Complete mitochondrial genome of Otis tarda (Gruiformes: Otididae) and phylogeny of Gruiformes inferred from mitochondrial DNA sequences

2009 ◽  
Vol 37 (7) ◽  
pp. 3057-3066 ◽  
Author(s):  
Rong Yang ◽  
Xiaobing Wu ◽  
Peng Yan ◽  
Xia Su ◽  
Banghe Yang
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Complete Mitochondrial Genome ◽  
Otis Tarda

scholarly journals The mitochondrial genome of the antarctic springtail Folsomotoma octooculata (Hexapoda; Collembola), and an update on the phylogeny of collembolan lineages based on mitogenomic data

Entomologia ◽  
2014 ◽  
Author(s):  
A. Carapelli ◽  
P. Convey ◽  
F. Nardi ◽  
F. Frati
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Gene Order ◽  
Dna Sequences ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Phylogenetic Reconstruction ◽  
Amino Acid Sequences ◽  
Specific Gene ◽  
The Antarctic

This study provides the description of the complete mitochondrial genome of the Antarctic collembola Folsomotoma octooculata. Since mitogenomic data are extensively used for phylogenetic reconstruction, we also provide a phylogenetic reconstruction of the internal relationships of some collembola taxa using the complete mitochondrial DNA data available at present for this group. The complete mitochondrial genome sequence of F. octooculata has been obtained using standard amplification and sequencing methods for long DNA templates. Sequence data are analyzed using bayesian methods based on the analysis of nucleotide and amino acid sequences. The complete set of available mitochondrial DNA sequences for ten species of the group is also analyzed for the presence of lineage-specific gene order of the 37 encoded genes. The results of the phylogenetic analysis are compared with previous morphological and molecular analyses, showing some intriguing outcomes, such as the paraphyly of Entomobryomorpha, the derived position of Podura aquatica within Poduromorpha, and the sister group relationships between the single Symphypleona species available for comparison and the entomobryid Orchesella villosa. The F. octooculata mitochondrial genome generally conforms with those observed in other basal hexapod species and displays the plesiomorphic gene order observed for Pancrustacea. Mitogenomic data are useful to reconstruct a molecular phylogeny of major collembolan taxa. In spite of the limited number of species for which entire mitochondrial genomes are known, the coverage of many of the major lineages allows some preliminary conclusions concerning the relationships among families and suborders.

Sequence amplification and gene rearrangement in parasitic nematode mitochondrial DNA.

Genetics ◽  
1988 ◽  
Vol 120 (3) ◽  
pp. 707-712
Author(s):  
B C Hyman ◽  
J L Beck ◽  
K C Weiss
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Gene Rearrangement ◽  
Tandem Repeats ◽  
Parasitic Nematode ◽  
Mitochondrial Gene ◽  
Sequence Organization ◽  
Large Size ◽  
Mitochondrial Gene Order

Abstract The nematode Romanomermis culicivorax, an obligate mosquito parasite, possesses a 26 kilobase (kb) mitochondrial genome. The unusually large size is due to transcriptionally active DNA sequences present as 3.0 kb direct tandem repeats and as inverted portions of the repeating unit located elsewhere in the mitochondrial DNA (mtDNA). The genome rearrangements involved in establishing this unusual sequence organization may have dramatically altered conventional mitochondrial gene order. Genes for subunits of the cytochrome c oxidase complex (COI and COII) are normally closely linked in animal mtDNAs, but are separated by approximately 8 kb in this mitochondrial genome.

Complete mitochondrial genome of wild aurochs (Bos primigenius) reconstructed from ancient DNA

2013 ◽  
Vol 16 (2) ◽  
pp. 265-273 ◽  
Author(s):  
J. Zeyland ◽  
Ł. Wolko ◽  
J. Bocianowski ◽  
M. Szalata ◽  
R. Słomski ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Ancient Dna ◽  
Dna Sequences ◽  
Demographic History ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Genetic Material ◽  
Gradual Process ◽  
Mtdna Sequence ◽  
History Of

Abstract Extinct aurochs (Bos primigenius), accepted as the ancestor of domestic cattle, was one of the largest wild animals inhabiting Europe, Asia and North Africa. The gradual process of aurochs extinction finished in Poland in 1627, were the last recorded aurochs, a female, died. Some aspects of cattle domestication history and the distribution of aurochs genetic material among modern cattle breeds still remain unclear. Analyses of ancient DNA (aDNA) from bone sample deliver new genetic information about extinct wild aurochs as well as modern cattle phylogeny. DNA was extracted from a fragment of aurochs fossil bone found in the Pisz Forest, Poland. The sample was radiocarbon- dated to about 1500 yBP. The aDNA was used for Whole Genome Amplification in order to form a DNA bank. Auroch mitochondrial DNA sequences were amplified using sets of 41 primers overlapping the whole mtDNA, cloned and sequenced. The sequence of the whole mitochondrial genome was reconstructed and deposed in GenBank [GenBank:JQ437479]. Based on the phylogenetic analyses of the Bovine mitochondrial genomes, a phylogenetic tree was created. As expected, the tree clearly shows that the mtDNA sequence of the analyzed PWA (Polish Wild Aurochs) individual belongs to haplogroup P. In the course of the comparative mtDNA analysis we identified 30 nucleotide marker positions for haplogroup P and nine unique PWA differences compared to the two remaining haplotype P representatives. Our analysis provides the next step to the reconstruction of the demographic history of this extinct but still exciting species.

Mitochondrial genome diversity and cytoplasmic male sterility in higher plants

1988 ◽  
Vol 319 (1193) ◽  
pp. 165-176 ◽  
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Genome Rearrangement ◽  
Recombinant Dna ◽  
Higher Plants ◽  
Current Evidence ◽  
Genome Diversity ◽  
Mitochondrial Translation ◽  
Mitochondrial Genome Diversity

Characteristic differences exist between the mitochondrial genome organization of fertile and cytoplasmic male-sterile (CMS) lines in a range of plant species. Current evidence suggests that these characteristic mitochondrial genotypes arose by aberrant recombination events, generating chimeric mitochondrial DNA sequences which have subsequently become stabilized, possibly by selective amplification. An investigation of the variation in stoichiometry of the four atp A gene types in maize have suggested evolutionary mechanisms for the generation of mitochondrial genome diversity which are based on amplification of pre-existing, rare recombinant DNA molecules. As with a number of other well-documented examples of genome rearrangement, those involving the atp A gene appear to have no obvious phenotypic significance. However, in a number of cases, recombination events have resulted in either modification of existing mitochondrial genes, leading to the synthesis of a modified polypeptide, e.g. the cox I gene in the 9E sorghum cytoplasm, or the generation of novel open reading frames. In the latter case the unique open reading frame found in the mitochondrial DNA of CMS-T maize plants encodes a 13 kDa polypeptide, previously identified as a CMS-T-specific mitochondrial translation product. Current studies are directed towards establishing a causal link between the 13 kDa polypeptide, mitochondrial enzyme complexes, and the CMS phenotype.

A path from mitochondria to the yeast nucleus

1988 ◽  
Vol 319 (1193) ◽  
pp. 127-133 ◽  
Keyword(s):  
Mitochondrial Dna ◽  
Control System ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Nuclear Ribosomal Dna ◽  
Regulatory Function ◽  
Dna Repeat ◽  
Elevated Expression ◽  
Respiratory Deficient

We have identified a path in yeast, from mitochondria to the nucleus, which may have a regulatory function in mitochondrial biogenesis. This path is evident as an elevated expression of a number of nuclear DNA sequences in response to specific defects in the mitochondrial genome, including the absence of mitochondrial DNA in p 0 petites. Among those nuclear sequences preferentially expressed in certain respiratory-deficient cells are stable poly (A) + transcripts derived from the so-called non-transcribed spacer region of the nuclear ribosomal DNA repeat, where they are most abundant in the p 0 petite. Although the function of these unusual RNAs is unclear, the observations may reflect the presence of a mitochondrial homeostatic control system in yeast, which we suggest could function to adjust the mass of mitochondria and mitochondrial DNA in the cell in response to inequities in organelle apportionment during cell budding.

scholarly journals Fin whale (Balaenoptera physalus) mitogenomics: A cautionary tale of defining sub-species from mitochondrial sequence monophyly

2018 ◽  
Author(s):  
Andrea A. Cabrera ◽  
Jeroen P. A. Hoekendijk ◽  
Alex Aguilar ◽  
Susan G. Barco ◽  
Simon Berrow ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genetic Drift ◽  
North Atlantic ◽  
Dna Sequences ◽  
Common Ancestor ◽  
Complete Mitochondrial Genome ◽  
Recent Common Ancestor ◽  
Balaenoptera Physalus ◽  
Fin Whale ◽  
Fin Whales

HighlightsMitochondrial monophyly is commonly employed to define evolutionary significant units.Monophyly may be caused by insufficient sampling or a recent common ancestor.Mitogenomic studies are generally based on few samples and prone to sampling issues.Expanded mitogenome sampling negates previous monophyly in fin whales.AbstractThe advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point is illustrated by a re-analysis of a global mitogenomic assessment of fin whales, Balaenoptera physalus spp., published by Archer et al. (2013) which proposed to further subdivide the Northern Hemisphere fin whale subspecies, B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para-or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to most recent common ancestor and hence the probability that individuals in a sample are monophyletic.

scholarly journals GENEBANK ANALYSIS: SINGLE NUCLEOTIDE POLYMORPHISMS OF ANIMALS MITOCHONDRIAL GENOME UKRAINIAN GRAY AND UKRAINIAN WHITEHEAD CATTLE BREEDS

2017 ◽  
Vol 53 ◽  
pp. 241-248
Author(s):  
Yu. V. Podoba ◽  
V. O. Pinchuk ◽  
V. P. Boroday
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Bos Taurus ◽  
Bos Indicus ◽  
Ex Situ ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
D Loop ◽  
Mtdna Haplogroup

Examination of variation in mitochondrial DNA (mtDNA) control region sequences has been pivotal in the elucidation of bovine phylogeography. Initial studies have demonstrated a deep bifurcation in bovine mtDNA phylogeny, which indicates a predomestic divergence between the two major taxa of cattle, humped zebu (Bos indicus) and humpless taurine (Bos taurus). Subsequent genetic investigations have yielded further inference regarding origins within the B. taurus lineage. B. taurus mtDNA sequences fall into one of five ancestral star-like haplotypic clusters, which are geographically distributed. Just one of these clusters, T3, predominates in Western Europe. Symmetrically, diversity within Africa is composed almost exclusively of members of a separate haplotypic cluster, T1, which is rarely detected elsewhere. The almost mutually exclusive geographic distribution of these two haplotypic clusters allows geographical exceptions to be securely identified as secondary introductions. We investigated a comparative analysis of mitochondrial genome sequences for different breeds of cattle (Bos taurus, Bos indicus) with global genetic bank. Mitochondrial DNA sequences from bovine animals (Bos taurus) breeds Ukrainian Whitehead and Ukrainian Gray freely available on the global genetic bank (http://www.ncbi.nlm.nih.gov/Genebank/). Local alignment of sequences for mitochondrial genome of different cattle breeds was performed using the program MEGA 4.0. For the detection of nucleotide replacements used mitochondrial DNA sequence of Bos taurus Hereford breed (Anderson S. at al., 1982) as a reference (accession number V00645). Here we report the analysis results of testing for 9 genotypes Ukrainian Gray mitochondrial DNA sequences showed that one animal (GQ129208) has haplotype Bos indicus, other belongs to haplogroup T1 with European origin mtDNA. Analysis of single nucleotide replacement in one of the hypervariable regions mtDNA (position number 16019-16339) shows, that among 10 submitted genotypes of Ukrainian Whitehead the 3 of them (FJ014303, FJ014298, FJ014294) relating to T1a mtDNA haplogroup of African origin, which characterized by replacement of T to C at position 16255. Also have been two animals (FJ014301, FJ014295) with single nucleotide replacements with relatives to Bos indicus mtDNA haplogroup. We performed alignment with reference sequences (Bos_taurus_v00654.1) and comparative nucleotide sequences analysis of another hypervariable D-loop (position number 1-240) mtDNA with 5 Ukrainian Whitehead genotypes and 5 Ukrainian Gray genotypes represented in genetics bank. Among the Ukrainian Whitehead genotypes (FJ014298, FJ014297, FJ014296, FJ014295, FJ014294) all were polymorphic that characterizes large differentiation these animals for maternal and describe deep heterogeneous parent population of studied group. We determined one animal with genotype FJ014295 was significantly different by the number of segregation sites. The analyzed sequences (FJ014290, FJ014289, FJ014288, FJ014287, FJ014286) of 5 Ukrainian Gray genotypes showed no polymorphism in hypervariable D-loop (position number 1-240) mtDNA. The mtDNA analysis of different species of animals allowed to distribute their mtDNA belonging to European, African and Asian haplogroups. The technique, which allows to differentiate the animals represented by their belonging to the respective haplogroups. The process that gave rise to different genotypes in one lineage is clearly of fundamental importance in understanding intraspecific mitochondrial polymorphism and evolution in mammals. Сomprehensive study genetic material provide more opportunities to optimize costs in-situ conservation of different cattle breeds, to optimize methods and techniques which used in ex-situ conservation programmes of National gene bank of animal genetic resources.

Mitochondrial Genome of Brugia malayi Microfilariae Isolated From a Clinical Sample

2021 ◽  
Vol 9 ◽  
Author(s):  
Xiong Qing ◽  
Kasem Kulkeaw ◽  
Sirichit Wongkamchai ◽  
Stephen Kwok-Wing Tsui
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Dna Sequences ◽  
Gene Annotation ◽  
Clinical Sample ◽  
Complete Mitochondrial Genome ◽  
Trna Genes ◽  
Human Patient ◽  
Close Relationship ◽  
Mt Genome

Lymphatic filariasis is a neglected parasitic disease that is a leading cause of long-term disability. Information obtained from genome sequencing of filarial worm can help us identify systems in the worm that are likely to be useful for novel drug design. Brugia (B.) malayi is still the only lymphatic-dwelling filarial parasite with a nearly complete, fully annotated, and published genome. However, most previous studies were based on the FR3 strain of B. malayi, which originally was isolated from a human patient, and was adapted to the rodent model, then maintained in laboratories for more than 60 years. It is uncertain whether genetic variation exists, thus, sequencing of clinical isolates of lymphatic dwelling filarial parasites is a high priority. Here, we report for the first time the complete mitochondrial genome of B. malayi microfilariae from clinical isolate. Complete mitochondrial (mt) genome of the microfilariae isolated from a blood sample taken from a Thai subject living in Narathiwat Province, which is an endemic area of brugian filariasis, was assembled with sequencing reads obtained by Illumina sequencing. Gene annotation, phylogenetic analysis and single nucleotide polymorphism (SNP) were deployed. A complete 13,658-bp mt genome of B. malayi microfilaria was obtained, and it shows 68x coverage. Based on gene annotation, the mt genome consists of 12 protein-coding, two rRNA, and 23 tRNA genes. Phylogenetic analysis using all protein sequences of DNA sequences of mt genome or cytochrome c oxidase subunit I (COX1) revealed a close relationship among three lymphatic filariae (i.e., B. timori, zoonotic B. pahangi, and Wuchereria spp.). The SNPs in the COX1 gene can differentiate microfilariae of B. malayi in human from those found in canine. Furthermore, the number, order and transcription, and direction of B. malayi microfilariae mitochondrial genes were the same as those found in the FR3 strain of B. malayi. The comparison on mitochondrial genome of B. malayi could have important implications on the development of a new intervention or vaccine to treat or prevent this disease in endemic areas/regions around the world.

Sign in / Sign up

Export Citation Format

Share Document