title: Localized Retroprocessing as a Model of Intron Loss in the Plant Mitochondrial Genome.
abstract: Loss of introns in plant mitochondrial genes is commonly explained by retroprocessing. Under this model, an mRNA is reverse transcribed and integrated back into the genome, simultaneously affecting the contents of introns and edited sites. To evaluate the extent to which retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing for whole mitochondrial genomes of 30 species in the monocot order Alismatales. In this group, we found an unusually high degree of variation in the intron content, even expanding the hitherto known variation among angiosperms. Some species have lost some two-third of the cis-spliced introns. We found a strong correlation between intron content and editing frequency, and detected 27 events in which intron loss is consistent with the presence of nucleotides in an edited state, supporting retroprocessing. However, we also detected seven cases of intron loss not readily being explained by retroprocession. Our analyses are also not consistent with the entire length of a fully processed cDNA copy being integrated into the genome, but instead indicate that retroprocessing usually occurs for only part of the gene. In some cases, several rounds of retroprocessing may explain intron loss in genes completely devoid of introns. A number of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome.
authors.affiliation: Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Argelia
authors.initials: A
authors.lastname: Cuenca
authors.affiliation: Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: T Gregory
authors.initials: TG
authors.lastname: Ross
authors.affiliation: Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, Canada UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada.
authors.forename: Sean W
authors.initials: SW
authors.lastname: Graham
authors.affiliation: Department of Biological Sciences, California State University, Los Angeles, California.
authors.forename: Craig F
authors.initials: CF
authors.lastname: Barrett
authors.affiliation: L.H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York.
authors.forename: Jerrold I
authors.initials: JI
authors.lastname: Davis
authors.affiliation: Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
authors.forename: Ole
authors.initials: O
authors.lastname: Seberg
authors.affiliation: Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark gittep@snm.ku.dk.
authors.forename: Gitte
authors.initials: G
authors.lastname: Petersen
mesh_terms: D035961:Alismatales / Q000235:genetics; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D007438:Introns; D017393:RNA Editing
keywords: Alismatales; RNA editing; intron loss; mitochondrial genome; retroprocessing