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.

scholarly journals Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kun Zhang ◽  
Kehua Zhu ◽  
Yifan Liu ◽  
Hua Zhang ◽  
Li Gong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Tandem Duplication ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Protein Coding ◽  
Muraenesox Cinereus ◽  
Complete Mitogenome ◽  
Relationship Of ◽  
Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

scholarly journals Reduced Variation in Drosophila simulans Mitochondrial DNA

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1519-1528
Author(s):  
J William O Ballad ◽  
Joy Hatzidakis ◽  
Timothy L Karr ◽  
Martin Kreitman
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Evolutionary Dynamics ◽  
Selective Sweep ◽  
Mitochondrial Gene ◽  
Drosophila Simulans ◽  
Dramatic Reduction ◽  
Nucleotide Variability ◽  
Pooled Samples ◽  
Mitochondrial Gene Mutation

We investigated the evolutionary dynamics of infection of a Drosophila simulans population by a maternally inherited insect bacterial parasite, Wolbachia, by analyzing nucleotide variability in three regions of the mitochondrial genome in four infected and 35 uninfected lines. Mitochondrial variability is significantly reduced compared to a noncoding region of a nuclear-encoded gene in both uninfected and pooled samples of flies, indicating a sweep of genetic variation. The selective sweep of mitochondrial DNA may have been generated by the fixation of an advantageous mitochondrial gene mutation in the mitochondrial genome. Alternatively, the dramatic reduction in mitochondrial diversity may be related to Wolbachia.

Genetic diversity within Scorpio maurus (Scorpiones: Scorpionidae) from morocco: Preliminary evidence based on CO1 mitochondrial DNA sequences

Biologia ◽  
2008 ◽  
Vol 63 (6) ◽  
Author(s):  
Elsa Froufe ◽  
Pedro Sousa ◽  
Paulo Alves ◽  
David Harris
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Cytochrome Oxidase ◽  
Dna Sequences ◽  
Preliminary Analysis ◽  
Mitochondrial Gene ◽  
Sequence Divergence ◽  
Preliminary Evidence ◽  
Evidence Based ◽  
Cytochrome Oxidase 1

AbstractThe large-clawed scorpion, Scorpio maurus, is a medically important scorpion and yet nothing is known regarding genetic diversity within this species. As a preliminary analysis we determined variation within the cytochrome oxidase 1 (CO1) mitochondrial gene from specimens from Morocco. High levels of genetic diversity were found that presented some geographical coherence. Of the two identified subspecies from Morocco, S. maurus birulai and S. maurus fuliginosus, the latter included genetically distinct lineages (8.0% uncorrected sequence divergence), indicating a detailed morphological and molecular revision is needed for this species.

scholarly journals Using high-resolution annotation of insect mitochondrial DNA to decipher tandem repeats in the control region

2018 ◽  
Author(s):  
Ji Haishuo ◽  
Xu Xiaofeng ◽  
Jin Xiufeng ◽  
Cheng Zhi ◽  
jin Hong ◽  
...  
Keyword(s):  
Steady State ◽  
High Resolution ◽  
Mitochondrial Genome ◽  
Control Region ◽  
Transcription Initiation ◽  
Tandem Repeats ◽  
Mitochondrial Gene ◽  
Mitochondrial Genomes ◽  
Small Rna Sequencing ◽  
Antisense Gene

In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. Most of the new annotations were consistent with the previous annotations which were obtained using PacBio full-length transcripts. Two important findings are that animals transcribe both entire strands of mitochondrial genomes and the tandem repeat in the control region of the E. fullo mitochondrial genome contains the repeated Transcription Initiation Sites (TISs) of the H-strand. In addition, we found that the copy numbers of tandem repeats showed a great diversity within an individual, enriching the fundamental knowledge of mitochondrial biology. This sRNA-seq based method uses 5′ and 3′ end small RNAs to annotate nuclear non-coding and mitochondrial genes at 1 bp resolution and can also be used to identify new steady-state RNAs, particularly long non-coding RNAs (lncRNAs). Animal mitochondrial genomes containing one control region only encode two steady-state lncRNAs, which are the Mitochondrial D-loop 1 (MDL1) and its antisense gene (MDL1AS), while all other reported mitochondrial lncRNAs could be degraded fragments of transient RNAs or random breaks during experimental processing. The high-resolution annotations of mitochondrial genomes can be used to study the phylogenetics and molecular evolution of animals or to investigate mitochondrial gene transcription, RNA processing, RNA maturation and several other related topics.

The cosmopolitan spider Cryptachaea blattea (Urquhart 1886) (Araneae: Theridiidae): Redescription, including COI sequence, and new synonymy

Zootaxa ◽  
2009 ◽  
Vol 2133 (1) ◽  
pp. 55-63 ◽  
Author(s):  
COR J. VINK ◽  
NADINE DUPÉRRÉ ◽  
PIERRE PAQUIN ◽  
BRIAN M. FITZGERALD ◽  
PHIL J. SIRVID
Keyword(s):  
Mitochondrial Dna ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Dna Sequences ◽  
Mitochondrial Gene ◽  
Junior Synonym ◽  
New Combination ◽  
Morphological Evidence ◽  
Cosmopolitan Species ◽  
New Synonymy

Cryptachaea blattea (Urquhart 1886) new combination, a cosmopolitan species of the spider family Theridiidae, is redescribed, including notes on its distribution and DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1. Based on morphological evidence and mitochondrial DNA sequences, Cryptachaea acoreensis Berland 1932 is a junior synonym of Cryptachaea blattea.

A one-megabase physical map provides insights on gene organization in the enormous mitochondrial genome of cucumber

Genome ◽  
2009 ◽  
Vol 52 (4) ◽  
pp. 299-307 ◽  
Author(s):  
Grzegorz Bartoszewski ◽  
Piotr Gawronski ◽  
Marek Szklarczyk ◽  
Henk Verbakel ◽  
Michael J. Havey
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Physical Map ◽  
Mitochondrial Gene ◽  
Mitochondrial Genes ◽  
Gene Organization ◽  
Mitochondrial Genomes ◽  
Bac Contig ◽  
Repetitive Dnas ◽  
Dna Motifs

Cucumber ( Cucumis sativus ) has one of the largest mitochondrial genomes known among all eukaryotes, due in part to the accumulation of short 20 to 60 bp repetitive DNA motifs. Recombination among these repetitive DNAs produces rearrangements affecting organization and expression of mitochondrial genes. To more efficiently identify rearrangements in the cucumber mitochondrial DNA, we built two nonoverlapping 800 and 220 kb BAC contigs and assigned major mitochondrial genes to these BACs. Polymorphism carried on the largest BAC contig was used to confirm paternal transmission. Mitochondrial genes were distributed across BACs and physically distant, although occasional clustering was observed. Introns in the nad1, nad4, and nad7 genes were larger than those reported in other plants, due in part to accumulation of short repetitive DNAs and indicating that increased intron sizes contributed to mitochondrial genome expansion in cucumber. Mitochondrial genes atp6 and atp9 are physically close to each other and cotranscribed. These physical contigs will be useful for eventual sequencing of the cucumber mitochondrial DNA, which can be exploited to more efficiently screen for unique rearrangements affecting mitochondrial gene expression.

scholarly journals Complete mitochondrial genome of Indian tent turtle, Pangshura tentoria and comparative mitochondriomics

2018 ◽  
Author(s):  
Shantanu Kundu ◽  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Iftikar Rahaman ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
Tandem Repeats ◽  
Synonymous Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Bootstrap Support ◽  
Nadh Dehydrogenase Subunit ◽  
Strong Negative Selection

Complete mitochondrial genomes of Indian tent turtle, Pangshura tentoria was sequenced and annotated as 16,657 bp in length. This first assembly was encoded by 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs) as similar to the typical vertebrate mitochondrial gene arrangement. The complete mitogenome has a base composition of A (33.30%), G (13.54%), C (27%), and T (26.13%). Most of the genes were encoded on major strand, except for the eight tRNAs and one PCG (nad6). Almost all PCGs were starting with an ATG initiation codon, except for cytochrome oxidase subunit 1 (cox1) with ‘GTG’ and NADH dehydrogenase subunit 5 (nad5) with ‘ATA’. The typical termination codons, ‘TAA’ and ‘AGA’ has been observed in NADH dehydrogenase subunit 4l (nad4l) and NADH dehydrogenase subunit 6 (nad6) respectively; and others were used incomplete stop codons. The Relative Synonymous Codon Usage (RSCU) analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine in P. tentoria. Codon distribution per thousand codon (CDsPT) values for all the amino acids showed the maximum values were present for Leucine in all geoemydid turtles. Further, the PCGs showed non-synonymous (Ka)/synonymous (Ks) values were <1 that indicated a strong negative selection among the studied species. The tRNAs were folded into classic clover-leaf secondary structures, except for trnS (GCT), lacking of the conventional DHU arm or stem. Further, the 10 tRNAs showed G-T mismatches and forming weak bonds. In the control region (CR) of P. tentoria, a single tandem repeat of eight base pairs (TTCTCTTT) was resulted with two copy numbers. The comparative study of CR with other geoemydid turtles revealed the numbers of tandem repeats were frequent in the 3´ end and structural characteristic were species-specific. The Maximum Likelihood (ML) phylogeny showed 32 geoemydid turtles were clustered distinctly with high bootstrap support and congruent with the previous phylogenetic hypothesis. Further, the representative mitogenome sequences of other family/suborder were depicted discrete clades in the ML tree. The study argued the complete mitochondrial genome sequence of P. tentoria and comparative mitochondriomics of geoemydid turtles would be useful for further phylogenetic reconciliation and evolutionary research.

scholarly journals Purifying selection can reduce intraspecific mitochondrial gene variation to that of nuclear rRNA

2020 ◽  
Author(s):  
Tshifhiwa G. Matumba ◽  
Jody Oliver ◽  
Nigel P. Barker ◽  
Christopher D. McQuaid ◽  
Peter R. Teske
Keyword(s):  
Mitochondrial Dna ◽  
Dna Barcoding ◽  
Dna Sequences ◽  
Mitochondrial Gene ◽  
Population Expansion ◽  
Purifying Selection ◽  
Species Level ◽  
Molecular Dating ◽  
Coi Gene ◽  
28S Rrna

AbstractMitochondrial DNA (mtDNA) has long been used to date the divergence between species, and to explore the time when species’ effective population sizes changed. The idea that mitochondrial DNA is useful for molecular dating rests on the premise that its evolution is neutral. This premise was questionable to begin with, and even though it has long been challenged, the evidence against clock-like evolution of mtDNA is usually ignored. Here, we present a particularly clear and simple example to illustrate the implications of violations of the assumption of selective neutrality. DNA sequences were generated for the mtDNA COI gene and the nuclear 28S rRNA of two closely related and widely distributed rocky shore snails whose geographical ranges are defined by different thermal preferences. To our knowledge, this is the first study to use nuclear rRNA sequence for studying species-level genealogies instead of phylogenetics, presumably because this marker is considered to be uninformative at this taxonomic level. Even though the COI gene evolves at least an order of magnitude faster, which was reflected in high inter-specific divergence, intraspecific genetic variation was similar for both markers. As a result, estimates of population expansion times based on mismatch distributions were completely different for the two markers. Assuming that 28S evolves effectively clock-like, these findings likely illustrate variation-reducing purifying selection in mtDNA at the species level, and an elevated divergence rate caused by divergent selection between the two species. Although these two selective forces together make mtDNA suitable as a DNA barcoding marker because they create a ‘barcoding gap’, estimates of demographic change can be expected to be highly unreliable. Our study contributes to the growing evidence that the utility of mtDNA beyond DNA barcoding is limited.

scholarly journals Cell-to-cell movement of mitochondria in plants

2016 ◽  
Vol 113 (12) ◽  
pp. 3395-3400 ◽  
Author(s):  
Csanad Gurdon ◽  
Zora Svab ◽  
Yaping Feng ◽  
Dibyendu Kumar ◽  
Pal Maliga
Keyword(s):  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Cell Movement ◽  
Evolutionary Process ◽  
Nicotiana Sylvestris ◽  
Dna Transfer ◽  
Male Sterile ◽  
Mitochondrial Movement ◽  
Homeotic Conversion

We report cell-to-cell movement of mitochondria through a graft junction. Mitochondrial movement was discovered in an experiment designed to select for chloroplast transfer from Nicotiana sylvestris into Nicotiana tabacum cells. The alloplasmic N. tabacum line we used carries Nicotiana undulata cytoplasmic genomes, and its flowers are male sterile due to the foreign mitochondrial genome. Thus, rare mitochondrial DNA transfer from N. sylvestris to N. tabacum could be recognized by restoration of fertile flower anatomy. Analyses of the mitochondrial genomes revealed extensive recombination, tentatively linking male sterility to orf293, a mitochondrial gene causing homeotic conversion of anthers into petals. Demonstrating cell-to-cell movement of mitochondria reconstructs the evolutionary process of horizontal mitochondrial DNA transfer and enables modification of the mitochondrial genome by DNA transmitted from a sexually incompatible species. Conversion of anthers into petals is a visual marker that can be useful for mitochondrial transformation.

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