Phylogenomics reveals multiple evolutionary lineages of marine crustacean-infecting gregarine apicomplexans

Apicomplexans are a diverse phylum of single-celled protists that are all obligate animal symbionts. The most well-studied members are severe pathogens of humans and livestock, such as the causative agents of malaria, cryptosporidiosis, toxoplasmosis, and coccidiosis, but comparatively little is known about their invertebrate-infecting counterparts, which are evolutionarily and ecologically important, but often overlooked. One of these groups is the Cephaloidophoroidea gregarine superfamily which is one of the most often-detected apicomplexan groups in molecular surveys of marine environments. The few members that have been isolated and molecularly characterized primarily infect crustaceans, and indeed all known crustacean-infecting gregarines phylogenetically branch within the Cephaloidophoroidea. Here we expand the phylogenomic data for gregarines from crustacean hosts, report 11 new species of crustacean-infecting gregarines, and perform phylogenomic analyses using transcriptome data to determine their position on the tree of Apicomplexa. The crustacean-infecting gregarines primarily do branch with the Cephaloidophoroidea, but not exclusively. Lentusidium euphilomedae n. gen. et sp., found in the seed shrimp Euphilomedes sp., branches very distantly to the Cephaloidophoroidea forming a strongly supported sister to Lecudinoidea. We show that crustacean-infecting gregarines comprise multiple evolutionary lineages providing important context for future interpretations of marine environmental surveys.