Mitochondrial genome organization and phylogeny of two vespid wasps

Genome ◽  
2008 ◽  
Vol 51 (10) ◽  
pp. 800-808 ◽  
Author(s):  
Stephen L. Cameron ◽  
Mark Dowton ◽  
Lyda R. Castro ◽  
Kalani Ruberu ◽  
Michael F. Whiting ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genome Organization ◽  
Trna Gene ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Genome Sequences ◽  
Entire Mitochondrial Genome

We sequenced the entire mitochondrial genome of Abispa ephippium (Hymenoptera: Vespoidea: Vespidae: Eumeninae) and most of the mitochondrial genome of Polistes humilis synoecus (Hymenoptera: Vespoidea: Vespidae: Polistinae). The arrangement of genes differed between the two genomes and also differed slightly from that inferred to be ancestral for the Hymenoptera. The genome organization for both vespids is different from that of all other mitochondrial genomes previously reported. A number of tRNA gene rearrangements were identified that represent potential synapomorphies for a subset of the Vespidae. Analysis of all available hymenopteran mitochondrial genome sequences recovered an uncontroversial phylogeny, one consistent with analyses of other types of data.

scholarly journals Frequent tRNA gene translocation towards the boundaries with control regions contributes to the highly dynamic mitochondrial genome organization of the parasitic lice of mammals

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wen-Ge Dong ◽  
Yalun Dong ◽  
Xian-Guo Guo ◽  
Renfu Shao
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Genome Organization ◽  
Trna Gene ◽  
Trna Genes ◽  
Single Chromosome ◽  
Gene Translocation ◽  
Sucking Lice ◽  
Different Types ◽  
Mt Genome

Abstract Background The typical single-chromosome mitochondrial (mt) genome of animals has fragmented into multiple minichromosomes in the lineage Mitodivisia, which contains most of the parasitic lice of eutherian mammals. These parasitic lice differ from each other even among congeneric species in mt karyotype, i.e. the number of minichromosomes, and the gene content and gene order in each minichromosome, which is in stark contrast to the extremely conserved single-chromosome mt genomes across most animal lineages. How fragmented mt genomes evolved is still poorly understood. We use Polyplax sucking lice as a model to investigate how tRNA gene translocation shapes the dynamic mt karyotypes. Results We sequenced the full mt genome of the Asian grey shrew louse, Polyplax reclinata. We then inferred the ancestral mt karyotype for Polyplax lice and compared it with the mt karyotypes of the three Polyplax species sequenced to date. We found that tRNA genes were entirely responsible for mt karyotype variation among these three species of Polyplax lice. Furthermore, tRNA gene translocation observed in Polyplax lice was only between different types of minichromosomes and towards the boundaries with the control region. A similar pattern of tRNA gene translocation can also been seen in other sucking lice with fragmented mt genomes. Conclusions We conclude that inter-minichromosomal tRNA gene translocation orientated towards the boundaries with the control region is a major contributing factor to the highly dynamic mitochondrial genome organization in the parasitic lice of mammals.

The mitochondrial genome organization of a maize fertile cmsT revertant line is generated through recombination between two sets of repeats.

Genetics ◽  
1990 ◽  
Vol 124 (2) ◽  
pp. 423-428 ◽  
Author(s):  
C M Fauron ◽  
M Havlik ◽  
R I Brettell
Keyword(s):  
Mitochondrial Genome ◽  
Genome Organization ◽  
Callus Tissue ◽  
Mitochondrial Genomes ◽  
Normal Type ◽  
Male Sterile ◽  
Sequence Complexity ◽  
Mtdna Organization ◽  
Callus Tissue Culture ◽  
Fertile Revertant

Abstract The mitochondrial genome (mtDNA) organization from a fertile revertant line (V3) derived from the maize cytoplasmic male sterile type T (cmsT) callus tissue culture has been determined. We report that the sequence complexity can be mapped on to a circular "master chromosome" of 705 kb which includes a duplication of 165 kb of DNA when compared to its male sterile progenitor. Associated with this event is also a 0.423-kb deletion, which removed the cmsT-associated urf13 gene. As found for the maize normal type (N) and cmsT mitochondrial genomes, the V3 master chromosome also exists as a multipartite structure generated by recombination through repeated sequences.

Novel tRNA gene rearrangements in the mitochondrial genome of Camarochiloides weiweii (Hemiptera: Pachynomidae)

2020 ◽  
Vol 165 ◽  
pp. 1738-1744 ◽  
Author(s):  
Zhuo Chen ◽  
Yingqi Liu ◽  
Yunfei Wu ◽  
Fan Song ◽  
Wanzhi Cai ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Trna Gene ◽  
Gene Rearrangements

scholarly journals Draft Plastid and Mitochondrial Genome Sequences from Antarctic Alga Prasiola crispa

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Evelise Leis Carvalho ◽  
Gabriel da Luz Wallau ◽  
Darlene Lopes Rangel ◽  
Laís Ceschini Machado ◽  
Alexandre Freitas da Silva ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Oxidative Metabolism ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Total Length ◽  
Organelle Genomes ◽  
Prasiola Crispa ◽  
The Antarctic

The organelle genomes of the Antarctic alga Prasiola crispa (Lightfoot) Kützing have been sequenced. The plastid and mitochondrial genomes have a total length of 196,502 bp and 89,819 bp, respectively. These genomes have 19 putative photosynthesis-related genes and 17 oxidative metabolism-related genes, respectively.

scholarly journals Mitochondrial genome organization and vertebrate phylogenetics

2000 ◽  
Vol 23 (4) ◽  
pp. 745-752 ◽  
Author(s):  
Sérgio Luiz Pereira
Keyword(s):  
Mitochondrial Genome ◽  
Genome Organization ◽  
Tandem Duplication ◽  
Probable Mechanism ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Use Of Data ◽  
New Gene ◽  
Conserved Gene

With the advent of DNA sequencing techniques the organization of the vertebrate mitochondrial genome shows variation between higher taxonomic levels. The most conserved gene order is found in placental mammals, turtles, fishes, some lizards and Xenopus. Birds, other species of lizards, crocodilians, marsupial mammals, snakes, tuatara, lamprey, and some other amphibians and one species of fish have gene orders that are less conserved. The most probable mechanism for new gene rearrangements seems to be tandem duplication and multiple deletion events, always associated with tRNA sequences. Some new rearrangements seem to be typical of monophyletic groups and the use of data from these groups may be useful for answering phylogenetic questions involving vertebrate higher taxonomic levels. Other features such as the secondary structure of tRNA, and the start and stop codons of protein-coding genes may also be useful in comparisons of vertebrate mitochondrial genomes.

scholarly journals Complete mitochondrial genome sequences of the northern spotted owl (Strix occidentalis caurina) and the barred owl (Strix varia; Aves: Strigiformes: Strigidae) confirm the presence of a duplicated control region

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3901 ◽  
Author(s):  
Zachary R. Hanna ◽  
James B. Henderson ◽  
Anna B. Sellas ◽  
Jérôme Fuchs ◽  
Rauri C.K. Bowie ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genes ◽  
Mitochondrial Genomes ◽  
Genome Sequences ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Strix Occidentalis Caurina ◽  
Control Regions

We report here the successful assembly of the complete mitochondrial genomes of the northern spotted owl (Strix occidentalis caurina) and the barred owl (S. varia). We utilized sequence data from two sequencing methodologies, Illumina paired-end sequence data with insert lengths ranging from approximately 250 nucleotides (nt) to 9,600 nt and read lengths from 100–375 nt and Sanger-derived sequences. We employed multiple assemblers and alignment methods to generate the final assemblies. The circular genomes of S. o. caurina and S. varia are comprised of 19,948 nt and 18,975 nt, respectively. Both code for two rRNAs, twenty-two tRNAs, and thirteen polypeptides. They both have duplicated control region sequences with complex repeat structures. We were not able to assemble the control regions solely using Illumina paired-end sequence data. By fully spanning the control regions, Sanger-derived sequences enabled accurate and complete assembly of these mitochondrial genomes. These are the first complete mitochondrial genome sequences of owls (Aves: Strigiformes) possessing duplicated control regions. We searched the nuclear genome of S. o. caurina for copies of mitochondrial genes and found at least nine separate stretches of nuclear copies of gene sequences originating in the mitochondrial genome (Numts). The Numts ranged from 226–19,522 nt in length and included copies of all mitochondrial genes except tRNAPro, ND6, and tRNAGlu. Strix occidentalis caurina and S. varia exhibited an average of 10.74% (8.68% uncorrected p-distance) divergence across the non-tRNA mitochondrial genes.

scholarly journals Vertebrate Mitochondrial Genome Organization: Evidence of Convergent Evolution

2021 ◽  
Author(s):  
Maria Paula Montaña Lozano ◽  
Manuela Alejandra MorenoCarmona ◽  
Jesus Mauricio Ochoa Capera ◽  
Natalia Sofía Medina Camacho ◽  
Jeffrey L. Boore ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genome Organization ◽  
Gene Rearrangement ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Sequencing Technology ◽  
Taxonomic Class ◽  
Evolutionary Studies

Abstract The evolution of the vertebrate mitochondrial genome has been the focus of numerous genetic and evolutionary studies over the last several decades. Initially, sampling was heavily biased toward taxonomic orders of greatest economic or health importance, but recent advances in DNA sequencing technology have facilitated a much broader phylogenetic sampling from which we can clarify general evolutionary trends such as patterns of gene rearrangement. Toward this end, we performed a comparative genomic analysis of the 2,831 vertebrate mitochondrial genomes representing 12 classes that are available in the NCBI database. Using a combination of bioinformatics methods, we determined that there is a great variation in the proportion of rearrangement by gene and by taxonomic class, with higher rates being observed in Reptilia, Amphibia, Petromyzonti, Mammalia, and Actinopteri. Further, within each class, there is large variation in proportion of reorganization among different orders or even taxonomic families. Eleven events of convergence in the genic order among different taxonomic orders were determined, most of them not previously reported.

Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'

2002 ◽  
Vol 16 (3) ◽  
pp. 345 ◽  
Author(s):  
M. Dowton ◽  
L. R. Castro ◽  
A. D. Austin
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Gene Rearrangement ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Genome Organisation ◽  
Rearrangement Mechanism ◽  
Molecular Characters

Mitochondrial gene rearrangements are the latest tool in the arsenal of phylogeneticists for investigating historical relationships. They are complex molecular characters that may provide more reliable evidence of ancestry than comparative molecular data. Here we review the phylogenetic utility of mitochondrial gene rearrangements, and find that despite isolated incidences of convergence, derived gene order appears highly congruent with phylogenies produced from other sources of data. We calculate that the chance of two mitochondrial genomes sharing the same derived genome organisation is only 1/2664, but caution that this ignores the possibility that the (as yet uncharacterised) gene rearrangement mechanism may greatly increase the chance of convergence. Broader taxonomic surveys of mitochondrial genome organisation will lead to a more realistic indication of the historical incidence of convergence in genome organisation.

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