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

The S. neurona apicoplast genome is well conserved with other Apicomplexa. In addition to its nuclear genome, the apicoplast genome of S. neurona SO SN1 was studied by reference mapping to the assembled S. neurona SN3 apicoplast sequence (see Fig. S1 in the supplemental material). Both organellar genome architectures are highly similar to those of Toxoplasma (GenBank accession no. U87145.2) and P. falciparum (22) . There are, however, a few key differences. As in Toxoplasma, both Sarcocystis apicoplast sequences are missing open reading frame A (ORFA). However, unlike Toxoplasma, both S. neurona sequences show a loss of rpl36 and a loss of one copy of tRNA-Met (from the tRNA cluster between rps4 and rpl4). S. neurona also has a feature first observed in the Piroplasmida that is not seen in Toxoplasma, namely, a division of the RNA polymerase C2 gene into two distinct genes (23) . Both S. neurona apicoplast genome sequences uniquely have the insertion of a fragment of rps4 between ORFG and one copy of the large-subunit rRNA in common (see Fig. S1 in the supplemental material). The insert was verified in S. neurona SN3 via PCR and sequencing across this region (see Fig. S2 , S3, and S4 in the supplemental material). The rps4 fragment insertion appears to be very recent because the S. neurona SN3 fragment insert is identical in sequence to the corresponding region in the full-length rps4 gene. Comparison of the S. neurona SO SN1 and SN3 nucleotide sequences to each other reveals a few indels but no single-nucleotide polymorphisms (see Text S1 in the supplemental material). Indels, when present, occur in up to one-third of the reads for the locus. The dominant sequence is identical to that determined for SN3. Each S. neurona apicoplast genome was sequenced to greater than 200Ï« coverage.