Genome Evolution and Meiotic Maps by Massively Parallel DNA Sequencing: Spotted Gar, an Outgroup for the Teleost Genome Duplication

Comparative genomics for hundreds of plant and animal species of evolutionary, agricultural, economic, and medical importance are unknown due to the expense of obtaining well-assembled sequenced genomes and difficulties in performing multi-generational studies. Teleost fish provide many medical models of human disease, but possess anciently duplicated genomes that are substantially rearranged in ways that can sometimes obfuscate genome connectivities. Here we exploit massively parallel DNA sequencing to develop strategies and software to construct, with thrift and speed, a meiotic map containing over 8,000 single nucleotide polymorphisms (SNPs), including nearly a thousand protein-coding markers, from individual wild-caught spotted gar, an ancient air-breathing fish. Results showed that the gar genome diverged from the teleost genome before the teleost genome duplication event and resembles more closely the organization of the human genome than that of the teleost genome; thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our mapping strategy promises to facilitate comparative genomic analysis in non-model species.