Data from: Phylogenomic Diversity of Marine Crustacean-Infecting Gregarine Apicomplexans Within and Outside the Cephaloidophoroidea

Apicomplexans are a phylum of diverse protists that are obligate animal symbionts. Gregarines are a widespread clade of apicomplexans dominating microbial communities in forest biomes and are the most represented apicomplexans in marine ecosystems. However, few members have been isolated and molecularly characterized from crustacean hosts. All known crustacean-infecting gregarines phylogenetically branch within the Cephaloidophoroidea. Here we expand the phylogenomic data for crustacean gregarines and report 11 new species of crustacean-infecting gregarines. We show that crustacean-infecting gregarines primarily do branch with the Cephaloidophoroidea, but not exclusively. Lentusidium euphilomedae, found in the seed shrimp Euphilomedes sp., branches very distantly to the Cephaloidophoroidea forming a strongly supported sister to Lecudinoidea. This dataset contains the multiple nuclear gene alignment used in the phylogenomic analysis, a SSU/LSU gene alignment of apicomplexans, and a SSU/LSU gene alignment of gregarines and environmental sequences.