Population data for 101 Austrian Caucasian mitochondrial DNA d-loop sequences: Application of mtDNA sequence analysis to a forensic case

1998 ◽  
Vol 111 (3) ◽  
pp. 124-132 ◽  
Author(s):  
W. Parson ◽  
T. J. Parsons ◽  
R. Scheithauer ◽  
M. M. Holland
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Analysis ◽  
Population Data ◽  
Mtdna Sequence ◽  
D Loop ◽  
Forensic Case

scholarly journals Identification of Mitochondrial DNA (NUMTs) in the Nuclear Genome of Daphnia Magna

2020 ◽  
Author(s):  
Krzysztof Kowal ◽  
Angelika Tkaczyk ◽  
Mariusz Pierzchała ◽  
Adam Bownik ◽  
Brygida Ślaska
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Daphnia Magna ◽  
Sequence Homology ◽  
Nuclear Genome ◽  
Complete Information ◽  
Trna Genes ◽  
Entire Genome ◽  
Mtdna Sequence ◽  
D Loop

Abstract Background: This is the first study in which the Daphnia magna (D. magna) nuclear genome deposited in the GenBank data-base was analyzed for pseudogene sequences of mitochondrial origin. The first complete information about the genome of D. magna was published by Lee et al. in 2019. To date, there is no information about pseudogenes localized in the genome of D. magna . The aim of the present study was to identify NUMTs, their length, homology, and location for potential use in evolutionary studies and to check whether their occurrence causes co-amplification during mitochondrial genome analyses.Results: Bioinformatic analysis showed 1909 fragments of the mitochondrial genome of D. magna , of which 1630 fragments were located in ten linkage groups (LG) of the nuclear genome (nDNA). The most frequently occurring fragments of the mtDNA sequence in the nuclear genome included ND2 (115), ND3 (113), and TRNA-CYS (110)). However, the highest number of NUMTs was observed for the D-loop (147). 253 fragments showed 100% homology (from 16 to 46 bp) with mtDNA gene sequences. The sequence homology for TRNA-MET was 100% for all 6 NUMTs (from 16 to 18 bp). The overall length of NUMTs in the nDNA was 44.391 bp (from 16 to 182 bp), which accounted for 0.042% of the entire genome.Conclusions: The best-matched NUMTs covering more than 90% of the mtDNA gene sequence have been identified for the TRNA-ARG (95%), TRNA-GLU (97%), and TRNA-THR (95%) genes, and they may be included in the functional nuclear tRNA genes. Using the product of total DNA isolation in mtDNA studies, coamplification of nDNA fragments is unlikely in the case of amplification of the whole tRNA genes as well as fragments of other genes and the D-loop with a length exceeding 200 bp. It was observed that TRNA-MET fragments had the highest level of sequence homology, which means that they could be evolutionarily the youngest. The lowest degree of homology was found in the pseudogene derived from the mtDNA D-loop sequence. It may probably be the oldest element of mitochondrial DNA incorporated into the nuclear genome; however, further analysis is necessary.

D-Loop sequence analysis of mitochondrial DNA in local goats of Odisha

2015 ◽  
Vol 21 (2) ◽  
pp. 211
Author(s):  
Bhakta Charan Dalai ◽  
Pragati Panda ◽  
P. Dash ◽  
P.K. Rao ◽  
Chinmoy Mishra ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Analysis ◽  
Loop Sequence ◽  
D Loop

Lack of Phylogeographic Structure in Nigerian Village Chickens Revealed by Mitochondrial DNA D-loop Sequence Analysis

2010 ◽  
Vol 9 (5) ◽  
pp. 503-507 ◽  
Author(s):  
A.O. Adebambo ◽  
V.A. Mobegi ◽  
J.M. Mwacharo ◽  
B.M. Oladejo ◽  
R.A. Adewale ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Analysis ◽  
Phylogeographic Structure ◽  
Village Chickens ◽  
Loop Sequence ◽  
D Loop

scholarly journals Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds

2019 ◽  
Vol 44 (4) ◽  
pp. 335
Author(s):  
J. Jakaria ◽  
T. Musyaddad ◽  
S. Rahayu ◽  
M. Muladno ◽  
C. Sumantri
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Distance ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Haplotype Diversity ◽  
Complete Sequence ◽  
Distance Method ◽  
Mtdna Sequence ◽  
D Loop ◽  
Bali Cattle

This study aimed to investigate the diversity of the complete sequence of D-loop mitochondrial DNA (mtDNA) in Bali and Sumba Ongole (SO) cattlebreeds. A total of 24 blood samples were collected from Bali cattle (19 heads) and SO cattle (5 heads), and were extracted and then analyzed to obtain the sequence of D-loop mt DNA.Multiple alignments of the whole sequence of D-loop mtDNA were determined using clustal W. Genetic distance was calculated using a p-distance method, while the genetic tree was constructed using neighbor-joining (NJ) based on MEGA 6. Haplotype number, haplotype diversity (Hd) and nucleotide diversity (Pi) were analyzed using DnaSP version 6. As a result, the sequence of D-loop mtDNA in Bali cattle (921-1119 bp) and SO cattle (913 bp) was reported to have 8 and 4 haplotypes. Hd and Pi of Bali cattle reached 0.625±0.139 and 0.0266±0.0145, respectively, which wwere different from that of SO cattle, namely 0.900±0.1610 and 0.0064±0.0015, respectively. Specifically, we found 22 bp-repetitive nucleotide in Bali cattle, existing 3-9 times with a length of 66-198 bp present in D-loop mtDNA. This unique feature did not exist in SO cattle. Genetic distance and genetic tree determined according to sequence in hypervariability (HV-1) region of D-loop mtDNA (166 bp) resulted in satisfied separation, successfully classifying Bos javanicus, Bos indicus, and Bos taurus cluster.

scholarly journals Mitochondrial DNA D‐loop sequence analysis reveals high variation and multiple maternal origins of indigenous Tanzanian goat populations

2021 ◽  
Author(s):  
Athumani Nguluma ◽  
Martina Kyallo ◽  
Getinet Mekuriaw Tarekegn ◽  
Rose Loina ◽  
Zabron Nziku ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Analysis ◽  
Loop Sequence ◽  
D Loop
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