| Ciona savignyi is an emerging model for chordate evolution, development, and gene regulation. However, its potential as a model has been somewhat hampered by the lack of a genetic map. In this work, we construct the first genetic map in this species. To do this we employ a combination of novel approaches, developing the first set of portable markers in this extremely polymorphic species, and tightly integrating the genetic map and the sequence assembly data. The resulting genetic map is complete, having just one linkage group for each one of the fourteen chromosomes, and 83% of the sequenced genome has been reconstructed into chromosomes. With chromosomes, we were then able compare the genome of C. savignyi to its highly divergent sister species, Ciona intestinalis, to reveal extensive intrachromosomal rearrangement, and a paucity of interchromosomal rearrangements. These results, when considered in the light of the very large effective population sizes of this species, strongly suggest that interchromosomal rearrangements are generally deleterious, which has important implications for the interpretation of the pattern of rearrangements observed among the vertebrates. |
