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 SO SN1 genome is more than twice the size of the T. gondii genome. Combining 7,020,033 reads from the 454 Life Sciences sequencing platform with 529,830,690 reads from the Illumina Hi-Seq sequencing platform, we generated 47,722 Mbp of sequence data from S. neurona SO SN1 DNA. By integrating a variety of assembly algorithms (see Materials and Methods), these data were assembled into 116 genomic scaffolds with a combined size of 127 Mbp, over twice the size of the Neospora caninum and T. gondii genomes ( Table 1 is a summary of the genome statistics obtained). An additional 3.1 Mbp of sequence is encoded in 2,950 unscaffolded contigs (each greater than 500 bp in length). The assembly N50 value was 3,117,290 bp, with a maximum scaffold length of 9,217,112 bp. To help annotation efforts, we generated an additional 59,622,019 reads from S. neurona RNA. From these data, we predict a complement of 7,093 genes, 5,853 of which are supported by RNA-Seq evidence (see Table S1 in the supplemental material). The number of genes predicted is comparable to that of the related coccidia T. gondii and Eimeria tenella. Comparisons of gene orderings reveal blocks of syntenic relationships between homologous genes in S. neurona and T. gondii, with the longest such block aligning 43 genes on scaffold 1 of S. neurona and chromosome IX of T. gondii (Fig. 1A) . Chromosome-wide synteny was not observed, suggesting a significant level of genome rearrangement between S. neurona and T. gondii. A more detailed view of the largest syntenic region reveals the extent of gene order preservation but also reveals differences in the structures of individual genes (Fig. 1B) .