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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 towhich retroprocessing explains intron loss, we analyzed patterns of intron content and predicted RNA editing forwhole mitochondrial genomesof 30 species in themonocot order Alismatales. In this group,wefound 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 andediting frequency, and detected27 events inwhich 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 cDNAcopy being integrated intothegenome,but instead indicate that retroprocessingusually occurs for onlypartof the gene. In some cases, several rounds of retroprocessingmay explain intron loss in genes completely devoid of introns.Anumber of taxa retroprocessing seem to be very common and a possibly ongoing process. It affects the entire mitochondrial genome. [ABSTRACT FROM AUTHOR]

Past phylogenetic studies of the monocot order Alismatales left several higher-order relationships unresolved. We addressed these uncertainties using a nearly complete genus-level sampling of whole plastid genomes (gene sets representing 83 protein-coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter- and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister-group of the rest of the order, one likelihood analysis indicated a contrasting Araceae-sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral-state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae. [ABSTRACT FROM AUTHOR]

A phylogenetic analysis of the early branching lineages of the monocotyledons is performed using data from two plastid genes ( rbcL and matK), five mitochondrial genes ( atp1, ccmB, cob, mttB and nad5) and morphology. The complete matrix includes 93 terminals representing Acorus, the 14 families currently recognized within Alismatales, and numerous lineages of monocotyledons and other angiosperms. Total evidence analysis results in an almost completely resolved strict consensus tree, but all data partitions, genomic as well as morphological, are incongruent. The effects of RNA editing and potentially processed paralogous sequences are explored and discussed. Despite a decrease in incongruence length differences after exclusion of edited sites, the major data partitions remain significantly incongruent. The 14 families of Alismatales are all found to be monophyletic, but Acorus is found to be included in Alismatales rather than being the sister group to all other monocotyledons. The placement is strongly supported by the mitochondrial data, atp1 in particular, but it cannot be explained as an artifact caused by patterns of editing or by sampling of processed paralogues. [ABSTRACT FROM AUTHOR]