Mitogenomics: digging deeper with complete mitochondrial genomes

Curole, Jason P.; Kocher, Thomas D.

doi:10.1016/s0169-5347(99)01660-2

Cited by 316 publications

(192 citation statements)

References 27 publications

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“…The traditional phenetic or pure divergence philosophy of classifying this genus as to its rank has not been successful because of the extreme morphological divergence of its included species. Curole and Kocher (1999) argued that mitochondrial genome sequences are most informative at deep nodes in phylogenetic studies, and hence the resolution of supraspecific taxa. Herein, for the first time, we incorporate nearly complete mitochondrial genome sequences of a species of Psilorhynchus in a phylogenetic analysis including representatives of all families of the Order Cypriniformes.…”

Section: Introductionmentioning

confidence: 99%

Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome

Mayden

et al. 2008

Molecular Phylogenetics and Evolution

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Section: Introductionmentioning

confidence: 99%

Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome

Mayden

et al. 2008

Molecular Phylogenetics and Evolution

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“…In this respect, tRNA-encoding genes are usually more frequently rearranged than either rRNAs and PCGs (Boore, 1999;Curole & Kocher, 1999), with most changes observed in arthropods involving tRNA genes near the control region or in the cluster that is most commonly ordered trnA, trnR, trnN, trnS, trnE, trnF (Boore, 1999).…”

Section: Introductionmentioning

confidence: 99%

The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera)

Carapelli

Vannini

Nardi

et al. 2006

Gene

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Abbreviations: atp6 and atp8, genes for ATP synthase subunits 6 and 8; cox1-3, genes for subunits I-III of cytochrome c oxidase; cob, gene for cytochrome b; nad1-6 and nad4L, genes for subunits 1-6 and 4L of NADH dehydrogenase; rrnL and rrnS, genes for the samll and large subunits of ribosomal RNA; trnX, genes encoding for transfer RNA molecules with corresponding amino acids denotaed by the one-letter code and anticodon indicated in parentheses (xxx) when necessary; tRNA-X, transfer RNA molecules with corresponding amino acids denoted with a one-letter code; bp, base pair; mtDNA, mitochondrial DNA; PCR, Polymerace Chain Reaction; Address for correspondence:Francesco AbstractIn this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward As and Ts, as is typical for insect mtDNAs. There is also significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and the N-strand showing an opposite skew for complementary pairs of nucleotides. The hypothetical secondary structure of the 16S rRNA has also been reconstructed, obtaining a structural model similar to that of other insects.

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“…Indeed, several problematic relationships have already been convincingly resolved using this dataset, including those among classes of echinoderms (Smith et al 1993) and of arthropods (Boore, Lavrov, and Brown 1998). However, our limited knowledge of gene rearrangement mechanisms hampers our ability to interpret this dataset and is an impediment to its broader acceptance for phylogenetic studies (Curole and Kocher 1999).…”

Section: Introductionmentioning

confidence: 99%

Complete mtDNA Sequences of Two Millipedes Suggest a New Model for Mitochondrial Gene Rearrangements: Duplication and Nonrandom Loss

Lavrov

Boore²,

Brown³

2002

Molecular Biology and Evolution

261

193

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We determined the complete mtDNA sequences of the millipedes Narceus annularus and Thyropygus sp. (Arthropoda: Diplopoda) and identified in both genomes all 37 genes typical for metazoan mtDNA. The arrangement of these genes is identical in the two millipedes, but differs from that inferred to be ancestral for arthropods by the location of four genes/gene clusters. This novel gene arrangement is unusual for animal mtDNA, in that genes with opposite transcriptional polarities are clustered in the genome and the two clusters are separated by two non-coding regions. The only exception to this pattern is the gene for cysteine tRNA, which is located in the part of the genome that otherwise contains all genes with the opposite transcriptional polarity. We suggest that a mechanism involving complete mtDNA duplication followed by the loss of genes, predetermined by their transcriptional polarity and location in the genome, could generate this gene arrangement from the one ancestral for arthropods. The proposed mechanism has important implications for phylogenetic inferences that are drawn on the basis of gene arrangement comparisons.

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Mitogenomics: digging deeper with complete mitochondrial genomes

Cited by 316 publications

References 27 publications

Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome

Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes): Evidence from the mitochondrial genome

The mitochondrial genome of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera)

Complete mtDNA Sequences of Two Millipedes Suggest a New Model for Mitochondrial Gene Rearrangements: Duplication and Nonrandom Loss

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