Construction of a Comprehensive Linkage Map in the Sea Lamprey, Petromyzon marinus

The sea lamprey (Petromyzon marinus) represents a critical outgroup for understanding the evolution of vertebrate genes, genomes, and development. Moreover, lampreys are one of the few vertebrates known to undergo large-scale rearrangements of its genome. To facilitate genome-scale analyses using lamprey and complement the existing somatic genome assembly, we generated the first comprehensive linkage map for the species.  We developed this genetic map using deep sequencing to identify single nucleotide polymorphisms and track their segregation in a controlled cross derived from two wild-captured lampreys. Specifically, restriction-site associated DNA (RAD) sequencing was used to genotype 5275 independent loci for 30 F1 siblings of the outbred cross.

            The resulting meiotic map yielded 95 linkage groups, which allowed us to map 71% of the scaffolds over 250 kb from the current genome assembly and 45% of the entire assembly. Analyses of conserved synteny reveal a strong signature of whole-genome duplication in the vertebrate lineage. Other notable features of the map include large differences between the maternal and paternal maps, four linkage groups that only segregated in the maternal germline, and one group that only segregated in the paternal germline. This map provides the first direct characterization of the chromosome-scale structure of an agnathan (jawless vertebrate) genome, sheds new light on the deep evolutionary history of vertebrate genomes, and provides new insight into structural variation within and among individual lampreys.