Joint assembly and genetic mapping of the Atlantic horseshoe crab genome reveals ancient whole genome duplication

摘要

Horseshoe crabs are marine arthropods with a fossil record extending backapproximately 450 million years. They exhibit remarkable morphologicalstability over their long evolutionary history, retaining a number of ancestralarthropod traits, and are often cited as examples of "living fossils." Asarthropods, they belong to the Ecdysozoa}, an ancient super-phylum whosesequenced genomes (including insects and nematodes) have thus far shown moredivergence from the ancestral pattern of eumetazoan genome organization thancnidarians, deuterostomes, and lophotrochozoans. However, much of ecdysozoandiversity remains unrepresented in comparative genomic analyses. Here we use anew strategy of combined de novo assembly and genetic mapping to examine thechromosome-scale genome organization of the Atlantic horseshoe crab Limuluspolyphemus. We constructed a genetic linkage map of this 2.7 Gbp genome bysequencing the nuclear DNA of 34 wild-collected, full-sibling embryos and theirparents at a mean redundancy of 1.1x per sample. The map includes 84,307sequence markers and 5,775 candidate conserved protein coding genes. Comparisonto other metazoan genomes shows that the L. polyphemus genome preservesancestral bilaterian linkage groups, and that a common ancestor of modernhorseshoe crabs underwent one or more ancient whole genome duplications (WGDs)~ 300 MYA, followed by extensive chromosome fusion.