Systems-Based Analysis of the Sarcocystis neurona Genome Identifies Pathways That Contribute to a Heteroxenous Life Cycle

Blazejewski, Tomasz; Nursimulu, Nirvana; Pszenny, Viviana; Dangoudoubiyam, Sriveny; Namasivayam, Sivaranjani; Chiasson, Melissa A.; Chessman, Kyle; Tonkin, Michelle; Swapna, Lakshmipuram S.; Hung, Stacy S.; Bridgers, Joshua; Ricklefs, Stacy M.; Boulanger, Martin J.; Dubey, Jitender P.; Porcella, Stephen F.; Kissinger, Jessica C.; Howe, Daniel K.; Grigg, Michael E.; Parkinson, John

Given the relative lack of repeats in the T. gondii genome, we explored whether the repeats identified in S. neurona are less active than those identified in E. tenella. When repeats are active, it is possible to identify clades of repeats with significant sequence similarity. Pairwise sequence alignments of members of five families of repeats (Fig. 2B) were highly divergent, indicating that the LINEs and DNA elements are no longer active in S. neurona. Further, the LINEs in S. neurona are more diverse and therefore likely to be more ancient than those in E. tenella. Interestingly, E. tenella, T. gondii, and P. falciparum all feature a bimodal distribution of simple repeats that is lacking in S. neurona. Finally, all three of the coccidian genomes analyzed here displayed similar distributions of sequence divergence of DNA elements, albeit with slightly different means (22.5, 28.1, and 27.8% for E. tenella, S. neurona, and S. neurona-like DNA repeats in T. gondii, respectively). This suggests that while DNA elements are no longer active in these genomes, they did remain active for slightly longer within E. tenella. From these analyses, we conclude that the maintenance of large numbers of LINEs and DNA elements in S. neurona (and E. tenella), even though they are inactive, likely plays a functional role, since T. gondii has removed most of these elements from its genome.