scholarly journals A nanopore based chromosome-level assembly representing Atlantic cod from the Celtic Sea

2019 ◽  
Author(s):  
Tina Graceline Kirubakaran ◽  
Øivind Andersen ◽  
Michel Moser ◽  
Mariann Arnyasi ◽  
Philip McGinnity ◽  
...  
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Population Based ◽  
Linkage Groups ◽  
Long Read ◽  
Study Population ◽  
Celtic Sea ◽  
Genome Assemblies ◽  
Inversion Breakpoints

ABSTRACTCurrently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed using DNA from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the cold Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. Structurally, the genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig size of 686 Mb with a N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize in detail large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step towards developing pan-genomic resources for Atlantic cod.

scholarly journals A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea

2020 ◽  
Vol 10 (9) ◽  
pp. 2903-2910 ◽  
Author(s):  
Tina Graceline Kirubakaran ◽  
Øivind Andersen ◽  
Michel Moser ◽  
Mariann Árnyasi ◽  
Philip McGinnity ◽  
...  
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Population Based ◽  
Linkage Groups ◽  
Long Read ◽  
Study Population ◽  
Celtic Sea ◽  
Genome Assemblies ◽  
Inversion Breakpoints

Abstract Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig length of 686 Mb with an N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize, to an extent not previously reported large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step toward developing pan-genomic resources for Atlantic cod.

scholarly journals Exploring the role of temperature in observed inter-population differences of Atlantic cod (Gadus morhua) growth with a 4-dimensional modelling approach

2021 ◽  
Author(s):  
Nadezhda Sokolova ◽  
Martin Butzin ◽  
Flemming Dahlke ◽  
Karl Michael Werner ◽  
Daniel Balting ◽  
...  
Keyword(s):  
Observational Data ◽  
North Sea ◽  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Growth Patterns ◽  
Integrative Approach ◽  
Continuous Growth ◽  
Celtic Sea

Abstract Atlantic cod (Gadus morhua) is one of the most commercially important fish species in the North Atlantic. Environmental factors, such as water temperatures, influence growth of individuals over time, thus forming population-specific growth patterns across climatic regions. Here we develop an integrative approach to investigate the role of temperature in shaping geographic differences of cod growth in the Celtic Sea, North Sea, Iceland, and Barents Sea. We combine a physiology-based growth model and 50-years observational temperature data of 0.5 × 0.5° spatial resolution to simulate continuous growth of cod. The model generated weight-at-age data for the period 1959–2007 which we compared to observational data from fishery-independent scientific surveys. In the Celtic and the northern North Sea, simulated growth matches well observational data. We also show that relatively warm temperatures in the Celtic Sea facilitate maximum growth rates; future warming is likely to have a negative impact on growth of these cod stocks. Growth simulations in Icelandic waters and the Barents Sea are less consistent with local observational data. More complex growth patterns in these regions are probably shaped by ontogenetic shifts in temperature regimes, feeding conditions and physiological adaptations. These findings should stimulate further research on critical processes to be considered in population-specific projections of growth of cod and productivity.

Otolith growth and zone formation during first maturity and spawning of Atlantic cod (Gadus morhua)

2020 ◽  
Vol 77 (1) ◽  
pp. 113-123 ◽  
Author(s):  
Christian Irgens ◽  
Arild Folkvord ◽  
Håkon Otterå ◽  
Olav S. Kjesbu
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Somatic Growth ◽  
Otolith Growth ◽  
Zone Formation ◽  
Stock Biomass ◽  
Tank Experiment ◽  
The Individual ◽  
First Maturity

Specific impacts of somatic growth, sexual maturation, and spawning events on otolith zone formation in Atlantic cod (Gadus morhua) were assessed in a 33-month tank experiment, using Barents Sea cod and Norwegian coastal cod. High and low feeding ration combinations were used to mimic environmental stressors in the field. For both stocks, apparent macrostructural “spawning zones” in otoliths are registered in statutory stock monitoring programs to estimate age at maturity, thus adding key information to stock biomass assessments. We found that substantial energy investments in reproduction caused reductions in otolith growth and altered proportional width between translucent and opaque zones. These effects, however, were only statistically significant among individuals with high reproductive investments, while otoliths from individuals with low investments did not differ from the otoliths for immatures. Reproduction may thus not necessarily induce spawning zones, and alternatively, spawning zones may not necessarily reflect reproduction. Altogether, this suggests that the individual energy level, as a premise for metabolic activity, plays a key role in the formation of such zones and thus is related to environmental conditions.

Pseudobranchial tumours in Atlantic cod, Gadus morhua L., from the Barents Sea

1981 ◽  
Vol 4 (6) ◽  
pp. 527-532 ◽  
Author(s):  
E. C. EGIDIUS ◽  
J. V. JOHANNESSEN ◽  
E. LANGE
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
The Barents Sea

Molecular systematics of gadid fishes: implications for the biogeographic origins of Pacific species

1999 ◽  
Vol 77 (1) ◽  
pp. 19-26 ◽  
Author(s):  
Steven M Carr ◽  
David S Kivlichan ◽  
Pierre Pepin ◽  
Dorothy C Crutcher
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Molecular Data ◽  
Pacific Basin ◽  
Bering Strait ◽  
Pacific Cod ◽  
The Pacific ◽  
Phylogenetic Lineages ◽  
Pacific Species

Phylogenetic relationships among 14 species of gadid fishes were investigated with portions of two mitochondrial DNA (mtDNA) genes, a 401 base pair (bp) segment of the cytochrome b gene, and a 495 bp segment of the cytochrome oxidase I gene. The molecular data indicate that the three species of gadids endemic to the Pacific Basin represent simultaneous invasions by separate phylogenetic lineages. The Alaskan or walleye pollock (Theragra chalcogramma) is about as closely related to the Atlantic cod (Gadus morhua) as is the Pacific cod (Gadus macrocephalus), which suggests that T. chalcogramma and G. macrocephalus represent separate invasions of the Pacific Basin. The Pacific tomcod (Microgadus proximus) is more closely related to the Barents Sea navaga (Eleginus navaga) than to the congeneric Atlantic tomcod (Microgadus tomcod), which suggests that the Pacific species is derived from the Eleginus lineage and that Eleginus should be synonymized with Microgadus. Molecular divergences between each of the three endemic Pacific species and their respective closest relatives are similar and consistent with contemporaneous speciation events following the reopening of the Bering Strait ca. 3.0-3.5 million years BP. In contrast, the Greenland cod (Gadus ogac) and the Pacific cod have essentially identical mtDNA sequences; differences between them are less than those found within G. morhua. The Greenland cod appears to represent a contemporary northward and eastward range extension of the Pacific cod, and should be synonymized with it as G. macrocephalus.

scholarly journals An improved genome assembly uncovers prolific tandem repeats in Atlantic cod

2016 ◽  
Author(s):  
Ole K. Tørresen ◽  
Bastiaan Star ◽  
Sissel Jentoft ◽  
William B. Reinar ◽  
Harald Grove ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Gadus Morhua ◽  
Tandem Repeats ◽  
Atlantic Cod ◽  
Genomic Variation ◽  
Promoter Regions ◽  
Sequencing Technologies ◽  
Combining Data ◽  
Genome Assemblies ◽  
Multiple Assembly

AbstractBackground: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.Results: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21 % of the TRs across the assembly, 19 % in the promoter regions and 12 % in the coding sequences are heterozygous in the sequenced individual.Conclusions: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

scholarly journals An outbreak of francisellosis in wild-caught Celtic Sea Atlantic cod, Gadus morhua L., juveniles reared in captivity

2013 ◽  
Vol 38 (1) ◽  
pp. 97-102 ◽  
Author(s):  
N M Ruane ◽  
M Bolton-Warberg ◽  
H D Rodger ◽  
D J Colquhoun ◽  
M Geary ◽  
...  
Keyword(s):  
Gadus Morhua ◽  
Atlantic Cod ◽  
In Captivity ◽  
Celtic Sea

scholarly journals Methods and results of in situ target-strength measurements of Atlantic cod (Gadus morhua) during combined trawl-acoustic surveys

2009 ◽  
Vol 66 (6) ◽  
pp. 1225-1232 ◽  
Author(s):  
Viacheslav A. Ermolchev
Keyword(s):  
Gadus Morhua ◽  
Barents Sea ◽  
Atlantic Cod ◽  
Biological Data ◽  
Target Strength ◽  
Fish Length ◽  
The Barents Sea ◽  
Total Fish ◽  
Acoustic Surveys

Abstract Ermolchev, V. A., 2009. Methods and results of in situ target-strength measurements of Atlantic cod (Gadus morhua) during combined trawl-acoustic surveys. – ICES Journal of Marine Science, 66: 1225–1232. This paper presents methods for collecting acoustic and biological data, including in situ target-strength (TS) estimates of fish, with results presented for Atlantic cod (Gadus morhua) obtained from combined trawl-acoustic surveys. These include fish in the small, average, and maximum length classes, within the range 5–136 cm (total fish length, LT). The investigations were done using Simrad EK500/EK60 echosounders with split-beam transducers and special post-processing software. Based on an analysis of data collected in the Barents Sea during 1998–2007, a relationship TS = 25.2 log10(LT) − 74.8 was obtained for Atlantic cod at 38 kHz, with TS in dB and LT in centimetres. Seasonally, and for depths between 50 and 500 m, the variability in cod TS was 3.1 dB, decreasing with depth. The largest day–night difference in mean TS was in August–September, with changes as large as 1.0–1.7 dB. In the other seasons, the day–night difference was <1.0 dB.

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