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The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Kris A Christensen1,2,3, Eric B Rondeau1,2, David R Minkley2
1Fisheries and Oceans Canada, Centre for Aquaculture and Environmental Research, West Vancouver, British Columbia, Canada.
Plos One
|September 14, 2018
Summary
This study presents a new Arctic charr genome assembly and genetic map, crucial for understanding local adaptation and anadromy in this resilient salmonid species. The findings offer insights into conserved gene expression across salmonids.
Area of Science:
- Genomics
- Aquatic Biology
- Evolutionary Biology
Background:
- Arctic charr (Salvelinus alpinus) exhibit remarkable resilience and longevity, with a genome structure potentially linked to adaptation and anadromy.
- The Salvelinus genus genome is considered more ancestral compared to related genera like Oncorhynchus and Salmo.
Purpose of the Study:
- To generate a new genetic map for Arctic charr.
- To sequence and assemble the Arctic charr genome using newly developed and previous genetic maps.
- To analyze the Arctic charr genes and genome assembly, including orthologous gene identification and expression profiles.
Main Methods:
- Generation of a high-density genetic map with 8,574 unique markers.
- Whole-genome sequencing and assembly utilizing both new and prior genetic maps.
- Comparative genomic analysis to identify orthologous genes and conserved expression patterns across salmonid species.
Main Results:
- A new Arctic charr genetic map was created, showing minor structural differences from previous maps.
- The Arctic charr genome assembly is comparable in size, N50, BUSCOs, and repetitive DNA content to other salmonid genomes.
- Numerous orthologous genes were identified between salmonid species, with many exhibiting conserved gene expression profiles.
Conclusions:
- The new Arctic charr genome assembly and genetic map provide a valuable resource for evolutionary and adaptation studies.
- Conserved gene expression profiles among salmonids suggest potential insights into species-specific phenotypic traits.
- Understanding these genomic features can illuminate the mechanisms behind Arctic charr's unique adaptations.
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