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The age of modern introns and the evolutionary forces controlling intron loss and gain remain matters of much debate. In the case of the apicomplexan malaria parasite  Plasmodium falciparum , previous studies have shown that while the positions of two thirds of  P. falciparum  introns are not shared with surveyed non-apicomplexans (leaving open the possibility that they were relatively recently gained), 99.1% are shared with  Plasmodium yoelii , which diverged from  P. falciparum  at least 100 Mya. We show here that 60.6% of  P. falciparum  intron positions in conserved regions are shared with the distantly related apicomplexan  Theileria parva , whereas only 18.2% of introns in the more intron-rich  T. parva  are shared with  P. falciparum . Comparison of 3305 pairs of orthologous genes between  T. parva  and  Theileria annulata  showed that 7089/7111 (99.7%) introns in conserved regions are shared between species. These levels of conservation imply significant differences in rates of intron loss and gain through apicomplexan history. Because transposable elements (TEs) and/or (often TE-encoded) reverse transcriptase are implicated in models of intron loss and gain, the observed low rates of intron loss and gain in recent  Plasmodium  and  Theileria  evolution are consistent with the lack of known TE in those groups. We suggest that intron loss/gain in some eukaryotic lineages may be concentrated in relatively short episodes coincident with occasional TE invasions.

Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution