Structure and evolution of the mitochondrial control region of the pollen beetle Meligethes thalassophilus (Coleoptera: Nitidulidae)

Genome ◽  
2008 ◽  
Vol 51 (3) ◽  
pp. 196-207 ◽  
Author(s):  
Emiliano Mancini ◽  
Alessio De Biase ◽  
Paolo Mariottini ◽  
Alessandro Bellini ◽  
Paolo Audisio
Keyword(s):  
Control Region ◽  
Tandem Repeats ◽  
Population Level ◽  
Mitochondrial Control Region ◽  
Variable Number ◽  
12S Rrna ◽  
Rrna Gene ◽  
Length Variation ◽  
Pollen Beetle ◽  
Repeat Elements

The organization of the mitochondrial DNA (mtDNA) control region (CR) of the pollen beetle Meligethes thalassophilus is described. This mtDNA CR represents the longest sequenced for beetles so far, since the entire nucleotide sequence ranges from ~5000 to ~5500 bp. The CR of M. thalassophilus is organized in three distinct domains: a conserved domain near the tRNAIle gene, a variable domain flanking the 12S rRNA gene, and a relatively large central tandem array made up of a variable number of ~170 bp repeats that is responsible for the intraspecific length variation observed. Like other CRs found in insects, the M. thalassophilus CR contains two long homopolymeric runs that may be involved in mtDNA replication. Furthermore, conserved stem-and-loop structures in the repetitive domain were identified and their possible role in generating length variation is examined. Intraspecific comparison of the tandem repeat elements of M. thalassophilus suggests mechanisms of concerted evolution leading to homogenization of the repetitive region. The utility of such an array of tandem repeats as a genetic marker for assessing population-level variability and evolutionary relationships among populations is discussed. Finally, the technical difficulties found in isolating the mtDNA CR in beetles are remarked upon.

Tandem repeats and length variation in the mitochondrial DNA control region of Epirrita autumnata (Lepidoptera: Geometridae)

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 855-861 ◽  
Author(s):  
N Snäll ◽  
K Huoponen ◽  
M -L Savontaus ◽  
K Ruohomäki
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Tandem Repeats ◽  
Repetitive Sequences ◽  
Distinct Type ◽  
Variable Number ◽  
Tandem Array ◽  
Epirrita Autumnata ◽  
Length Variation ◽  
Mitochondrial Dna Control Region

The organization of the mitochondrial DNA (mtDNA) control region (CR) of the autumnal moth, Epirrita autumnata, is described. The E. autumnata CR presents a distinct type of lepidopteran CR with domains of non-repetitive and repetitive sequences. The CRs show considerable length variation owing to a variable number of short ~29-bp sequence blocks that are repeated between 6 and 14 times in tandem. The organization of such a tandem array is unique among the insect CRs examined so far. Furthermore, the E. autumnata CR, which may reach 1075 bp in length, is considerably longer than previously reported lepidopteran CRs, which reach 311–499 bp in length. Like other lepidopteran CRs, the E. autumnata CR contains two long homopolymer runs that may be involved in mtDNA replication and (or) transcription.Key words: Lepidoptera, Epirrita autumnata, mitochondrial DNA, control region, tandem array.

scholarly journals Unusual mtDNA Control Region Length Heteroplasmy in the COS-7 Cell Line

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 607
Author(s):  
Nataliya Kozhukhar ◽  
Sunil Mitta ◽  
Mikhail F. Alexeyev
Keyword(s):  
Mitochondrial Genome ◽  
Cell Line ◽  
Control Region ◽  
Tandem Repeats ◽  
Variable Number ◽  
Length Heteroplasmy ◽  
Repeat Units ◽  
Chlorocebus Aethiops ◽  
Region Length ◽  
Transcription And Replication

The COS-7 cell line is a workhorse of virology research. To expand this cell line’s utility and to enable studies on mitochondrial DNA (mtDNA) transcription and replication, we determined the complete nucleotide sequence of its mitochondrial genome by Sanger sequencing. In contrast to other available mtDNA sequences from Chlorocebus aethiops, the mtDNA of the COS-7 cell line was found to contain a variable number of perfect copies of a 108 bp unit tandemly repeated in the control region. We established that COS-7 cells are heteroplasmic with at least two variants being present: with four and five repeat units. The analysis of the mitochondrial genome sequences from other primates revealed that tandem repeats are absent from examined mtDNA control regions of humans and great apes, but appear in lower primates, where they are present in a homoplasmic state. To our knowledge, this is the first report of mtDNA length heteroplasmy in primates.

scholarly journals B Chromosomes of the Asian Seabass (Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 464 ◽  
Author(s):  
Aleksey Komissarov ◽  
Shubha Vij ◽  
Andrey Yurchenko ◽  
Vladimir Trifonov ◽  
Natascha Thevasagayam ◽  
...  
Keyword(s):  
Dna Content ◽  
Copy Number ◽  
Population Level ◽  
18S Rrna Gene ◽  
Variable Number ◽  
B Chromosomes ◽  
Female Gonad ◽  
Rrna Gene ◽  
Lates Calcarifer ◽  
Asian Seabass

The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing.

scholarly journals High Sequence Variations in Mitochondrial DNA Control Region among Worldwide Populations of Flathead MulletMugil cephalus

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Brian Wade Jamandre ◽  
Jean-Dominique Durand ◽  
Wann-Nian Tzeng
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Tandem Repeats ◽  
Evolutionary Rate ◽  
Variable Number ◽  
Rapid Radiation ◽  
Mitochondrial Dna Control Region ◽  
Good Marker ◽  
Sequence Variations ◽  
Complete Mtdna

The sequence and structure of the complete mtDNA control region (CR) ofM. cephalusfrom African, Pacific, and Atlantic populations are presented in this study to assess its usefulness in phylogeographic studies of this species. The mtDNA CR sequence variations amongM. cephaluspopulations largely exceeded intraspecific polymorphisms that are generally observed in other vertebrates. The length of CR sequence varied amongM. cephaluspopulations due to the presence of indels and variable number of tandem repeats at the3′hypervariable domain. The high evolutionary rate of the CR in this species probably originated from these mutations. However, no excessive homoplasic mutations were noticed. Finally, the star shaped tree inferred from the CR polymorphism stresses a rapid radiation worldwide, in this species. The CR still appears as a good marker for phylogeographic investigations and additional worldwide samples are warranted to further investigate the genetic structure and evolution inM. cephalus.

Assessing the phylogenetic signal of the nuclear β-Fibrinogen intron 7 in salamandrids (Amphibia: Salamandridae)

2006 ◽  
Vol 27 (3) ◽  
pp. 409-418 ◽  
Author(s):  
Fernando Sequeira ◽  
Nuno Ferrand ◽  
D. James Harris
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
12S Rrna ◽  
Rrna Gene ◽  
Length Variation ◽  
Β Subunit ◽  
Phylogenetic Studies ◽  
12S Rrna Gene ◽  
Considerable Length ◽  
Mitochondrial 12S Rrna

AbstractThe potential of the seventh intron of the β-subunit of the fibrinogen gene (β-fibint 7) for phylogenetic analysis within the Salamandridae family was explored, comparing the topologies of trees based on this marker to those based on mitochondrial 12S rRNA gene previously published. Using primers designed specifically for amphibians, we amplified 25 sequences of β-fibint 7 corresponding to 15 species of salamandrids and one plethodontid species. There was considerable length variation among the β-fibint 7 sequences examined, ranging from 1123 bp in S. atra to 400 bp in P. waltl. Many aspects of the phylogenetic relationships estimated by the two independent loci were congruent and corroborate current taxonomic hypothesis. Although the number of taxa analysed is small, the data obtained in this work suggested that β-fibint 7 is a useful marker for assessing phylogenetic relationships within the Salamandridae family, and is probably appropriate for phylogenetic studies among closely related salamanders that have diverged over the last 20 Myr.

Structural organization of the mitochondrial DNA control region in Aedes aegypti

Genome ◽  
2006 ◽  
Vol 49 (8) ◽  
pp. 931-937 ◽  
Author(s):  
Juan C. Rondan Dueñas ◽  
Cristina N Gardenal ◽  
Guillermo Albrieu Llinás ◽  
Graciela M Panzetta-Dutari
Keyword(s):  
Mitochondrial Dna ◽  
Aedes Aegypti ◽  
Control Region ◽  
Sequence Similarity ◽  
Mosquito Species ◽  
Repeat Unit ◽  
12S Rrna ◽  
Rrna Gene ◽  
Rich Region ◽  
Stem Loop

The complete A+T - rich region of Aedes aegypti mitochondrial DNA has been cloned and sequenced. In Argentinean populations of the species, a polymorphism in the length of the amplified fragment was observed. Nucleotide sequence comparison of the shortest and longest A+T - rich amplified fragments detected revealed the presence of 2 types of tandemly repeated blocks. The size variation observed in natural populations is mainly due to the presence of a variable number of a 181 bp tandem repeat unit, located toward the 12S rRNA gene end. The size of the longest A+T - rich region was of 2070 bp, representing the largest control sequence reported for any mosquito species. Few relevant short blocks of primary-sequence similarity conserved in the control region of mosquitoes and other insects were detected scattered throughout the whole region. Five putative stem-loop secondary structures were found, one of them flanked by conserved sequences described in other insects. Our results suggest that there are no universal models of structure–function relations in the control region of insect mtDNA. In addition, we identified a short A+T - rich variable segment in the Ae. aegyti control region that would be suitable for population genetic studies.Key words: mitochondrial DNA, A+T - rich region, repeated elements, conserved blocks, Aedes aegypti.

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