scholarly journals Evolution of Duplicate Control Regions in the Mitochondrial Genomes of Metazoa: A Case Study with Australasian Ixodes Ticks

2004 ◽  
Vol 22 (3) ◽  
pp. 620-629 ◽  
Author(s):  
Renfu Shao ◽  
Stephen C. Barker ◽  
Harumi Mitani ◽  
Yayoi Aoki ◽  
Masahito Fukunaga
Keyword(s):  
Mitochondrial Genomes ◽  
Ixodes Ticks ◽  
Control Regions

A protocol for isolating insect mitochondrial genomes: a case study of NUMT in Melipona flavolineata (Hymenoptera: Apidae)

2015 ◽  
Vol 27 (4) ◽  
pp. 2401-2404 ◽  
Author(s):  
Elaine Françoso ◽  
Fernando Gomes ◽  
Maria Cristina Arias
Keyword(s):  
Mitochondrial Genomes

scholarly journals Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 148
Author(s):  
Watcharaporn Thapana ◽  
Nattakan Ariyaraphong ◽  
Parinya Wongtienchai ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Analyses ◽  
Evolutionary Patterns ◽  
Evolutionary Pattern ◽  
Independent Evolution ◽  
Substitution Saturation ◽  
Varanus Salvator ◽  
Monitor Lizards ◽  
Control Regions

Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

scholarly journals Mitochondrial Ecophysiology: Assessing the Evolutionary Forces That Shape Mitochondrial Variation

2019 ◽  
Vol 59 (4) ◽  
pp. 925-937 ◽  
Author(s):  
Jessica L McKenzie ◽  
Dillon J Chung ◽  
Timothy M Healy ◽  
Reid S Brennan ◽  
Heather J Bryant ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Mitochondrial Function ◽  
Fundulus Heteroclitus ◽  
Secondary Contact ◽  
Mitochondrial Genomes ◽  
Evolutionary Forces ◽  
Population Genomic ◽  
Genomic Studies

Abstract The mitonuclear species concept hypothesizes that incompatibilities between interacting gene products of the nuclear and mitochondrial genomes are a major factor establishing and maintaining species boundaries. However, most of the data available to test this concept come from studies of genetic variation in mitochondrial DNA, and clines in the mitochondrial genome across contact zones can be produced by a variety of forces. Here, we show that using a combination of population genomic analyses of the nuclear and mitochondrial genomes and studies of mitochondrial function can provide insight into the relative roles of neutral processes, adaptive evolution, and mitonuclear incompatibility in establishing and maintaining mitochondrial clines, using Atlantic killifish (Fundulus heteroclitus) as a case study. There is strong evidence for a role of secondary contact following the last glaciation in shaping a steep mitochondrial cline across a contact zone between northern and southern subspecies of killifish, but there is also evidence for a role of adaptive evolution in driving differentiation between the subspecies in a variety of traits from the level of the whole organism to the level of mitochondrial function. In addition, studies are beginning to address the potential for mitonuclear incompatibilities in admixed populations. However, population genomic studies have failed to detect evidence for a strong and pervasive influence of mitonuclear incompatibilities, and we suggest that polygenic selection may be responsible for the complex patterns observed. This case study demonstrates that multiple forces can act together in shaping mitochondrial clines, and illustrates the challenge of disentangling their relative roles.

scholarly journals Repeated sequence homogenization between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae

2009 ◽  
Vol 312B (3) ◽  
pp. 171-185 ◽  
Author(s):  
Luis Cadahía ◽  
Wilhelm Pinsker ◽  
Juan José Negro ◽  
Mihaela Pavlicev ◽  
Vicente Urios ◽  
...  
Keyword(s):  
Repeated Sequence ◽  
Mitochondrial Genomes ◽  
Control Regions

From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity

2016 ◽  
Vol 61 ◽  
pp. 258-269 ◽  
Author(s):  
Elizabeth Misas ◽  
José Fernando Muñoz ◽  
Juan Esteban Gallo ◽  
Juan Guillermo McEwen ◽  
Oliver Keatinge Clay
Keyword(s):  
Mitochondrial Genomes ◽  
Genome Complexity

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 The Complete Nucleotide Sequence of a Snake (Dinodon semicarinatus) Mitochondrial Genome With Two Identical Control Regions

Genetics ◽  
1998 ◽  
Vol 150 (1) ◽  
pp. 313-329 ◽  
Author(s):  
Yoshinori Kumazawa ◽  
Hidetoshi Ota ◽  
Mutsumi Nishida ◽  
Tomowo Ozawa
Keyword(s):  
Southern Hybridization ◽  
Gene Organization ◽  
Amino Acid Sequences ◽  
High Rate ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Chain Reaction ◽  
Rate Of Molecular Evolution ◽  
Polymerase Chain ◽  
Control Regions

Abstract The 17,191-bp mitochondrial DNA (mtDNA) of a Japanese colubrid snake, akamata (Dinodon semicarinatus), was cloned and sequenced. The snake mtDNA has some peculiar features that were found in our previous study using polymerase chain reaction: duplicate control regions that have completely identical sequences over 1 kbp, translocation of tRNALeu(UUR) gene, shortened TψC arm for most tRNA genes, and a pseudogene for tRNAPro. Phylogenetic analysis of amino acid sequences of protein genes suggested an unusually high rate of molecular evolution in the snake compared to other vertebrates. Southern hybridization experiments using mtDNAs purified from multiple akamata individuals showed that the duplicate state of the control region is not a transient or unstable feature found in a particular individual, but that it stably occurs in mitochondrial genomes of the species. This may, therefore, be regarded as an unprecedented example of stable functional redundancy in animal mtDNA. However, some of the examined individuals contain a rather scanty proportion of heteroplasmic mtDNAs with an organization of genes distinct from that of the major mtDNA. The gene organization of the minor mtDNA is in agreement with one of models that we present to account for the concerted evolution of duplicate control regions.

scholarly journals Linear Mitochondrial genome in Anthozoa (Cnidaria): A case study in Ceriantharia

2018 ◽  
Author(s):  
Sergio N Stampar ◽  
Michael B Broe ◽  
Jason Macrander ◽  
Adam M Reitzel ◽  
Marymegan Daly
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Mitochondrial Gene ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Gene Sequences ◽  
Phylogenetic Placement ◽  
Organellar Genome ◽  
Linear Mitochondrial Genome

Sequences and structural attributes of mitochondrial genomes have played a key role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic groups in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both ceriantharian species studied, the mitochondrial gene sequences could not be assembled into a circular genome. Instead, our analyses suggest both species have fragmented mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The number of fragments and the variation in gene order between species is much greater in Ceriantharia than among Medusozoa. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other anthozoan groups.

Reconstruction of mitochondrial genomes from raw sequencing data provides insights on the phylogeny of Ixodes ticks and cautions for species misidentification

2022 ◽  
Vol 13 (1) ◽  
pp. 101832
Author(s):  
Wessam Mohamed Ahmed Mohamed ◽  
Mohamed Abdallah Mohamed Moustafa ◽  
Samuel Kelava ◽  
Dayana Barker ◽  
Keita Matsuno ◽  
...  
Keyword(s):  
Mitochondrial Genomes ◽  
Sequencing Data ◽  
Ixodes Ticks
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