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

Luis Cadahía; Wilhelm Pinsker; Juan José Negro; Mihaela Pavlicev; Vicente Urios; Elisabeth Haring

doi:10.1002/jez.b.21282

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

Journal of Experimental Zoology Part B Molecular and Developmental Evolution ◽

10.1002/jez.b.21282 ◽

2009 ◽

Vol 312B (3) ◽

pp. 171-185 ◽

Cited By ~ 15

Author(s):

Luis Cadahía ◽

Wilhelm Pinsker ◽

Juan José Negro ◽

Mihaela Pavlicev ◽

Vicente Urios ◽

...

Keyword(s):

Repeated Sequence ◽

Mitochondrial Genomes ◽

Control Regions

Download Full-text

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

Animals ◽

10.3390/ani12020148 ◽

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.

Download Full-text

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 ◽

10.7717/peerj.3901 ◽

2017 ◽

Vol 5 ◽

pp. e3901 ◽

Cited By ~ 9

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.

Download Full-text

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

Genetics ◽

10.1093/genetics/150.1.313 ◽

1998 ◽

Vol 150 (1) ◽

pp. 313-329 ◽

Cited By ~ 4

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.

Download Full-text