Phylogenetic Implications of the Multiple Losses of the Mitochondrial coxII.i3 Intron in the Angiosperms

Abstract

Previous studies have shown that the mitochondrial coxII.i3 intron is absent in all rosids examined, in Philadelphus (Hydrangeaceae, Cornales), and in Catharanthus and Vinca (Apocynaceae, Gentianales). We surveyed for the presence or absence of this intron in 177 species representing all orders of angiosperms, where it is primitively present. The intron appears to have been lost independently in Gnetales, Laurales, Zingiberales, Ranunculales, Saxifragales, rosids, Santalales, Caryophyllales, Ericales, Cornales, Gentianales, Lamiales, Boraginales, Aquifoliales, Asterales, Dipsacales, as well as in the genus Escallonia. Depending upon the phylogenies used to interpret the losses, and due to lack of resolution in some groups, the intron could have been lost up to 27 times in the angiosperms (excluding the loss in Gnetales). The losses sometimes corroborate the monophyly of groups (rosids and Lamiales) or of subgroups within orders (in the Ranunculales, Caryophyllales, Cornales, Gentianales, and Asterales). In other groups, such as the Saxifragales, Ericales, and Dipsacales, the patterns of losses are more complex and would require further study. The presence or absence of the coxII.i3 mitochondrial intron seems a useful phylogenetic marker in some groups, but caution in interpretation is needed as multiple parallel losses have occurred throughout the angiosperms.

Extensive Loss of RNA Editing Sites in Rapidly Evolving Silene Mitochondrial Genomes: Selectionvs. Retroprocessing as the Driving Force

“…Therefore, additional RNA editing sites surrounding the second cox2 intron may have been lost in parallel between these lineages ( Figure 5A). Overall, the cox2 introns appear to have been lost independently numerous times during angiosperm evolution ( Figure S1) (Joly et al 2001). In the second case of intron loss, S. noctiflora lacks the third nad7 intron along with two adjacent editing sites ( Figure 5B).…”

Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia

“…All 19 introns are found in protein genes, and all but one occur in genes that encode subunits of complex I (NADH dehydrogenase). The S. latifolia lineage has lost the second nad4 intron and both of the cox2 introns found in other angiosperms [ 51 ]. It also lacks the group I intron in cox1 , which has been widely distributed across the angiosperm phylogeny by numerous horizontal transfer events [ 52 ].…”

Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome

“…Over evolutionary time intron loss has occurred in virtually all organisms with spliced genes ( Joly et al 2001 ; Lambowitz and Zimmerly 2004 ; Odom and Herrin 2013 ). However, the mechanisms underlying intron loss remain poorly understood.…”

“…A number of lineage-specific intron losses have, however, been detected, and multiple losses were recently found in the genus Geranium ( Park et al 2015 ). In addition, a few genes (e.g., nad 1 and cox 2) seem to have a very dynamic evolutionary history, with frequent intron loss among angiosperm groups ( Gugerli et al 2001 ; Joly et al 2001 ; Hepburn et al 2012 ).…”