RNA splicing of a long cox2i691 and the evolution of cox2 introns in angiosperm mitochondria

Abstract In angiosperms, the mitochondrial cox2 gene harbors up to two introns, commonly referred to as cox2i373 and cox2i691. Although each of these introns is ~1.5 kb in length, a cox2i691 of 4.2 kb has been reported in Acacia ligulata (Fabaceae). It is still unclear whether its unusual length is due to a trans-splicing arrangement, the loss of functionality of the interrupted cox2, or a rare elongation of a cis-spliced intron. Here, we tried to shed light on these hypotheses by thoroughly analyzing short-read RNA sequencing with a multi-step computational strategy. The results revealed that the Acacia cox2 is very likely functional and its long intron is spliced in cis in a very efficient manner despite its length. To better characterize how conserved cox2i691 is among angiosperms, we studied 222 fully-sequenced mitogenomes from 30 plant orders. Unlike cox2i373, our results point out that cox2i691 shows a distribution among plants that is shaped by frequent intron loss events driven by localized retroprocessing. In addition, cox2i691 undergoes episodic elongations that are taxonomically scattered and poorly related to genome-wide repeat content. Such elongations were found to occur within domain IV and seem to be due to the incorporation of exogenous DNA. Surprisingly, we found that cox2i691 is erroneously annotated as absent in 30 mitogenomes deposited in public databases.