ArticleBMC genomics2017
An improved genome assembly uncovers prolific tandem repeats in Atlantic cod.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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86 citing papers in PubMed, 169 citations in OpenAlex.
- Article
- Coexisting Atlantic Cod Ecotypes in the Barents Sea: An Issue for Managing Fisheries.Evolutionary applications · 2026Article
- Rapid genome modifications including chromosomal fusions and large-scale inversions are key features in Arctic codfish species.Genome biology · 2026Article
- Reference genome bias in light of species-specific chromosomal reorganization and translocations.Genome biology · 2025Article
- Chromosome-level genome assembly for Sichuan taimen (Hucho bleekeri) reveals the extraordinary tandem repeat proportions and its persistent population shrinkage.BMC genomics · 2025Article
- A century of anthropogenic perturbations impact genomic signatures of the iconic migratory Atlantic cod.Science advances · 2025Article
- Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA.Proceedings. Biological sciences · 2024Article
- The Atlantic Cod MHC I compartment has the properties needed for cross-presentation in the absence of MHC II.Scientific reports · 2024Article
- Interaction of Bisphenol A and Its Analogs with Estrogen and Androgen Receptor from Atlantic Cod (Environmental science & technology · 2024Article
- Maptcha: an efficient parallel workflow for hybrid genome scaffolding.BMC bioinformatics · 2024Article
- Article
- High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl.Heliyon · 2023Article
- Evidence of hybridization between genetically distinct Baltic cod stocks during peak population abundance(s).Evolutionary applications · 2023Article
- The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling.Science China. Life sciences · 2023Article
- Adaptive protein evolution through length variation of short tandem repeats inScience advances · 2023Article
- Atlantic cod (Frontiers in cell and developmental biology · 2023Article
- Ancestral reconstruction reveals catalytic inactivation of activation-induced cytidine deaminase concomitant with cold water adaption in the Gadiformes bony fish.BMC biology · 2022Article
- Immunogenetic losses co-occurred with seahorse male pregnancy and mutation in tlx1 accompanied functional asplenia.Nature communications · 2022Article
- Genomic differentiation in Pacific cod using Pool-Seq.Evolutionary applications · 2022Article
- Ancient DNA evidence for the ecological globalization of cod fishing in medieval and post-medieval Europe.Proceedings. Biological sciences · 2022Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors at 8 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsBy 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.
conclusionsThe 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.
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