Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome

Macey, Jonathan R.; Larson, Allan; Ananjeva, Natalia B.; Fang, Zhi-Li; Papenfuss, Theodore J.

doi:10.1093/oxfordjournals.molbev.a025706

Cited by 575 publications

(414 citation statements)

References 63 publications

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“…In particular, the 3'-GCC-5' heavy strand template sequence identified as the point of light-strand elongation in mouse (Brennicke and Clayton, 1981) is not present in these structures for the Bipedidae. Bipes tridactylus has an eight base stem and the other two species 13 have a seven base stem, which is less than that normally found among squamate reptiles and these stem regions show little base compositional similarity with that observed across other squamates (Macey et al, 1997a). …”

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confidence: 67%

“…Bipes biporus has an unusual stem and loop structure atypical of vertebrates between trnN and trnC (Macey et al, 1997a) where light-strand replication usually initiates. This character has been linked to mitochondrial genomic rearrangement among vertebrates (Macey et al, 1997a).…”

Section: Introductionmentioning

confidence: 99%

“…Although no character can be asserted to be completely free from the possibility of homoplasious change, parallelisms or reversals of gene rearrangements seem, in principle, to be unlikely, and have not been observed to date in sampling approximately 300 complete mtDNA sequences. A common mode of mitochondrial genomic rearrangement appears to be a tandem duplication of genes with random loss of extra copies (Boore 2000;Macey et al, 1997a;. Hence, the pattern of pseudogene formation in a tandemly duplicated segment is causative in establishing novel gene orders.…”

Section: Introductionmentioning

confidence: 99%

“…3F). Mitochondrial gene order is a highly robust phylogenetic character for reconstructing evolutionary relationships among animals (Boore, 1999;Boore and Brown 1998;Macey et al, 1997aMacey et al, , 2000. Although no character can be asserted to be completely free from the possibility of homoplasious change, parallelisms or reversals of gene rearrangements seem, in principle, to be unlikely, and have not been observed to date in sampling approximately 300 complete mtDNA sequences.…”

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confidence: 99%

“…A common mode of mitochondrial genomic rearrangement appears to be a tandem duplication of genes with random loss of extra copies (Boore 2000;Macey et al, 1997a;. Hence, the pattern of pseudogene formation in a tandemly duplicated segment is causative in establishing novel gene orders.Amphisbaenian reptiles are known to have several novel mitochondrial genomic features.Bipes biporus has an unusual stem and loop structure atypical of vertebrates between trnN and trnC (Macey et al, 1997a) where light-strand replication usually initiates. This character has been linked to mitochondrial genomic rearrangement among vertebrates (Macey et al, 1997a).…”

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confidence: 99%

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Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences

Macey

Papenfuss

Kuehl

et al. 2004

Molecular Phylogenetics and Evolution

106

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Key Words: Reptilia; Amphisbaenia; Bipes; phylogeny; mitochondrial DNA; genomics; limb evolution; biogeography; Pangaea. 3 INTRODUCTIONAmphisbaenians are fossorial reptiles that inhabit tropical and semitropical regions of the world (Fig. 1). The vast majority of species occur on land masses of Gondwanan origin in South America, Africa and Arabia. However, two of the four families are restricted to regions associated with Laurasia, the Bipedidae, with three species in Mexico (Fig. 2), and the Rhineuridae, with a single species in Florida. These taxa have pleurodont dentition (Gans, 1968) and were originally placed in the family Amphisbaenidae which now primarily includes taxa distributed in Gondwanan regions of South America and Africa (Gans, 1978). The fourth family of Amphisbaenia, the Trogonophidae, is the only one to have acrodont dentition and is restricted to Gondwanan plates of North Africa, Arabia and the island of Socotra. By superimposing a phylogeny of these groups on their distribution relative to the breakup of these major land masses, it is possible to test hypotheses about their origins. For example, monophyly of taxa found in Laurasia or Gondwana may reflect their isolation stemming from the breakup of Pangaea 200 million years before present (MYBP), (Fig. 3C, D).A phylogeny of Amphisbaenia is also important for reconstructing patterns of morphological change. Among the four families of Amphisbaenia, all taxa are limbless except the Bipedidae, which contains reptiles with two forelimbs. If gradual reduction in limbs were to have occurred from an ancestor with both hind and forelimbs, then the Bipedidae, with its presumed intermediate state, would be thought to be the sister taxon to the remaining families as has been suggested by morphological data (Kearney, 2003; Fig. 3B).Within the Bipedidae, species are variable for the number of digits on a limb (Papenfuss, 1982). The Baja California taxon, Bipes biporus, always has five digits on each limb. In mainland Mexico, the more northern taxon, B. canaliculatus, is variable, with either four or five 4 digits, while the more southern species, B. tridactylus, always has three digits on each limb. If digits are being gradually lost from an ancestor with five digits then B. biporus is predicted to be the sister taxon to the other two species (Fig. 3E). This phylogenetic hypothesis is consistent with an initial splitting of Bipes by the separation of peninsular Baja California from the west coast of Mexico (12-14 MYBP;Ferrari, 1995), with the two mainland species later diverging.Alternatively, tectonic activity along the west coast of Mexico in the Cretaceous to Paleocene (Ferrari, 1995) may have isolated the more northern taxa, B. biporus and B. canaliculatus, from B. tridactylus to the south (Fig. 3F).Mitochondrial gene order is a highly robust phylogenetic character for reconstructing evolutionary relationships among animals (Boore, 1999;Boore and Brown 1998;Macey et al., 1997aMacey et al., , 2000. Although no character can be asserted to be completely ...

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confidence: 67%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences

Macey

Papenfuss

Kuehl

et al. 2004

Molecular Phylogenetics and Evolution

106

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Mitochondrial Genome Evolution

Bernt

Machné²,

Sahyoun

et al. 2013

Encyclopedia of Life Sciences

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Mitochondria are membrane‐enclosed organelles present in most eukaryotic cells that generate most of the cell's adenosine triphosphate (ATP) supply. Derived from a proteobacterial ancestor, mitochondria harbour their own, drastically reduced genome. Starting from a prokaryote‐like ancestral state encoding a complete ribosomal ribonucleic acid (rRNA) operon, a complete set of transfer RNAs (tRNAs) required for translation, and key enzymes of the respiratory chain as well as some ribosomal proteins, the mitogenome has been dramatically restructured and further reduced in many of the eukaryotic lineages. The loss and transfer to the nucleus of mitochondrial genes is a common trend in most phyla, in particular in Metazoa and Alveolata. In extreme, phylogenetically dispersed cases, often associated with parasitic or anaerobic life styles, mitochondria have been transformed to the so‐called mitosomes or hydrogenosomes devoid of their own genetic material. Ancestrally a single circular deoxyribonucleic acid (DNA) , mitogenomes have evolved to complex, fragmented architectures in particular in Euglenozoa. Key Concepts: Mitochondria have an endosymbiotic origin deriving from a proteobacterial ancestor. Various evolutionary mechanisms operate on mitochondrial genomes. Mitochondrial genomes have developed very diverse properties during eukaryote evolution. Mitogenomic gene content declines in most eukaryotic lineages by horizontal transfer to the nuclear genome. Complex idiosyncratic genome organisations have independently evolved in several eukaryotic phyla.

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The extraordinary rearrangement of mitochondrial genome of the wheat pest, Aptinothrips stylifer and the mitochondrial phylogeny of Thripidae (Thysanoptera)

Li,

Gao,

Wang

et al. 2024

Arch Insect Biochem Physiol

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The mitochondrial gene order in Thysanoptera is notably distinct and highly rearranged, with each species exhibiting its own unique arrangement. To elucidate the relationship between gene rearrangements and phylogeny, the complete mitochondrial genome (mitogenome) of the wheat pest, Aptinothrips stylifer, was sequenced and assembled, spanning a total length of 16,033 bp. Compared with the ancestral arthropod mitogenome, significant rearrangement differences were evident in A. stylifer, whereas the gene order between A. stylifer and Anaphothrips obscurus was similar. Phylogenetic trees were reconstructed based on all 13 protein‐coding gene sequences using Bayesian inference and maximum‐likelihood methods, both yielding similar topological structures. Notably, A. stylifer was robustly clustered with A. obscurus, affirming its classification within Anaphothrips genus group. This exemplifies the potential correlation between gene rearrangements and phylogeny in the Thripidae family. Additionally, the mitogenome of A. stylifer exhibited several atypical features, including: (1) Three putative control regions (CRs) in close proximity, with CR2 and CR3 displaying partial similarity, and CR1 differing in base composition; (2) Two transfer RNAs (tRNAs), trnS1 and trnV, lacking the DHU arm; (3) Two ribosomal RNA (rRNA) genes inverted and positioned distant from each other; (4) Negative AT and GC skew (AT skew = −0.001, GC skew = −0.077); (5) One transposition (nad6), one inverse transposition (trnQ), four inversions (trnF, trnH, trnC, and gene block nad1‐trnL1‐rrnL‐trnV‐rrnS), and four tandem duplication random loss events; and (6) Two protein‐coding genes, nad2 and atp8, terminated with an incomplete stop codon “T”.

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Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome

Cited by 575 publications

References 63 publications

Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences

Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences

Mitochondrial Genome Evolution

The extraordinary rearrangement of mitochondrial genome of the wheat pest, Aptinothrips stylifer and the mitochondrial phylogeny of Thripidae (Thysanoptera)

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