A linkage map of the Hydractinia symbiolongicarpus genome

Hydractinia symbiolongicarpus is a colonial cnidarian. In previous work, the genome of a single male colony, 291-10, has been sequenced and assembled. In this project, we sought to create a linkage map of the genome. To do so, we crossed colony 291-10 to a female colony (ID=295-8), to create a population of 90 F1 offspring. We then re-sequenced the genomes of the female parent and all offspring, each via a separate library. These sequences were then mapped to 291-10 genome assembly, and variants identified using GATK. Variants were then used in pseudotestcross strategy to create a linkage map consisting of 15 linkage groups, which corresponds to the expected haploid number of chromosomes. Subsequent analysis of this map was also used to show that Hydractinia symbiolongicarpus has XX/XY genetic sex determination.