Tomasz Furmanek

• Institute of Marine Research in Norway

The architecture underpinning genomic divergence is still a largely uncharted territory and likely case-dependent. Here, we investigated genome-wide variation in Ballan wrasse, a northeastern Atlantic fish species that displays two sympatric colour morphs, spotty and plain, that have been suggested to represent subspecies. We produced a chromosome-...

Light cues vary along the axis of periodicity, intensity and spectrum and perception of light is dependent on the photoreceptive capacity encoded within the genome and the opsins expressed. A global approach was taken to analyze the photoreceptive capacity and the effect of differing light conditions on a developing teleost prior to first feeding....

Background Tandem mass tag spectrometry (TMT labeling-LC-MS/MS) was utilized to examine the global proteomes of Atlantic halibut eggs at the 1-cell-stage post fertilization. Comparisons were made between eggs judged to be of good quality (GQ) versus poor quality (BQ) as evidenced by their subsequent rates of survival for 12 days. Altered abundance...

Using germ cell-free (GCF), sterile, dnd-knockout salmon for farming could solve the problems associated with precocious maturation and genetic introgression of farmed breeds into wild populations. However, prior to using GCF fish in the salmon farming industry, it is crucial to understand if, or how, the GCF phenotype differs from wild type (WT) c...

Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known. We produced a high-quality genome assembly from a male and identified parts of chromosome 13 as the Y chromosome due to sequence divergence between sexes and segregation of sex genotypes in pedigrees. Linkage analysi...

Developing organisms are especially vulnerable to environmental stressors. Crude oil exposure in early life stages of fish result in multiple functional and developmental defects, including cardiac dysfunction and abnormal and smaller eyes. Phenanthrene (Phe) has a reversible impact on cardiac function, and under exposure Phe reduces cardiac contra...

Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetit...

This is a duplicate, see https://www.researchgate.net/publication/350106692_The_salmon_louse_genome_copepod_features_and_parasitic_adaptations for full text.

Developing organisms are especially vulnerable to environmental stressors. We aimed to understand the underlying mechanisms of phenanthrene (Phe) and crude oil induced eye malformations. We exposed Atlantic haddock (Melanogrammus aeglefinus) embryos to a known L-type calcium channel blocker, nicardipine hydrochloride (Nic), and compared to early em...

Copepods encompass a range of ecological roles from parasites to phytoplankton grazers linking primary producers to higher trophic levels. Despite these important roles, copepod genome assemblies are scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod. We present the 695.4 Mbp L. salmonis genome assem...

Pituitary hormones can use local signaling molecules to regulate target tissue functions. In adult zebrafish testes, follicle-stimulating hormone (Fsh) strongly increases the production of insulin-like 3 (Insl3), a Leydig cell-derived growth factor found in all vertebrates. Little information is available regarding Insl3 function in adult spermatog...

Monitoring of planktonic salmon louse (Lepeophtheirus salmonis salmonis) abundance and parameterization of key life-history traits has been hindered by labour-intensive and error-prone quantification using traditional light microscopy. Fluorescence illumination has been proposed as a means of improving visualization, but prior to this study adequat...

Atlantic Halibut (Hippoglossus hippoglossus) has a X/Y genetic sex determination system, but the sex determining factor is not known. We produced a high-quality genome assembly and identified parts of chromosome 13 as the Y chromosome due to sequence divergence between sexes and segregation of sex genotypes in pedigrees. Linkage analysis revealed t...

The availability of genome sequences, annotations, and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotyp...

Pituitary hormones can use local signaling molecules to regulate target tissue functions. In adult zebrafish testes, follicle-stimulating hormone (Fsh) strongly increases the production of insulin-like 3 (Insl3), a Leydig cell-derived growth factor found in all vertebrates. Little information is available regarding Insl3 function in adult spermatog...

Most Atlantic salmon (Salmo salar L.) populations follow an anadromous life cycle, spending early life in freshwater, migrating to the sea for feeding, and returning to rivers to spawn. At the end of the last ice age ~10,000 years ago, several populations of Atlantic salmon became landlocked. Comparing their genomes to their anadromous counterparts...

The availability of genome sequences, annotations and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype...

Background: Sustainability challenges are currently hampering an increase in salmon production. Using sterile salmon can solve problems with precocious puberty and genetic introgression from farmed escapees to wild populations. Recently sterile salmon was produced by knocking out the germ cell-specific dead end (dnd). Several approaches may be app...

Background Sustainability challenges are currently hampering an increase in salmon production. Using sterile salmon can solve problems with precocious puberty and genetic introgression from farmed escapees to wild populations. Recently sterile salmon was produced by knocking out the germ cell-specific dead end (dnd). Several approaches may be appli...

The epidermal mucus protects fish against harmful environmental factors and the loss of physiological metabolites and water. It is an efficient barrier between the fish and the biosphere. The integrity of the skin mucus is thus of vital importance for the welfare and survival of the fish. Since excreted proteins and small molecules in the mucus can...

Background Sustainability challenges are currently hampering an increase in salmon production. Using sterile salmon can solve problems with precocious puberty and genetic introgression from farmed escapees to wild populations. Recently sterile salmon was produced by knocking out the germ cell-specific dead end (dnd). Several approaches may be appli...

Background: Enormous variability in skin colour and patterning is a characteristic of teleost fish, including Salmonidae fishes, which present themselves as a suitable model for studying mechanisms of pigment patterning. In order to screen for candidate genes potentially involved in the specific skin pigment pattern in marble trout (labyrinthine s...

Transcriptomics of skin colour patterning in Salmo, with emphasis on red spot Ida Djurdjevič1, Tomasz Furmanek2, Seita Miyazawa3 and Simona Susnik Bajec1* 1 Biotechnical Faculty, University of Ljubljana, Slovenia 2 Norwegian Institute of Marine Research (IMR), Norway 3 Graduate School of Frontier Biosciences, Osaka University, Japan Great variabili...

We performed RNA sequencing, identified components of the immune system and mapped early immune responses of lumpfish (Cyclopterus lumpus) leukocytes following in vitro exposure to the pathogenic bacterium Vibrio anguillarum O1. This is the first characterization of immune molecules in lumpfish at the gene level. In silico analyses revealed that ge...

Vgll3 is linked to age at maturity in Atlantic salmon (Salmo salar). However, the molecular mechanisms involving Vgll3 in controlling timing of puberty as well as relevant tissue and cell types are currently unknown. Vgll3 and the associated Hippo pathway has been linked to reduced proliferation activity in different tissues. Analysis of gene expre...

Background Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty negatively impacts animal welfare and growth. We hypothesize that certain miRNAs modulate mRNAs relevant for the initiation of pube...

Tables. (A) Read count data for a selection of genes expressed in distinct tissues. (B) Ten most regulated Ingenuity Pathway Analysis (Categories: Development, Lipid metabolism, Molecular transport) in high dose at stages E1-E6. #, number of molecules (C) Ingenuity Pathway Analysis. Top five pathways in low, pulse and high dose at all time points d...

Crude oil spills are a worldwide ocean conservation threat. Fish are particularly vulnerable to the oiling of spawning habitats, and crude oil causes severe abnormalities in embryos and larvae. However, the underlying mechanisms for these developmental defects are not well understood. Here, we explore the transcriptional basis for four discrete cru...

Atlantic salmon is a valuable commercial aquaculture species that would benefit economically and environmentally by controlling precocious puberty and preventing escapees from reproducing with wild populations. One solution to both these challenges is the production of sterile individuals by inhibiting the formation of germ cells, but achieving thi...

Background Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplica...

Spermatogonial stem cells are quiescent, undergo self-renewal or differentiating divisions, thereby forming the cellular basis of spermatogenesis. This cellular development is orchestrated by follicle-stimulating hormone (FSH), through the production of Sertoli cell-derived factors, and by Leydig cell-released androgens. Here, we investigate the tr...

In Atlantic salmon, a species of great relevance for aquaculture in Northern Europe, precocious puberty in males increases susceptibility to disease, affects flesh quality, reduces growth and cause hypo-osmoregulatory problems (Taranger et al. 2010). It is therefore of high importance to understand the underlying causative molecular processes invol...

Unlike in mammals, persistent postembryonic retinal growth is a characteristic feature of fish, which includes major remodeling events that affect all cell types including photoreceptors. Consequently, visual capabilities change during development, where retinal sensitivity to different wavelengths of light (photopic vision), -and to limited photon...

To our knowledge, there is no report on microRNA (miRNA) expression and their target analysis in relation to the type of the first feed and its effect on the further growth of fish. Atlantic cod (Gadus morhua) larvae have better growth and development performance when fed natural zooplankton as a start-feed, as compared with those fed typical aquac...

Gadiforms such as Atlantic haddock comprise some of the world's most economically important fisheries. Understanding the early life history of these fish is a prerequisite for predicting effects of a changing environment and increased human activities. Robust assessment of the effects of environmental impacts on the embryos of non-model vertebrates...

Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1-5 years. Previous studies have uncovered a genetic predisposition for variation of age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify...

Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1-5 years. Previous studies have uncovered a genetic predisposition for age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify associated g...

The growth and development of marine fish larvae fed copepods is superior to those fed rotifers, but the underlying molecular reasons for this are unclear. In the following study we compared the effects of such diets on redox regulation pathways during development of Atlantic cod (Gadus morhua) larvae. Cod larvae were fed a control diet of copepods...

Fish in use in aquaculture display large variation in gamete biology. To reach better understanding around this issue, this study aims at identifying if species specific "egg life history traits" can be hidden in the unfertilized egg. This was done by investigating egg transcriptome differences between Atlantic salmon and Atlantic cod. Salmon and c...

The Atlantic salmon, Salmo salar L, is an important species both for traditional fishery and fish farming. Many Atlantic salmon stocks have been declining and a suspected main contributor to this decline is the salmon louse (Lepeophtheirus salmonis); a parasitic copepod living off the salmonid hosts epidermal tissues and blood. Contributing to the...

The molecular mechanisms underlying oogenesis and maternally controlled embryogenesis in fish are not fully understood, especially in marine species. Our aim was to study the egg and embryo transcriptome during oogenesis and early embryogenesis in Atlantic cod. Follicles from oogenesis stages (pre-, early-, and late-vitellogenic), ovulated eggs, an...

Introduction Previous studies have revealed a differential expression of small RNA repertoires between immature and mature testis, however no such global small RNA expression studies have been performed in salmonides. Since both precocious maturation and fertility are current problems in salmon aquaculture, increased knowledge about molecular regul...

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In teleosts such as Atlantic salmon (Salmo salar L.), segmentation and subsequent mineralisation of the notochord during embryonic stages are essential for normal vertebrae formation. However, the molecular mechanisms leading to segmentation and mineralisation of the notochord are poorly understood. The aim of this study was to identify genes/pathw...

Atlantic cod displays a range of phenotypic and genotypic variations, which includes the differentiation into coastal stationary and offshore migratory types of cod that co-occur in several parts of its distribution range and are often sympatric on the spawning grounds. Differentiation of these ecotypes may involve both historical separation and ad...

We performed a sequential morphological and molecular biological study of the development of the vertebral bodies in Atlantic salmon (Salmo salar L.). Mineralization starts in separate bony elements which fuse to form complete segmental rings within the notochord sheath. The nucleation and growth of hydroxyapatite crystals in both the lamellar type...

Sequence alignment is an important bioinformatics tool for identifying homology, but searching against the full set of available sequences is likely to result in many hits to poorly annotated sequences providing very little information. Consequently, we often want alignments against a specific subset of sequences: for instance, we are looking for s...

Zygotic transcription in fish embryos initiates around the time of gastrulation, and all prior development is initiated and controlled by maternally derived messenger RNAs. Atlantic cod egg and embryo viability is variable, and it is hypothesized that the early development depends upon the feature of these maternal RNAs. Both the length and the pre...

Gene expression of reference genes in oocyte, 1-2 cell, blastula and gastrula stage in cod. mRNA levels are shown as cycle threshold (Ct)-values when 250 ng RNA was used for cDNA synthesis. All data are shown as mean with SEM. N = 2.

Results from repeated 3’UTR structure analyses, with less strict criteria for classification and excluding all ribosomal genes. Results from repeated analyses on 3’UTR structure, with less strict classification of gene groups and excluding all ribosomal genes. In addition to genes with above 95% of transcripts present in oocyte until blastula stage...

Distribution of nuclear genes with and without transcript number threshold. The bar to the left represents the proportion of nuclear genes that were expressed exclusively in maternal stages, gastrula or in all four stages, when analyzing the dataset with a transcript number threshold (n > 8). The bar to the right represents the dataset when no thre...

Gene Ontology annotation based on UniRef90 BLAST hits. This file contains Gene Ontology annotation based on UniRef90 BLAST hits. 1) UniRef hit, 2) Ensembl gene, 3) Ensembl annotation, 4) UniRef90 hit, 5) UniRef90 hit e-value, 6) UniRef90 hit score, 7) Total UniRef90 hits in the whole predicted gene set, 8) GO UniRef, 9) GO gene name, 10) GO number,...

Gene expression levels of candidate genes to reveal timing of midblastula transition in cod. mRNA levels of 3 candidate genes were measured in oocyte, 1-2 cell, blastula and gastrula stage. mRNA levels are relative to hba. Bars with different letters represent significant different mRNA levels for each gene. All data are shown as mean with SEM. N =...

Functional profile of transcripts that showed a difference in abundance between maternal and zygotic stages. Three levels of function (parent ontologies) are shown: cellular component, molecular function and biological process. The number on top of each bar represents the total number of transcripts in that stage, which could be coupled to the pare...

Contig annotations. This file shows the mapping of EST-contigs to the Atlantic cod genome. Contig annotations for the 257 genes analysed in this study are shown.

Contigs based on clustered sequences. This file contains clustered sequences from all libraries, with given contig name. The contig name can be linked to annotation and accession number in [Additional file 7].

MicroRNAs (miRNAs) play a major role in animal ontogenesis. Size variants of miRNAs, isomiRs, are observed along with the main miRNA types, but their origin and possible biological role are uncovered yet. Developmental profiles of miRNAs have been reported in few fish species only and, to our knowledge, differential expressions of isomiRs have not...

IsomiR occurrence during early development of Atlantic halibut. All miRNAs having ≥ 0.01% truncation/s or addition/s in 5' and/or 3' ends are listed. The percentage of both template and non-template nucleotide changes (A, U, C, and G) are shown as percentage of total reads of a given miRNA.

Cloned miRNA sequences and their frequency. Indentified conserved miRNAs using cloning technique and their frequencies. Nucleotide mismatches (green), additions (blue) or modifications (red) are found in some miRNAs.

Size distribution of mapped reads in Atlantic halibut deep sequencing data. Reads mapped to different databases: A) mitochondrial transcripts, rRNA, tRNA, other non-coding RNA; B) miRBase 16 and C) Atlantic halibut ESTs. The size distribution of mapped reads for each database is given.

Identified conserved miRNAs. All identified conserved Atlantic halibut miRNAs along with miRBase name, nucleotide sequences and read counts for each investigated developmental stages are given. Lower case letters indicate mismatches comparing to references.

miRNA diversity during early development of Atlantic halibut. The number of different types of miRNAs identified during 8 stages of Atlantic halibut development; increasing as the development progressed.

Read counts for 8 developmental stages of Atlantic halibut. The total number of raw sequence reads obtained from SOLiD sequencing and the number of usable reads for each developmental stage is given.

The Atlantic cod (Gadus morhua) is an emerging aquaculture species. Efforts to develop and characterize its genomic recourses, including draft-grade genome sequencing, have been initiated by the research community. The transcriptome represents the whole complement of RNA transcripts in cells and tissues and reflects the expressed genes at various l...

To investigate and compare the cellular expression of non-secreted Fgf11-14 and secreted Fgf15-18 and -20 mRNAs during tooth formation. mRNA expression was analyzed from the morphological initiation of the mouse mandibular first molar development to the onset of crown calcification using sectional in situ hybridization. This study found distinct, d...

The Atlantic cod (Gadus morhua) is a key species in the North Atlantic ecosystem and commercial fisheries, with increasing aquacultural production in several countries. A Norwegian effort to sequence the complete 0.9Gbp genome by the 454 pyrosequencing technology has been initiated and is in progress. Here we review recent progress in large-scale s...

Glutamate, the main excitatory neurotransmitter in the brain, may cause excitotoxic damage through excessive release during a number of pathological conditions. We have developed an immunocytochemical assay to investigate the mechanisms and regulation of glutamate release from intact, cultured neurons. Our results indicate that cultured hippocampal...

During embryogenesis, dental trigeminal axon navigation and patterning in the developing tooth take place in a highly spatio-temporally directed manner that is tightly linked to tooth morphogenesis and cell differentiation. Tooth formation is regulated by sequential and reciprocal tissue interactions between dental epithelium and neural crest-deriv...

Dental trigeminal nerve fiber growth and patterning are strictly integrated with tooth morphogenesis, but it is still unknown, how these two developmental processes are coordinated. Here we show that targeted inactivation of the dental epithelium expressed Fgfr2b results in cessation of the mouse mandibular first molar development at the degenerate...

Murine retroviral vectors carrying an enhancer detection cassette were used to generate 95 transgenic lines of fish in which reporter expression is observed in distinct patterns during embryonic development. We mapped 65 insertion sites to the as yet unfinished zebrafish genome sequence. Many integrations map close to previously known developmental...

Wnt signaling is essential for tooth formation. Members of the Dickkopf (Dkk) family modulate the Wnt signaling pathway by binding to the Wnt receptor complex. Comparison of Dkk1, -2, and -3 mRNA expression during mouse tooth formation revealed that all three genes showed distinct spatiotemporally regulated expression patterns. Dkk1 was prominently...