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A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea.
Tina Graceline Kirubakaran1, Øivind Andersen1,2, Michel Moser1
1Centre for Integrative Genetics and Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
G3 (Bethesda, Md.)
|July 10, 2020
Summary
A new high-quality Atlantic cod genome assembly (gadMor_Celtic) from a southern population was created using long-read nanopore data. This resource complements existing northern assemblies and reveals large chromosomal inversions, aiding population differentiation studies.
Area of Science:
- Genomics
- Population Genetics
- Marine Biology
Background:
- Existing Atlantic cod (Gadus morhua) genome assemblies are from the Northeast Arctic Cod (NEAC) population.
- These assemblies have facilitated studies on population differentiation and adaptive evolution, identifying genomic divergence on specific linkage groups.
Purpose of the Study:
- To present a high-quality reference genome assembly for a southern Atlantic cod population from the Celtic Sea.
- To complement existing northern population genome assemblies and support pan-genomic resource development for Atlantic cod.
Main Methods:
- Genome assembly using long-read nanopore data from a male Celtic Sea Atlantic cod.
- Integration of contigs with genetic linkage mapping data to construct chromosome sequences.
- Characterization of chromosomal inversions and repetitive elements.
Main Results:
- A high-quality genome assembly (gadMor_Celtic) with a contig length of 686 Mb and N50 of 10 Mb was generated.
- Twenty-three chromosome sequences were constructed, showing high confidence mapping to the NEAC assembly (gadMor3).
- Large chromosomal inversions were characterized on linkage groups 1, 2, 7, and 12, with potential inversions identified on linkage groups 6, 11, and 21. A repetitive element enriched at centromeric regions was also identified.
Conclusions:
- The gadMor_Celtic assembly provides a valuable resource for a southern Atlantic cod population, complementing existing northern assemblies.
- This assembly enables detailed characterization of chromosomal structures like inversions, advancing our understanding of cod population genomics.
- The study represents a significant step towards developing comprehensive pan-genomic resources for Atlantic cod.
