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At least 1,657 records · Page 92Linked to original sources
PubMed1997

Evolution of the mitochondrial cytochrome oxidase II gene in collembola.

The sequence of the mitochondrial COII gene has been widely used to estimate phylogenetic relationships at different taxomonic levels across insects. We investigated the molecular evolution of the COII gene and its usefulness for reconstructing phylogenetic relationships within and among four collembolan families. The collembolan COII gene showed the lowest A + T content of all insects so far examined, confirming that the well-known A + T bias in insect mitochondrial genes tends to increase from the basal to apical orders. Fifty-seven percent of all nucleotide positions were variable and most of the third codon positions appeared free to vary. Values of genetic distance between congeneric species and between families were remarkably high; in some cases the latter were higher than divergence values between other orders of insects. The remarkably high divergence levels observed here provide evidence that collembolan taxa are quite old; divergence levels among collembolan families equaled or exceeded divergences among pterygote insect orders. Once the saturated third-codon positions (which violated stationarity of base frequencies) were removed, the COII sequences contained phylogenetic information, but the extent of that information was overestimated by parsimony methods relative to likelihood methods. In the phylogenetic analysis, consistent statistical support was obtained for the monophyly of all four genera examined, but relationships among genera/families were not well supported. Within the genus Orchesella, relationships were well resolved and agreed with allozyme data. Within the genus Isotomurus, although three pairs of populations were consistently identified, these appeared to have arisen in a burst of evolution from an earlier ancestor. Isotomurus italicus always appeared as basal and I. palustris appeared to harbor a cryptic species, corroborating allozyme data.

Amino Acid Sequence↗
PubMed2003

Codon usage patterns in cytochrome oxidase I across multiple insect orders.

Synonymous codon usage bias is determined by a combination of mutational biases, selection at the level of translation, and genetic drift. In a study of mtDNA in insects, we analyzed patterns of codon usage across a phylogeny of 88 insect species spanning 12 orders. We employed a likelihood-based method for estimating levels of codon bias and determining major codon preference that removes the possible effects of genome nucleotide composition bias. Three questions are addressed: (1) How variable are codon bias levels across the phylogeny? (2) How variable are major codon preferences? and (3) Are there phylogenetic constraints on codon bias or preference? There is high variation in the level of codon bias values among the 88 taxa, but few readily apparent phylogenetic patterns. Bias level shifts within the lepidopteran genus Papilio are most likely a result of population size effects. Shifts in major codon preference occur across the tree in all of the amino acids in which there was bias of some level. The vast majority of changes involves double-preference models, however, and shifts between single preferred codons within orders occur only 11 times. These shifts among codons in double-preference models are phylogenetically conservative.

Animals↗
PubMed2002

Transcription of succinate dehydrogenase subunit 4 (sdh4) gene in potato: detection of extensive RNA editing and co-transcription with cytochrome oxidase subunit III (cox3) gene.

The potato (Solanum tuberosum L.) mitochondrial cox3/ sdh4 gene cluster was previously identified by heterologous hybridization using a Marchantia polymorpha sdh4 probe. In this work, this potato gene cluster was cloned, sequenced and its expression was evaluated. The gene sequence and gene locus organization were found to be similar to the corresponding gene cluster in other dicot species, where known. Northern hybridizations with potato and cauliflower (Brassica oleraceae) mtRNA and RT-PCR analyses using potato mtRNA indicated that cox3 and sdh4 are co-transcribed in both species, generating a complex transcription pattern, where several transcripts from 1.1 kb to 4.4 kb are found. The potato transcript from this cluster displayed 14 and 13 RNA-editing sites, in the cox3 and sdh4 genes respectively, which changed the codon identity to amino acids and created a sdh4 partially edited stop codon. Forty-three cDNA clones were analyzed for editing process and revealed different partial-editing with no apparent sequential processing in the sdh4 gene.

Arabidopsis Proteins↗