Salmonid Chromosome Evolution as Revealed by a Novel Method for Comparing RADseq Linkage Maps

Area of Science:

• Evolutionary biology
• Genomics
• Comparative genomics

Background:

• The Salmonidae family is an excellent model for studying whole genome duplication (WGD) due to a relatively recent WGD event followed by rediploidization and diversification.
• Extensive synteny exists between homologous chromosome arms in extant salmonids, yet each species exhibits unique chromosome arm fusions and fissions.
• Investigating structural rearrangements in large, outbred eukaryotic genomes is challenging, but linkage maps offer a viable approach.

Purpose of the Study:

• To generate a high-density linkage map for Brook Charr (Salvelinus fontinalis).
• To identify homologous chromosome arms across diverse salmonid species and their sister group, Northern Pike (Esox lucius).
• To characterize the history of chromosomal rearrangements and conserved inversions following WGD in salmonids.

Main Methods:

• Generation of a high-density linkage map using RAD sequencing for Brook Charr (3,826 markers).
• Development and application of MapComp software to identify homologous markers between multiple salmonid linkage maps, utilizing a reference genome for intermediate comparison.
• Comparative analysis of linkage maps from Salvelinus, Oncorhynchus, Salmo, Coregonus, and Esox lucius.

Main Results:

• A high-density linkage map for Brook Charr was successfully created.
• The MapComp tool increased marker comparability between linkage maps by five-fold, facilitating cross-species comparisons.
• The study characterized the likely history of chromosomal rearrangements and identified several conserved chromosomal inversions post-WGD in salmonids.

Conclusions:

• The developed MapComp tool significantly enhances the ability to compare linkage maps across related species, aiding the study of genome evolution.
• This research provides insights into the chromosomal evolutionary history of salmonids following whole genome duplication.
• The findings and methodology are applicable to RADseq-based linkage map analyses in other taxa.