scholarly journals Characterization of the mitochondrial Huso huso genome with new aspects into its organization with presence of tandem repeat in the 12SrRNA and tRNA-Glu

2021 ◽  
Author(s):  
Khadijeh Dadkhah ◽  
Ghodrat Rahimi Mianji ◽  
Ali barzegar ◽  
Ayoub Farhadia
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeat ◽  
Duplication Event ◽  
Regulatory Elements ◽  
Repeat Sequence ◽  
Loop Control ◽  
Coding Regions ◽  
Genes Encoding ◽  
D Loop

Abstract The sturgeon group is an economically important group in the world due to the production of caviar, and they are also a suitable old species for researching on the evolution of the mitochondrial genome. In H.huso sequencing, we identified a distinct genome organization relative to other species that has never been reported before. In this specie, the mitochondrial genome consisted of 13 genes encoding proteins, 22tRNA and 2rRNA, and two non-coding regions that followed other vertebrates. In addition, H.huso had an pseudo tRNA-Glu between ND6 and Cytb and also had a 52-nucleotide tandem repeat with two replications in the 12SrRNA. This duplication event is related to the slipped strand during replication, which can remain in the strand as a result of mispairing during replication. Furthermore, an 82 bp repeat sequence with three replications was observed in the D-loop control region, which is usually visible in different species. Regulatory elements are also visible in the control region of the mitochondrial genome that include termination sequences and conserved regulatory blocks. Genomic compounds showed the highest conservation in terms of rRNA and tRNA, while protein-encoded genes and non-encoded regions had the highest divergence. The mitochondrial genome was phylogenetically assayed using 13 protein-encoding genes.

Study on Tandem Repeat Sequence Variation in Sheep mtDNA D-loop Region

2006 ◽  
Vol 33 (12) ◽  
pp. 1087-1095 ◽  
Author(s):  
LI Xiang-Long ◽  
GONG Yuan-Fang ◽  
LIU Zheng-Zhu ◽  
ZHENG Gui-Ru ◽  
ZHOU Rong-Yan ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Sequence Variation ◽  
Repeat Sequence ◽  
Tandem Repeat Sequence ◽  
Loop Region ◽  
D Loop

scholarly journals Genetic diversity and population structure of the African catfish, Clarias gariepinus (Burchell, 1822) in Kenya: implication for conservation and aquaculture

2017 ◽  
Vol 147 (2) ◽  
Author(s):  
James E. Barasa ◽  
Sinebongo Mdyogolo ◽  
Romulus Abila ◽  
Johannes Paul Grobler ◽  
Robert A. Skilton ◽  
...  
Keyword(s):  
Population Structure ◽  
Control Region ◽  
Clarias Gariepinus ◽  
Natural Populations ◽  
Fish Farm ◽  
African Catfish ◽  
Important Species ◽  
Loop Control ◽  
D Loop ◽  
Hardy Weinberg Equilibrium

African catfish, Clarias gariepinus, is an important species in aquaculture and fisheries in Kenya. Mitochondrial D-loop control region was used to determine genetic variation and population structure in samples of C. gariepinus from 10 sites including five natural populations (Lakes Victoria (LVG), Kanyaboli (LKG), Turkana (LTA), Baringo (LBA) and Jipe (LJP), and five farms (Sangoro Aquaculture Center (SAN), Sagana Aquaculture Centre (SAG), University of Eldoret Fish Farm (UoE), Kibos Fish Farm (KIB), and Wakhungu Fish Farm (WKU)) in Kenya. Similarly, samples from eight localities (four natural populations: LVG/LKG, LTA, LBA, and four farmed: SAN, SAG, KIB, UoE) were genotyped using six microsatellite DNA loci. For the D-loop control region, samples from natural sites exhibited higher numbers of haplotypes and haplotype diversities compared to farmed samples, and 88.2% of haplotypes were private. All except LJP and LTA shared haplotypes, and the highest number of shared haplotypes (8) was detected in KIB. The 68 haplotypes we found in 268 individuals grouped into five phylogenetic clades: LVG/LKG, LTA, LBA, LJP and SAG. Haplotypes of farmed C. gariepinus mostly have haplotypes typical of LVG/LKG, and some shared haplotypes of the LBA population. Microsatellite analysis showed farmed samples have higher numbers of alleles than natural samples, but higher observed and expected heterozygosity levels were found in samples of natural populations. Fifteen pair-wise comparisons had significantly different FST values. All samples were in Hardy-Weinberg equilibrium. Samples from the eight localities grouped into four genetic clusters (LVG/LKG, LTA, LBA and SAG), indicating genetically distinct populations, which should be considered for aquaculture and conservation.

The mitochondrial genome structure of the clouded leopard (Neofelis nebulosa)

Genome ◽  
2007 ◽  
Vol 50 (2) ◽  
pp. 252-257 ◽  
Author(s):  
Xiaobing Wu ◽  
Tao Zheng ◽  
Zhigang Jiang ◽  
Lei Wei
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Repetitive Sequences ◽  
Genome Structure ◽  
Protein Coding ◽  
Acinonyx Jubatus ◽  
Clouded Leopard ◽  
Coding Regions ◽  
Neofelis Nebulosa ◽  
Complete Mitochondrial Genomes

The complete 16 844 bp mitochondrial genome of Neofelis nebulosa has been sequenced and compared with the complete mitochondrial genomes of Felis catus and the Acinonyx jubatus . The base composition of the mitochondrial genome of N. nebulosa is as follows: A, 5343 bp (31.7%); C, 4441 bp (26.4%); G, 2491 bp (14.8%); T, 4569 bp (27.1%). The genome complement and the gene order of this mitochondrial genome was found to be typical of those reported for other mammals. Several unusual features of this genome, however, were found. First, in protein-coding regions, AT bias in the genome was not prevalent in the third position of codons, as it is in most other mammals, but was found in the second position of codons. Second, in tRNA regions, tRNASer (AGY), which lacked the “DHU” arm, could not be folded into the typical cloverleaf-shaped structure. Third, in the control region, no repetitive sequences (RS)-2 were found. However, RS-2 repetitive motifs usually occurr in the control regions of most great cats. In addition, 4 variable sites were found in CSB-3 of the control region. Fourth, AT content in the control region of the mtDNA from the clouded leopard was lower than it is in other regions.

A very compact mt-DNA control region in the widely distributed goby Pomatoschistus minutus (Teleostei: Gobiidae)

2002 ◽  
Vol 82 (6) ◽  
pp. 1001-1003 ◽  
Author(s):  
S. STEFANNI ◽  
I.-S. CHEN ◽  
P.J. MILLER
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Divergence ◽  
Mt Dna ◽  
Conserved Sequence ◽  
Sequence Block ◽  
Pomatoschistus Minutus ◽  
Region Length ◽  
D Loop

The control region of the mitochondrial genome was amplified and sequenced for six individuals of the gobioid fish Pomatoschistus minutus, from several European localities, and one specimen of the related Deltentosteus quadrimaculatus. The length of this region for the former species was found to be 773 bp, 7·1% shorter than that previously described as the most compact D-loop known among teleosts. Sequences from other fish have been compared and the largest gap falls in the section between the conserved sequence block and the pyrimidine tract. Alignment of P. minutus sequences was done with D. quadrimaculatus, whose control region length was 853 bp, and this gap was found to be of 61 bp. For the P. minutus sample, the intraspecific sequence divergence is 0·07%.

scholarly journals Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9569
Author(s):  
Osman İbiş
Keyword(s):  
Mitochondrial Genome ◽  
Intergenic Spacer ◽  
Species Level ◽  
Mitochondrial Genomes ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Coding Regions ◽  
Protein Coding Genes ◽  
D Loop ◽  
High Genetic Distance

Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia.

scholarly journals The very low genetic variability on Aceh Tamiang’s (Indonesia) population of Painted Terrapin (Batagur borneoensis) inferred by cytochrome oxidase I (CO I) and D-loop (control region)

2020 ◽  
Vol 21 (6) ◽  
Author(s):  
JOKO GUNTORO ◽  
WIRDATETI ◽  
AWAL RIYANTO
Keyword(s):  
Genetic Variability ◽  
Cytochrome Oxidase ◽  
Control Region ◽  
Haplotype Diversity ◽  
Cytochrome Oxidase I ◽  
Conservation Strategy ◽  
Wild Populations ◽  
Loop Control ◽  
Loop Region ◽  
D Loop

Abstract. Guntoro J, Wirdateti, Riyanto A. 2020. The very low genetic variability on Aceh Tamiang’s (Indonesia) population of Painted Terrapin (Batagur borneoensis) inferred by cytochrome oxidase I (CO I) and D-loop (control region). Biodiversitas 21: 2514-2520. Populations of Batagur borneoensis have been rapidly decreasing due to the harvesting of adults and eggs for food and the construction of beachfront property causing the loss of nesting areas. By the new Indonesian regulation, since 2018 this turtle listed in the protected animal. Meanwhile, IUCN placed as critically endangered which indicating a high risk of extinction in the wild in the near future (www.iucnredlist.org). We used cytochrome oxidase I (COI) and control region D-loop region to investigate intraspecific variations on Aceh Tamiang’s population of painted terrapin, Batagur borneoensis. DNA material was gathered from saliva collected from 90 juveniles in the reaching facility of Sukacita Lestari Indonesia Foundation which hatched from eggs collected from December 2015 to April 2016 from 30 nests on beach area at Aceh Tamiang. The population showed very low genetic variability (haplotype diversity, Hd = 0.457 based on COI and 0.405 based on D-loop; nucleotide diversity, π = 0.00089 based on COI and 0.00076 based on D-loop). So, we suggested that further study such as more exploration to find new wild populations and genetic study across wild populations should be done to reveal genetic variability and genetic structure which important to decide the conservation strategy. At the time for Aceh Tamiang's population, the ranching conservation program should be maintained at least to keep the successful hatchling from hunters and natural predators both during eggs laying and hatching.

Tandem repeat sequence segments in control region of bronze featherback Notopterus notopterus mitochondrial DNA

2006 ◽  
Vol 72 (6) ◽  
pp. 1319-1321 ◽  
Author(s):  
Akira P TAKAGI ◽  
Satoshi ISHIKAWA ◽  
Thuok NAO ◽  
Sitha HORT ◽  
Masanori NAKATANI ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Control Region ◽  
Tandem Repeat ◽  
Repeat Sequence ◽  
Tandem Repeat Sequence ◽  
Notopterus Notopterus
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