunity. Among teleost ISGs, the grass carp reovirus-induced gene (gig) families 1 and 2 (gig1 and gig2, respectively) are absent in mammals but conserved in fishes and amphibians, and they have been implicated in resistance to viral infections across several aquaculture species. In particular, gig1 and gig2 genes are transcriptionally induced by viral stimuli in teleosts such as zebrafish, grass carp, and salmonids, and recent studies have highlighted their potential involvement in resistance to economically important diseases like pancreas disease in Atlantic salmon. Yet, the rapid evolution of these genes hinders a comprehensive understanding of their diversification process and regulatory mechanisms. This study investigated gig gene evolution across teleosts, with a focus on Atlantic salmon (Salmo salar). Phylogenetic analysis across representative ray-finned fishes (Actinopterygii), including both teleosts and non-teleost outgroups such as the spotted gar (Holostei), indicated that gig1 is restricted to teleosts, with no identifiable homologs in non-teleost lineages. In contrast, gig2 genes are present in both teleosts and the spotted gar, suggesting an origin prior to the teleost-specific whole genome duplication (Ts3R), likely in early non-amniote vertebrates. Whole-genome duplication drove lineage-specific expansions, particularly of gig2 in salmonids. Structural and transcriptomic analyses showed that gig1 and gig2 differ in domain composition, repeat content, and regulation. Our findings suggest the complex interplay of duplication history, structural divergence, and transcriptional regulation in shaping immune gene repertoires in teleosts, with implications for understanding host-pathogen interactions and aquaculture disease responses. Article summaryThis study investigates the evolutionary history and diversification of the gig immune gene families in aquatic species, with particular focus on Atlantic salmon. Phylogenetic and structural analyses revealed that gig1 and gig2 follow distinct evolutionary trajectories, shaped by whole-genome and tandem duplications. Further analysis of Atlantic salmon gig genes showed divergent structures and regulation, highlighting a general role of gig genes in antiviral Interferon-mediated immunity and additionally suggesting functional specialization across gig paralogs. Together, these findings improve our understanding of immune gene evolution in fishes and provide insights relevant to antiviral defense and disease management in aquaculture species.

genomics↗

bioRxiv2025

Metatranscriptomic Insights into Microbial Dynamics Prior to Disease Onset in Atlantic Salmon Aquaculture

Poly(A)-selected RNA-seq datasets are routinely generated in aquaculture research, yet the microbial information contained in unmapped reads is seldom explored due to the low abundance of nonhost transcripts and concerns about contamination. In this study, we repurposed Atlantic salmon gill RNA-seq data to assess whether meaningful microbial signals can be recovered using a contamination-aware and compositionally appropriate framework. Unmapped reads were analyzed with a custom Kraken2 database composed exclusively of complete, circularized salmon-associated bacterial genomes together with all available Atlantic salmon assemblies and the human genome. Although microbial sequences represented only a small fraction of total reads, 21 genera were detectable across samples. Genus-level profiles, Jaccard-based ordination, and ANCOM-BC analyses consistently revealed clear differences between tanks, whereas no associations were observed for sex or survival status. Three species exhibited significant tank-specific effects, indicating that environmental factors contributed the strongest detectable structure in the data. The limited microbial diversity recovered here reflects the expected constraints of poly(A)-enriched libraries, yet the results demonstrate that unmapped reads from host-derived RNA-seq can still provide informative environmental signatures when analyzed with curated reference databases and compositional statistical approaches. This strategy offers a practical means to extract exploratory microbiome information from existing transcriptomic datasets.

microbiology↗

bioRxiv2024

Transcriptomic profiling of gill biopsies to define predictive markers for seawater survival in farmed Atlantic salmon

Wild Atlantic salmon migrate to sea following completion of a developmental process known as parr - smolt transformation (PST), which establishes a seawater (SW) tolerant phenotype. Effective imitation of this aspect of anadromous life-history is a crucial aspect of commercial salmon production, with current industry practice being marred by significant losses during transition from the freshwater (FW) to SW phase of production. The natural photoperiodic control of PST can be mimicked by exposing farmed juvenile fish to a reduced duration photoperiod for at least 6 weeks before increasing the photoperiod in the last 1 - 2 months before SW transfer. While it is known that variations in this general protocol affect subsequent SW performance, there is no uniformly accepted industry standard; moreover, reliable prediction of SW performance from fish attributes in the FW phase remains a major challenge. Here we describe an experiment in which we took gill biopsies 1 week prior to SW transfer from 3000 individually tagged fish raised on 3 different photoperiod regimes during the FW phase. Biopsies were subjected to RNA profiling by Illumina sequencing, while individual fish growth and survival was monitored over 300 days in a SW cage environment, run as a common garden experiment. Using a random forest machine learning algorithm, we developed gene expression-based predictive models for initial survival and stunted growth in SW. Stunted growth phenotypes could not be predicted based on gill transcriptomes, but survival the first 40 days in SW could be predicted with moderate accuracy. While several previously identified marker genes contribute to this model, a surprisingly low weighting is ascribed to sodium potassium ATPase subunit genes, contradicting advocacy for their use as SW readiness markers. However, genes with photoperiod-history sensitive regulation were highly enriched among the genes with highest importance in the prediction model. This work opens new avenues for understanding and exploiting developmental changes in gill physiology during smolt development.

genomics↗

bioRxiv2024

Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions

Aquaculture has a considerably shorter history compared to the domestication of plants and animals. Among aquatic species, those that have undergone whole genome duplication events (WGD) seem particularly successful. This suggests that genetic redundancy from WGD is important for domestication, possibly similar to plant domestication. Atlantic salmon (Salmo salar), which has experienced a lineage-specific WGD, has undergone rapid domestication through intensive breeding since the 1960s. Here, we examined the genomic responses to the domestication of Atlantic salmon, including the impacts of WGD, by comparing the whole genome sequence data of aquaculture and wild populations from two lineages: the Eastern and Western Atlantic (Western Norway and North America). Our analysis revealed shared selective sweeps on identical SNPs in major histocompatibility complex (MHC) genes across distinct aquaculture populations compared to their wild counterparts. This SNP level parallelism suggests that a combination of long-term balancing selection and recent human-induced selection has significantly shaped the evolutionary trajectory of MHC genes. In addition, we observed selective sweeps on gene pairs in the homeologous regions originating from WGD, highlighting WGDs role in maintaining genomic variation and potentially reducing pleiotropy through sub-functionalization. This unique type of "parallel" selection contributes to adapting to the intensive artificial conditions of aquaculture. These findings provide valuable insights into the genetic mechanisms of domestication and adaptive responses in Atlantic salmon, suggesting that the salmonid whole genome duplication has underpinned their successful rapid domestication. Our research emphasizes the importance of maintaining genetic diversity to support sustainable aquaculture practices.

genomics↗

bioRxiv2023

Functional and regulatory diversification of circadian rhythm period genes during the evolution of vertebrates

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events of Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa. SignificanceThe Period (Per) genes play essential roles in the circadian rhythm in animals. In this study, we comprehensively investigated the evolutionary diversification of the three types of Period genes in vertebrates. As a result, we observed a rapid evolution and sub-functionalization of these genes, especially adaptive diversification signatures in the protein-binding region, which plays a crucial role in regulating circadian rhythms. This underscores the fine-tuned contribution of Per genes in the biological clocks precision and adaptability across various vertebrate taxa.

evolutionary biology↗