spyridok

• Baalsrud, Helle T; Tørresen, Ole K; Danneels, Bram; Ferrari, Giada; Tooming-Klunderud, Ave & Skage, Morten [Show all 12 contributors for this article] (2026). Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758). Journal of Heredity. ISSN 0022-1503. 117(4), p. 750–760. doi: https:/academic.oup.com/jhered/article/117/4/750/8497176. Full text in Research Archive Show summary

  The phylum Bryozoa is an understudied, yet commonly occurring, globally distributed bilaterian metazoan organismal group. They have a colonial lifestyle and an evolutionary history that spans at least 480 million years but likely longer. Despite their contentious phylogenetic affinities among metazoans, disproportionately few genomic investigations have been performed thus far. Here, we describe the first chromosome-level genome assembly of an individual Flustra foliacea colony belonging to the order Cheilostomatida, collected in southern Norway. The haplotype-resolved assembly of F. foliacea contains two pseudo-haplotypes spanning 956 megabases and 880 megabases, respectively. Both assemblies are highly complete both in terms of scaffolding (>90% of sequences placed in eight autosomal chromosomal pseudomolecules), and gene content (BUSCO completeness scores >90%). We also present gene and repeat annotations of the two assemblies. A comparison of our newly sequenced F. foliacea with five previously published bryozoan genomes supports the hypothesis that the group has undergone extensive genome rearrangements. This includes multiple chromosomal fusions in F. foliacea since their split with other cheilostome bryozoans. These fusions were enriched with long terminal repeat retrotransposons, highlighting the complex interplay between genome organization and genomic repeats. Our study contributes to a deeper understanding of bryozoan genome evolution and the role of repeats in metazoan genome organization.

• Samaras, Athanasios; Kollias, Spyridon & Pavlidis, Michail (2025). Molecular regulation of chronic stress responses in European sea bass, Dicentrarchus labrax. Frontiers in Endocrinology. 16. doi: 10.3389/fendo.2025.1611667. Full text in Research Archive Show summary

  Introduction: This study examines the effects of predictable repeated chronic stress on the stress response and cortisol metabolism in European sea bass. Methods: Fish were exposed to daily stress for 11 days and sampled the next day before or after an additional stressor. Chronically stressed fish showed an attenuated acute cortisol response and altered circulating cortisone levels. Results and Discussion: Gene expression analyses revealed stress-induced regulatory changes. In the brain, pomc and bdnf mRNA expression was affected by chronic stress, while crf by acute stress. In the head kidney, gr2 was affected by both stress types, whereas gr1 and mr responded only to acute stress. Neither mc2r, encoding the ACTH receptor, nor hsd11b2, responsible for cortisol inactivation, were affected. In the liver, gr2 and hsd11b2 were upregulated under chronic stress, suggesting an adaptive mechanism to regulate cortisol metabolism. In contrast, gill receptor expression remained largely unchanged, except for acute stress-induced gr2, gr1, and mr downregulation in chronically stressed fish, potentially modulating cortisol signaling. These findings suggest that chronic stress alters neuroendocrine regulation, desensitizing the HPI axis and impairing the acute stress response. Understanding these mechanisms provides insights into chronic stress adaptation in fish, with implications for aquaculture and stress physiology research.

• Martin, Sarah Louise; Torre, Renato La; Danneels, Bram; Tooming-Klunderud, Ave; Skage, Morten & Kollias, Spyridon [Show all 12 contributors for this article] (2025). Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids. GigaScience. doi: 10.1093/gigascience/giaf160. Full text in Research Archive Show summary

  Background Arctic and alpine insects experience extreme environmental stressors, yet the genomic basis of their adaptation is poorly understood. Diamesa midges (Diptera: Chironomidae) are cold-adapted insects inhabiting glacial and high-altitude freshwater ecosystems, but no chromosome-level genomes have been available to date. Findings We present the first haplotype-resolved, chromosome-level genomes for four Diamesa species (D. hyperborea, D. lindrothi, D. serratosioi and D. tonsa), assembled using PacBio HiFi sequencing and Hi-C scaffolding. The assemblies show high completeness and k-mer representation. Phylogenomic analyses place Diamesinae as sister to other Chironomidae except Podonominae, and comparisons suggest introgression between the distinct species D. hyperborea and D. tonsa. Comparative genomic analyses across 20 Diptera species identified significant gene family contractions in Diamesa related to oxygen transport and metabolism, consistent with adaptation to high-altitude, low-oxygen environments. Expansions were observed in histone-related and Toll-like receptor gene families, suggesting roles in chromatin remodeling and immune regulation under cold stress. A glucose dehydrogenase gene family was significantly expanded across all cold-adapted species studied, implicating it in cryoprotectant synthesis and oxidative stress mitigation. Diamesa exhibited the largest gene family contraction at any phylogenetic node, with limited overlap in expansions with other cold-adapted Diptera, indicating lineage-specific adaptation. Conclusions Our findings support the hypothesis that genome size condensation and selective gene family changes underpin survival in cold environments. These new genome assemblies provide a valuable resource for studying adaptation, speciation, and conservation in cold-specialist insects. Future integration of gene expression and population genomics will further clarify the evolutionary resilience of Diamesa in a warming world.

• Cobb, Lauren Louise; Muinck, Eric de; Kollias, Spyridon; Skage, Morten; Gilfillan, Gregor & Sydenham, Markus A. K. [Show all 8 contributors for this article] (2024). High-throughput sequencing of insect specimens with sub-optimal DNA preservation using a practical, plate-based Illumina-compatible Tn5 transposase library preparation method. PLOS ONE. 19(3). doi: 10.1371/journal.pone.0300865. Full text in Research Archive Show summary

  Entomological sampling and storage conditions often prioritise efficiency, practicality and conservation of morphological characteristics, and may therefore be suboptimal for DNA preservation. This practice can impact downstream molecular applications, such as the generation of high-throughput genomic libraries, which often requires substantial DNA input amounts. Here, we use a practical Tn5 transposase tagmentation-based library preparation method optimised for 96-well plates and low yield DNA extracts from insect legs that were stored under sub-optimal conditions for DNA preservation. The samples were kept in field vehicles for extended periods of time, before long-term storage in ethanol in the freezer, or dry at room temperature. By reducing DNA input to 6ng, more samples with sub-optimal DNA yields could be processed. We matched this low DNA input with a 6-fold dilution of a commercially available tagmentation enzyme, significantly reducing library preparation costs. Costs and workload were further suppressed by direct post-amplification pooling of individual libraries. We generated medium coverage (>3-fold) genomes for 88 out of 90 specimens, with an average of approximately 10-fold coverage. While samples stored in ethanol yielded significantly less DNA compared to those which were stored dry, these samples had superior sequencing statistics, with longer sequencing reads and higher rates of endogenous DNA. Furthermore, we find that the efficiency of tagmentation-based library preparation can be improved by a thorough post-amplification bead clean-up which selects against both short and large DNA fragments. By opening opportunities for the use of sub-optimally preserved, low yield DNA extracts, we broaden the scope of whole genome studies of insect specimens. We therefore expect these results and this protocol to be valuable for a range of applications in the field of entomology.

• Jentoft, Sissel; Tørresen, Ole K.; Tooming-Klunderud, Ave; Skage, Morten; Kollias, Spyridon & Jakobsen, Kjetill Sigurd (2024). The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758). Wellcome Open Research. 9. doi: 10.12688/wellcomeopenres.21122.1. Full text in Research Archive Show summary

  We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.

• Samaras, Athanasios; Dimitroglou, Arkadios; Kollias, Spyridon; Skouradakis, Grigorios; Papadakis, Ioannis E. & Pavlidis, Michail (2021). Cortisol concentration in scales is a valid indicator for the assessment of chronic stress in European sea bass, Dicentrarchus labrax L. Aquaculture. ISSN 0044-8486. 545, p. 1–8. doi: 10.1016/j.aquaculture.2021.737257. Full text in Research Archive
• Koutsouveli, Vasiliki; Manousaki, Tereza; Riesgo, Ana; Lagnel, Jacques; Kollias, Spyridon & Tsigenopoulos, Costas S. [Show all 10 contributors for this article] (2020). Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience. Frontiers in Marine Science. 6, p. 1–14. doi: 10.3389/fmars.2019.00786. Full text in Research Archive Show summary

  The emblematic sponge Spongia officinalis is currently threatened by recurrent mortality incidents in its native habitats. Elevated temperature has been indicated as a major triggering factor, but the molecular mechanisms recruited for the organism’s response to thermal shifts are yet unknown. Here, we experimentally tested the effect of exposure to temperatures of varying intensity and span on its gene expression profile, replicating gradients encountered in the species’ native habitat. Analysis revealed major shifts in the organism’s transcriptomic profile induced by temperatures corresponding to the standard seasonal maximum, triggering processes related to signal transduction, inflammation, and apoptotic pathway. Further elevation of temperature corresponding to local extremes activated further the immune response of the sponge along with protein ubiquitination. Following prolonged exposure, activation of endoplasmic reticulum stress related to accumulation of misfolded proteins and signs of resilience were observed. In the latter condition, categories such as cellular response to stress, wound repair, and diminution of pathological inflammation as also genes related to cell regeneration and cell growth were upregulated. Our results highlight the acknowledged sensitivity of S. officinalis to environmental shifts, providing an insight into the molecular mechanisms involved in the process. Furthermore, they suggest innate capacity for resilience at the current thermal extremes, implying a combination of factors and not temperature per se as the lethal agent. This sheds light on the mechanisms of pressure induced by the ongoing ocean warming trend to coastal sessile invertebrates.

• Manousaki, Tereza; Koutsouveli, Vasiliki; Lagnel, Jacques; Kollias, Spyridon; Tsigenopoulos, Costas S. & Arvanitidis, Christos [Show all 9 contributors for this article] (2019). A de novo transcriptome assembly for the bath sponge Spongia officinalis, adjusting for microsymbionts. BMC Research Notes. 12(1), p. 1–3. doi: 10.1186/s13104-019-4843-6. Full text in Research Archive Show summary

  Objectives We report a transcriptome acquisition for the bath sponge Spongia officinalis, a non-model marine organism that hosts rich symbiotic microbial communities. To this end, a pipeline was developed to efficiently separate between bacterial expressed genes from those of eukaryotic origin. The transcriptome was produced to support the assessment of gene expression and, thus, the response of the sponge, to elevated temperatures, replicating conditions currently occurring in its native habitat. Data description We describe the assembled transcriptome along with the bioinformatic pipeline used to discriminate between signals of metazoan and prokaryotic origin. The pipeline involves standard read pre-processing steps and incorporates extra analyses to identify and filter prokaryotic reads out of the analysis. The proposed pipeline can be followed to overcome the technical RNASeq problems characteristic for symbiont-rich metazoan organisms with low or non-existent tissue differentiation, such as sponges and cnidarians. At the same time, it can be valuable towards the development of approaches for parallel transcriptomic studies of symbiotic communities and the host.

• Batista, Sonia; Ozorio, Rodrigo; Kollias, Spyridon; Dhanasiri, Anusha; Lokesh, Jep & Kiron, Viswanath [Show all 8 contributors for this article] (2016). Changes in intestinal microbiota, immune- and stress-related transcript levels in Senegalese sole (Solea senegalensis) fed plant ingredient diets intercropped with probiotics or immunostimulants. Aquaculture. ISSN 0044-8486. 458, p. 149–157. doi: 10.1016/j.aquaculture.2016.03.002. Full text in Research Archive Show summary

  Senegalese sole (Solea senegalensis) is a highly valued flatfish that grows well with diets containing plant ingredients but their effects on immune competence is still a matter of debate. The current study aimed to examine changes in innate immune parameters and gut microbiota in Senegalese sole fed with 35% or 72% of plant ingredients with or without probiotic or yeast supplementation. Overall, fish fed diets with 72% of plant ingredients showed lower transcript levels of key immune- and stress-related genes in distal intestine, rectum and head-kidney than the 35% diets. In particular, hsp90b mRNA levels in distal intestine were down-regulated by 70% and 60% with the use of high content of plant ingredients in the diet containing the multispecies probiotic and autolyzed yeast, respectively. Denaturing gradient gel electrophoresis showed lower similarity values for distal intestine than rectum. Also fish fed high content of plant ingredients displayed lower similarity values, pointing to a difference in the microbial populations between fish fed different plant ingredients content on the diet. Our data revealed that inclusion of plant ingredients was associated with differences in gene expression and a more diverse microbiota profile but without a significant effect on growth performance. Moreover, probiotic supplementation resulted in up-regulation of hsp90b, gpx, cat and apoa1 transcript levels in distal intestine concomitantly with a growth rate reduction compared to non-supplemented fish.

• Smolina, Irina; Kollias, Spyridon; Jüterbock, Alexander; Coyer, James A. & Hoarau, Galice Guillaume (2016). Variation in thermal stress response in two populations of the brown seaweed, Fucus distichus, from the Arctic and subarctic intertidal. Royal Society Open Science. 3. doi: 10.1098/rsos.150429. Full text in Research Archive Show summary

  It is unclear whether intertidal organisms are ‘preadapted’ to cope with the increase of temperature and temperature variability or if they are currently at their thermal tolerance limits. To address the dichotomy, we focused on an important ecosystem engineer of the Arctic intertidal rocky shores, the seaweed Fucus distichus and investigated thermal stress responses of two populations from different temperature regimes (Svalbard and Kirkenes, Norway). Thermal stress responses at 20°C, 24°C and 28°C were assessed by measuring photosynthetic performance and expression of heat shock protein (HSP) genes (shsp, hsp90 and hsp70). We detected population-specific responses between the two populations of F. distichus, as the Svalbard population revealed a smaller decrease in photosynthesis performance but a greater activation of molecular defence mechanisms (indicated by a wider repertoire of HSP genes and their stronger upregulation) compared with the Kirkenes population. Although the temperatures used in our study exceed temperatures encountered by F. distichus at the study sites, we believe response to these temperatures may serve as a proxy for the species’ potential to respond to climate-related stresses.

• Kollias, Spyros; Poortvliet, Marloes; Smolina, Irina & Hoarau, Galice (2015). Low cost sequencing of mitogenomes from museum samples using baits capture and Ion Torrent. Conservation Genetics Resources. ISSN 1877-7252. 7(2), p. 345–348. doi: 10.1007/s12686-015-0433-7. Full text in Research Archive
• Poortvliet, Marloes; Olsen, Jeanine L.; Croll, Donald A; Bernardi, Giacomo; Newton, Kelly & Kollias, Spyros [Show all 13 contributors for this article] (2015). A dated molecular phylogeny of manta and devil rays (Mobulidae) based on mitogenome and nuclear sequences. Molecular Phylogenetics and Evolution. ISSN 1055-7903. 83, p. 72–85. doi: 10.1016/j.ympev.2014.10.012. Full text in Research Archive
• Smolina, Irina; Kollias, Spyros; Møller, Eva Friis; Lindeque, Penelope K.; Sundaram, Arvind & Fernandes, Jorge [Show all 7 contributors for this article] (2015). Contrasting transcriptome response to thermal stress in two key zooplankton species, Calanus finmarchicus and C. glacialis. Marine Ecology Progress Series. ISSN 0171-8630. 534, p. 79–93. doi: 10.3354/meps11398. Full text in Research Archive Show summary

  Climate change has already led to the range expansion of warm-water plankton assemblages in the northeast Atlantic and the corresponding range contraction of colder-water species. The temperate copepod Calanus finmarchicus is predicted to shift farther northward into polar waters traditionally dominated by the arctic copepod C. glacialis. To identify temperature-mediated changes in gene expression that may be critical for the thermal acclimation and resilience of the 2 Calanus spp., we conducted a whole transcriptome profiling using RNA-seq on an Ion Torrent platform. Transcriptome responses of C. finmarchicus and C. glacialis from Disko Bay, west Greenland, were investigated under realistic thermal stresses (at +5, +10 and +15°C) for 4 h and 6 d. C. finmarchicus showed a strong response to temperature and duration of stress, involving up-regulation of genes related to protein folding, transcription, translation and metabolism. In sharp contrast, C. glacialis displayed only low-magnitude changes in gene expression in response to temperature and duration of stress. Differences in the thermal responses of the 2 species, particularly the lack of thermal stress response in C. glacialis, are in line with laboratory and field observations and suggest a vulnerability of C. glacialis to climate change.

• Jüterbock, Alexander; Kollias, Spyros; Smolina, Irina; Fernandes, Jorge; Coyer, James A. & Olsen, Jeanine L [Show all 7 contributors for this article] (2014). Thermal stress resistance of the brown alga Fucus serratus along the North-Atlantic coast: Acclimatization potential to climate change. Marine Genomics. ISSN 1874-7787. 13, p. 27–36. doi: 10.1016/j.margen.2013.12.008. Full text in Research Archive Show summary

  Seaweed-dominated communities are predicted to disappear south of 45° latitude on North-Atlantic rocky shores by 2200 because of climate change. The extent of predicted habitat loss, however, could be mitigated if the seaweeds' physiology is sufficiently plastic to rapidly acclimatize to the warmer temperatures. The main objectives of this study were to identify whether the thermal tolerance of the canopy-forming seaweed Fucus serratus is population-specific and where temperatures are likely to exceed its tolerance limits in the next 200 years. We measured the stress response of seaweed samples from four populations (Norway, Denmark, Brittany and Spain) to common-garden heat stress (20 °C–36 °C) in both photosynthetic performance and transcriptomic upregulation of heat shock protein genes. The two stress indicators did not correlate and likely measured different cellular components of the stress response, but both indicators revealed population-specific differences, suggesting ecotypic differentiation. Our results confirmed that thermal extremes will regularly reach physiologically stressful levels in Brittany (France) and further south by the end of the 22nd century. Although heat stress resilience in photosynthetic performance was higher at the species' southern distributional edge in Spain, the hsp expression pattern suggested that this edge-population experienced reduced fitness and limited responsiveness to further stressors. Thus, F. serratus may be unable to mitigate its predicted northward shift and may be at high risk to lose its center of genetic diversity and adaptability in Brittany (France). As it is an important intertidal key species, the disappearance of this seaweed will likely trigger major ecological changes in the entire associated ecosystem.

• Smolina, Irina; Kollias, Spyros; Poortvliet, Marloes; Nielsen, Torkel Gissel; Lindeque, Penelope & Castellani, Claudia [Show all 9 contributors for this article] (2014). Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification. Molecular Ecology Resources. ISSN 1755-098X. 14(5), p. 1072–1079. doi: 10.1111/1755-0998.12241. Full text in Research Archive

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• Martin, Sarah Louise; Torre, Renato La; Danneels, Bram; Tooming-Klunderud, Ave; Skage, Morten & Kollias, Spyridon [Show all 12 contributors for this article] (2025). Genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance adaptations and species boundaries. Full text in Research Archive
• Smolina, Irina; Kollias, Spyros; Møller, Eva Friis; Lindeque, Penelope & Hoarau, Galice (2014). Transcriptome response to thermal stress in two key zooplankton species, Calanus finmarchicus and C. glacialis. Full text in Research Archive
• Lazado, Carlo Cabacang; Nagasawa, Kazue; Kollias, Spyros; Babiak, Igor & Fernandes, Jorge (2013). Photic sensitivity and circadian rhythmicity of the fast muscle transcriptome in Atlantic cod, Gadus morhua. Full text in Research Archive
• Lazado, Carlo Cabacang; Nagasawa, Kazue; Kumaratunga, Hiruni; Babiak, Igor; Kollias, Spyros & Fernandes, Jorge (2013). Exploring the transcriptional landscape of the circadian rhythm in the fast skeletal muscle of Atlantic cod using next-generation sequencing technologies. Full text in Research Archive
• Smolina, Irina; Kollias, Spyros; Nielsen, Torkel Gissel; Lindeque, Penelope & Hoarau, Galice (2013). Genome- and transcriptome-assisted development of InDel markers for solving identification challenge of calanoid copepode Calanus finmarchicus and C. glacialis. Full text in Research Archive

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