Faculty Opinions recommendation of The genome sequence of Atlantic cod reveals a unique immune system.

2011 ◽  
Author(s):  
Seiamak Bahram
Keyword(s):  
Immune System ◽  
Genome Sequence ◽  
Atlantic Cod

scholarly journals The genome sequence of Atlantic cod reveals a unique immune system

Nature ◽  
2011 ◽  
Vol 477 (7363) ◽  
pp. 207-210 ◽  
Author(s):  
Bastiaan Star ◽  
Alexander J. Nederbragt ◽  
Sissel Jentoft ◽  
Unni Grimholt ◽  
Martin Malmstrøm ◽  
...  
Keyword(s):  
Immune System ◽  
Genome Sequence ◽  
Atlantic Cod

scholarly journals Commensal and Opportunistic Bacteria Present in the Microbiota in Atlantic Cod (Gadus morhua) Larvae Differentially Alter the Hosts’ Innate Immune Responses

2021 ◽  
Vol 10 (1) ◽  
pp. 24
Author(s):  
Ragnhild Inderberg Vestrum ◽  
Torunn Forberg ◽  
Birgit Luef ◽  
Ingrid Bakke ◽  
Per Winge ◽  
...  
Keyword(s):  
Immune System ◽  
Immune Responses ◽  
Atlantic Cod ◽  
Innate Immune ◽  
Rrna Gene ◽  
Innate Immune Responses ◽  
Transcriptional Responses ◽  
Gut Morphology ◽  
Germ Free ◽  
Opportunistic Bacteria

The roles of host-associated bacteria have gained attention lately, and we now recognise that the microbiota is essential in processes such as digestion, development of the immune system and gut function. In this study, Atlantic cod larvae were reared under germ-free, gnotobiotic and conventional conditions. Water and fish microbiota were characterised by 16S rRNA gene analyses. The cod larvae’s transcriptional responses to the different microbial conditions were analysed by a custom Agilent 44 k oligo microarray. Gut development was assessed by transmission electron microscopy (TEM). Water and fish microbiota differed significantly in the conventional treatment and were dominated by different fast-growing bacteria. Our study indicates that components of the innate immune system of cod larvae are downregulated by the presence of non-pathogenic bacteria, and thus may be turned on by default in the early larval stages. We see indications of decreased nutrient uptake in the absence of bacteria. The bacteria also influence the gut morphology, reflected in shorter microvilli with higher density in the conventional larvae than in the germ-free larvae. The fact that the microbiota alters innate immune responses and gut morphology demonstrates its important role in marine larval development.

scholarly journals Why does the immune system of Atlantic cod lack MHC II?

BioEssays ◽  
2012 ◽  
Vol 34 (8) ◽  
pp. 648-651 ◽  
Author(s):  
Bastiaan Star ◽  
Sissel Jentoft
Keyword(s):  
Immune System ◽  
Atlantic Cod ◽  
Mhc Ii

scholarly journals Single cell transcriptome profiling of the Atlantic cod immune system

2020 ◽  
Author(s):  
Naomi Guslund ◽  
Monica Hongrø Solbakken ◽  
Kjetill S. Jakobsen ◽  
Shuo-Wang Qiao
Keyword(s):  
Immune System ◽  
Single Cell ◽  
Peripheral Blood ◽  
Bacterial Infections ◽  
Immune Cell ◽  
Atlantic Cod ◽  
Peripheral Blood Leukocytes ◽  
Blood Leukocytes ◽  
Gene Markers ◽  
Putative Gene

AbstractThe Atlantic cod’s unusual immune system, entirely lacking the Major Histocompatibility class II pathway, has prompted intriguing questions about what mechanisms are used to combat bacterial infections and how immunological memory is generated. Here, we examine the diversity of 8,180 spleen cells and peripheral blood leukocytes by single cell RNA sequencing. Unbiased transcriptional clustering revealed eleven distinct immune cell signatures. Resolution at the single cell level enabled characterisation of the major cell subsets including the cytotoxic T cells, B cells, erythrocytes, thrombocytes, neutrophils and macrophages. Further, we describe for the first time rare cell subsets which may represent dendritic cells, natural killer-like cells and a population of cytotoxic cells expressing GATA-3. We propose putative gene markers for each cluster and describe the relative proportions of each cell type in the spleen and peripheral blood leukocytes. By single cell analysis, this study provides the most detailed molecular and cellular characterization of the immune system of the Atlantic cod so far.

scholarly journals Innovation in NLR and TLR sensing drives the MHC-II free Atlantic cod immune system

2020 ◽  
Author(s):  
Xingkun Jin ◽  
Bernat Morro ◽  
Ole K. Tørresen ◽  
Visila Moiche ◽  
Monica H. Solbakken ◽  
...  
Keyword(s):  
Immune System ◽  
Mhc Class Ii ◽  
Atlantic Cod ◽  
Ex Vivo ◽  
Specific Cell ◽  
Major Response ◽  
History Of ◽  
Underlying Mechanisms ◽  
Molecular Patterns ◽  
Cluster Of Differentiation

AbstractThe genome sequencing of Atlantic cod revealed an immune system absent of specific cell surface toll-like receptors (TLRs), major histocompatibility complex (MHC) class II, invariant chain (CD74) and the CD4 (cluster of differentiation 4) receptor. Despite the loss of these major components considered as critical to vertebrate innate and adaptive immune systems the cod system is fully functional, however the underlying mechanisms of the immune response in cod remain largely unknown. In this study, ex vivo cod macrophages were challenged with various bacterial and viral microbe-associated molecular patterns (MAMP) to identify major response pathways. Cytosolic MAMP-PRR pathways based upon the NOD-like receptors (NLRs) and RIG-I-like receptors (RLRs) were identified as the critical response pathways. Our analyses suggest that internalization of exogenous ligands through scavenger receptors drives both pathways activating transcription factors like NF-kB (Nuclear factor-kappa B) and interferon regulatory factors (IRFs). Further, ligand-dependent differential expression of a unique TLR25 isoform and multiple NLR paralogues suggests (sub)neofunctionalisation toward specific immune defensive strategies. Our results further demonstrate that the unique immune system of the Atlantic cod provides an unprecedented opportunity to explore the evolutionary history of PRR-based signalling in vertebrate immunity.

scholarly journals An accurate assignment test for extremely low-coverage whole-genome sequence data

2021 ◽  
Author(s):  
Giada Ferrari ◽  
Lane M Atmore ◽  
Sissel Jentoft ◽  
Kjetill S Jakobsen ◽  
Daniel Makowiecki ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Atlantic Cod ◽  
Sequence Data ◽  
Biological Characteristics ◽  
Assignment Test ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Assignment Tests ◽  
Low Coverage

Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. In ancient DNA research, such characters can provide further information on population continuity, evolution, climate change, species migration, or trade, depending on archaeological context. Yet, assignment tests often rely on moderate- to high-coverage sequence data, which can be difficult to obtain for many ancient specimens and in ecological studies, which often use sequencing techniques such as ddRAD to bypass the need for costly whole-genome sequencing. We have developed a novel approach that efficiently assigns biologically relevant information (such as population identity or structural variants) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic Single Nucleotide Polymorphisms (SNPs) associated with a biological characteristic. Low coverage alignment files from ancient specimens are subsequently compared to these databases to ascertain allelic state yielding a joint probability for each association. To assess the efficacy of this approach, we assigned inversion haplotypes and population identity in several species including Heliconius butterflies, Atlantic herring, and Atlantic cod. We used both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage (e.g. 0.0001x fold) based on genome-wide SNPs. This approach will therefore increase the number of ancient samples in ecological and bioarchaeological research for which relevant biological information can be obtained.

scholarly journals Genomic architecture of codfishes featured by expansions of innate immune genes and short tandem repeats

2017 ◽  
Author(s):  
Ole K. Tørresen ◽  
Marine S. O. Brieuc ◽  
Monica H. Solbakken ◽  
Elin Sørhus ◽  
Alexander J. Nederbragt ◽  
...  
Keyword(s):  
Immune System ◽  
Genome Assembly ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Atlantic Cod ◽  
High Density ◽  
Innate Immune ◽  
Immune Gene ◽  
Genome Assemblies ◽  
Short Tandem

AbstractBackgroundIncreased availability of genome assemblies for non-model organisms has resulted in invaluable biological and genomic insight into numerous vertebrates including teleosts. The sequencing and assembly of the Atlantic cod (Gadus morhua) genome and the genomes of many of its relatives (Gadiformes) demonstrated a shared loss 100 million years ago of the major histocompatibility complex (MHC) II genes. The recent publication of an improved version of the Atlantic cod genome assembly reported an extreme density of tandem repeats compared to other vertebrate genome assemblies. Highly contiguous genome assemblies are needed to further investigate the unusual immune system of the Gadiformes, and the high density of tandem repeats in this group.ResultsHere, we have sequenced and assembled the genome of haddock (Melanogrammus aeglefinus) - a relative of Atlantic cod - using a combination of PacBio and Illumina reads. Comparative analyses uncover that the haddock genome contains an even higher density of tandem repeats outside and within protein coding sequences than Atlantic cod. Further, both species show an elevated number of tandem repeats in genes mainly involved in signal transduction compared to other teleosts. An in-depth characterization of the immune gene repertoire demonstrates a substantial expansion of MCHI in Atlantic cod compared to haddock. In contrast, the Toll-like receptors show a similar pattern of gene losses and expansions. For another gene family associated with the innate immune system, the NOD-like receptors (NLRs), we find a large expansion common to all teleosts, with possible lineage-specific expansions in zebrafish, stickleback and the codfishes.ConclusionsThe generation of a highly contiguous genome assembly of haddock revealed that the high density of short tandem repeats as well as expanded immune gene families is not unique to Atlantic cod – but most likely a feature common to all codfishes. A shared expansion of NLR genes in teleosts suggests that the NLRs have a more substantial role in the innate immunity of teleosts than other vertebrates. Moreover, we find that high copy number genes combined with variable genome assembly qualities may impede complete characterization, i.e. the number of NLRs might be underestimates in the different teleost species.

scholarly journals Innovation in Nucleotide-Binding Oligomerization-Like Receptor and Toll-Like Receptor Sensing Drives the Major Histocompatibility Complex-II Free Atlantic Cod Immune System

2020 ◽  
Vol 11 ◽  
Author(s):  
Xingkun Jin ◽  
Bernat Morro ◽  
Ole K. Tørresen ◽  
Visila Moiche ◽  
Monica H. Solbakken ◽  
...  
Keyword(s):  
Immune System ◽  
Mhc Class Ii ◽  
Atlantic Cod ◽  
Ex Vivo ◽  
Major Response ◽  
History Of ◽  
Pathogen Recognition Receptors ◽  
Underlying Mechanisms ◽  
Class Ii Antigen ◽  
Molecular Patterns

The absence of MHC class II antigen presentation and multiple pathogen recognition receptors in the Atlantic cod has not impaired its immune response however how underlying mechanisms have adapted remains largely unknown. In this study, ex vivo cod macrophages were challenged with various bacterial and viral microbe-associated molecular patterns (MAMP) to identify major response pathways. Cytosolic MAMP-PRR pathways based upon the NOD-like receptors (NLRs) and RIG-I-like receptors (RLRs) were identified as the critical response pathways. Our analyses suggest that internalization of exogenous ligands through scavenger receptors drives both pathways activating transcription factors like NF-kB (Nuclear factor-kappa B) and interferon regulatory factors (IRFs). Further, ligand-dependent differential expression of a unique TLR25 isoform and multiple NLR paralogues suggests (sub)neofunctionalization toward specific immune defensive strategies. Our results further demonstrate that the unique immune system of the Atlantic cod provides an unprecedented opportunity to explore the evolutionary history of PRR-based signaling in vertebrate immunity.

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