In metazoans, alternative splicing is a well-established phenomenon that regulates multiple layers of gene regulation. Recent studies demonstrate that alternative splicing is more common than previously thought in some apicomplexans, particularly Plasmodium and Toxoplasma. One of the most studied alternative-splicing factor is the serine/arginine-rich (SR) protein family and their associated kinases. Previous work on P. berghei indicates that alternative splicing regulates gender differentiation into sexual gametocytes, and that ablation of one of the SR proteins produces a gender specific defect. Taking advantage of CRISPR/Cas technologies, we have now generated constitutive and inducible gene knockouts of these proteins in T. gondii. Importantly, ablation of these proteins appear to produce stage specific defects in the parasites, mirroring the P. berghei study. Current efforts are underway to investigate the transcriptional landscape of these parasite using RNA-seq. Traditionally, transcriptomic studies employing RNA-seq have relied on short read technologies. Despite the power of very high sequencing depth, the short reads present a limitation in studying the complexity of alternative splicing in individual transcripts. We are now applying third generation sequencing technologies with longer reads, including Oxford Nanopore and PacBio, which will allow us to obtain a fuller picture of splicing information than was previously possible.