scholarly journals Some maternal lineages of domestic horses may have origins in East Asia revealed with further evidence of mitochondrial genomes and HVR-1 sequences

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4896 ◽  
Author(s):  
Hongying Ma ◽  
Yajiang Wu ◽  
Hai Xiang ◽  
Yunzhou Yang ◽  
Min Wang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
East Asia ◽  
Dna Sequences ◽  
De Novo ◽  
Divergence Time ◽  
Upper Paleolithic ◽  
Phylogenetic Study ◽  
Mitochondrial Genomes ◽  
Domestic Horses ◽  
Matrilineal Inheritance

Objectives There are large populations of indigenous horse (Equus caballus) in China and some other parts of East Asia. However, their matrilineal genetic diversity and origin remained poorly understood. Using a combination of mitochondrial DNA (mtDNA) and hypervariable region (HVR-1) sequences, we aim to investigate the origin of matrilineal inheritance in these domestic horses. Methods To investigate patterns of matrilineal inheritance in domestic horses, we conducted a phylogenetic study using 31 de novo mtDNA genomes together with 317 others from the GenBank. In terms of the updated phylogeny, a total of 5,180 horse mitochondrial HVR-1 sequences were analyzed. Results Eightteen haplogroups (Aw-Rw) were uncovered from the analysis of the whole mitochondrial genomes. Most of which have a divergence time before the earliest domestication of wild horses (about 5,800 years ago) and during the Upper Paleolithic (35–10 KYA). The distribution of some haplogroups shows geographic patterns. The Lw haplogroup contained a significantly higher proportion of European horses than the horses from other regions, while haplogroups Jw, Rw, and some maternal lineages of Cw, have a higher frequency in the horses from East Asia. The 5,180 sequences of horse mitochondrial HVR-1 form nine major haplogroups (A-I). We revealed a corresponding relationship between the haplotypes of HVR-1 and those of whole mitochondrial DNA sequences. The data of the HVR-1 sequences also suggests that Jw, Rw, and some haplotypes of Cw may have originated in East Asia while Lw probably formed in Europe. Conclusions Our study supports the hypothesis of the multiple origins of the maternal lineage of domestic horses and some maternal lineages of domestic horses may have originated from East Asia.

The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

2020 ◽  
Author(s):  
Liyan Qu ◽  
Heng Zhang ◽  
Fengying Zhang ◽  
Wei Wang ◽  
Fenghua Tang ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Flying Fishes ◽  
Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

scholarly journals Population genetic structure of the kuruma prawn (Penaeus japonicus) in East Asia inferred from mitochondrial DNA sequences

2004 ◽  
Vol 61 (6) ◽  
pp. 913-920 ◽  
Author(s):  
Tzong-Der Tzeng ◽  
Shean-Yeh Yeh ◽  
Cho-Fat Hui
Keyword(s):  
Mitochondrial Dna ◽  
East Asia ◽  
Dna Sequences ◽  
Genetic Difference ◽  
Japan Sea ◽  
China Sea ◽  
The Third ◽  
The North ◽  
Penaeus Japonicus ◽  
The Taiwan Strait

Abstract Sequence analyses on the complete mitochondrial DNA (mtDNA) control region (992 bp) were conducted to elucidate the population structure of kuruma prawns (Penaeus japonicus) in East Asia. Five populations including 95 individuals were collected. They are separated into the Japan Sea (JS), the north and south of the East China Sea (NECS and SECS), the Taiwan Strait (TS), and the north of the South China Sea (NSCS) populations. There are 292 variable sites without any insertions and deletions. Nucleotide diversity in the total populations is 2.51 ± 0.07%, and the variations within populations ranged from 2.61 ± 0.93% (SECS) to 2.29 ± 0.16% (JS). FST values between the JS and the rest of the populations, between the NECS and NSCS populations, and between the SECS and NSCS populations show significant differences. The UPGMA tree of these five populations shows three distinct clusters; one includes the JS population; another includes the NECS population; the third includes populations from the rest of the areas. The analysis of molecular variance (AMOVA) shows clear genetic difference between the JS and the rest of the populations. Additional AMOVA analysis excluding the JS population indicates significant variation between the NECS population and the other three populations. We, therefore, conclude that three distinct populations exist in East Asia; one is in the JS; another is in the NECS; and the third is distributed in SECS, TS and NSCS.

Cytochrome b gene based phylogeny and genetic divergence of Tetraophasis of China

2010 ◽  
Vol 60 (2) ◽  
pp. 133-144 ◽  
Author(s):  
Longying Wen ◽  
Naifa Liu
Keyword(s):  
Cytochrome B ◽  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Divergence Time ◽  
Tibet Plateau ◽  
Phylogenetic Study ◽  
Sequence Difference ◽  
Molecular Clock Estimate ◽  
Mitochondrial Cytochrome B

AbstractTetraophasis (Galliformes; Phasianidae) includes T. obscurus and T. szechenyii, which are endemic and distributed in the west and central parts of China. The phylogenetic status of Tetraophasis in the Phasianidae and the divergence of the two species are still controversial. We performed a phylogenetic study using DNA sequences of 828bp of the mitochondrial cytochrome b (Cytb) genes of Tetraophasis and of selected species of several other genera of Phasianidae. The phylogenetic trees suggest that Tetraophasis species belong to Phasianinae, which is inconsistent with the traditional taxonomic view that these species belong to Perdicinae. Sequence difference between T. obscurus and T. szechenyii was 3.0-3.1% and the divergence time was 1.88-1.94 Myr based on molecular clock estimate. Compared with other genera, T. obscurus and T. szechenyii should be classified as two distinct species. Our data suggest that the divergence of Tetraophasis may have been induced by the uplift of the Qinghai-Tibet Plateau and by environmental changes.

scholarly journals A method for calibrating molecular clocks and its application to animal mitochondrial DNA.

Genetics ◽  
1993 ◽  
Vol 135 (4) ◽  
pp. 1197-1208 ◽  
Author(s):  
M Lynch ◽  
P E Jarrell
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
Substitution Rate ◽  
Nuclear Dna ◽  
Average Rate ◽  
Divergence Time ◽  
Poisson Model ◽  
Generalized Least Squares ◽  
Molecular Clocks ◽  
Empirical Estimates

Abstract A generalized least-squares procedure is introduced for the calibration of molecular clocks and applied to the complete mitochondrial DNA sequences of 13 animal species. The proposed technique accounts for both nonindependence and heteroscedasticity of molecular-distance data, problems that have not been taken into to account in such analyses in the past. When sequence-identity data are transformed to account for multiple substitutions/site, the molecular divergence scales linearly with time, but with substantially more variation in the substitution rate than expected under a Poisson model. Significant levels of divergence are predicted at zero divergence time for most loci, suggesting high levels of site-specific heterozygosity among mtDNA molecules establishing in sister taxa. For nearly all loci, the baseline heterozygosity is lower and the substitution rate is higher in mammals relative to other animals. There is considerable variation in the evolutionary rate among loci but no compelling evidence that the average rate of mtDNA evolution is elevated with respect to that of nuclear DNA. Using the observed patterns of interspecific divergence, empirical estimates are derived for the mean coalescence times of organelles colonizing sister taxa.

Divergence time estimates of East Asian and European pigs based on multiple near complete mitochondrial DNA sequences

2011 ◽  
Vol 42 (1) ◽  
pp. 86-88 ◽  
Author(s):  
A. I. Fernández ◽  
E. Alves ◽  
C. Óvilo ◽  
M. C. Rodríguez ◽  
L. Silió
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequences ◽  
East Asian ◽  
Divergence Time ◽  
Divergence Time Estimates ◽  
Time Estimates

scholarly journals Mitochondrial DNA duplication, recombination, and introgression during interspecific hybridization

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Silvia Bágeľová Poláková ◽  
Žaneta Lichtner ◽  
Tomáš Szemes ◽  
Martina Smolejová ◽  
Pavol Sulo
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mitochondrial Dna ◽  
Interspecific Hybridization ◽  
Mobile Elements ◽  
Variable Length ◽  
Mitochondrial Genomes ◽  
Free Standing ◽  
Saccharomyces Paradoxus ◽  
Mtdna Recombination

AbstractmtDNA recombination events in yeasts are known, but altered mitochondrial genomes were not completed. Therefore, we analyzed recombined mtDNAs in six Saccharomyces cerevisiae × Saccharomyces paradoxus hybrids in detail. Assembled molecules contain mostly segments with variable length introgressed to other mtDNA. All recombination sites are in the vicinity of the mobile elements, introns in cox1, cob genes and free standing ORF1, ORF4. The transplaced regions involve co-converted proximal exon regions. Thus, these selfish elements are beneficial to the host if the mother molecule is challenged with another molecule for transmission to the progeny. They trigger mtDNA recombination ensuring the transfer of adjacent regions, into the progeny of recombinant molecules. The recombination of the large segments may result in mitotically stable duplication of several genes.

scholarly journals Cellular pyrimidine imbalance triggers mitochondrial DNA–dependent innate immunity

2021 ◽  
Author(s):  
Hans-Georg Sprenger ◽  
Thomas MacVicar ◽  
Amir Bahat ◽  
Kai Uwe Fiedler ◽  
Steffen Hermans ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Cultured Cells ◽  
De Novo ◽  
Metabolic Response ◽  
Interferon Response ◽  
Type I ◽  
Nucleotide Synthesis ◽  
Pyrimidine Synthesis ◽  
Pyrimidine Nucleotide ◽  
De Novo Pyrimidine Synthesis

AbstractCytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. Here, we show that mtDNA-dependent immune signalling via the cyclic GMP–AMP synthase‒stimulator of interferon genes‒TANK-binding kinase 1 (cGAS–STING–TBK1) pathway is under metabolic control and is induced by cellular pyrimidine deficiency. The mitochondrial protease YME1L preserves pyrimidine pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC25A33. Deficiency of YME1L causes inflammation in mouse retinas and in cultured cells. It drives the release of mtDNA and a cGAS–STING–TBK1-dependent inflammatory response, which requires SLC25A33 and is suppressed upon replenishment of cellular pyrimidine pools. Overexpression of SLC25A33 is sufficient to induce immune signalling by mtDNA. Similarly, depletion of cytosolic nucleotides upon inhibition of de novo pyrimidine synthesis triggers mtDNA-dependent immune responses in wild-type cells. Our results thus identify mtDNA release and innate immune signalling as a metabolic response to cellular pyrimidine deficiencies.

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