The first mitochondrial genome of the model echinoid Lytechinus variegatus and insights into Odontophoran phylogenetics

Assembly of publically available next-generation sequence data facilitated the generation of three camarodont echinoid mitogenomes: two for the Green Urchin (Lytechinus variegatus) and one for the Red Urchin (Mesocentrotus franciscanus). The data generated are exploited in a phylogenomic analysis of the superfamily Odontophora, originally proposed for echinoids with tooth supports on the epiphyses of the jaw. The analysis highly supports this taxon and its current subdivision into three families: the Echinometridae, Toxopneustidae, and Strongylocentrotidae. The analysis furthermore implies that historical taxonomic issues between two members of the genus Strongylocentrotus (S. pallidus and S. droebachiensis) may have a genetic basis. The novel mitogenomes for the model species L. variegatus complements the draft genome available for this taxon, one of only three genome-enabled echinoid species. The assembly method applied herein, follows a divide-and-conquer approach that provides for reduced computational requirements and facilitates resolving assembly problems when processing ultra-high coverage next-generation sequence data.