scholarly journals The Mitochondrial Genome of Paraminabea aldersladei (Cnidaria: Anthozoa: Octocorallia) Supports Intramolecular Recombination as the Primary Mechanism of Gene Rearrangement in Octocoral Mitochondrial Genomes

2012 ◽  
Vol 4 (9) ◽  
pp. 994-1006 ◽  
Author(s):  
Stephanie A. Brockman ◽  
Catherine S. McFadden
Keyword(s):  
Mitochondrial Genome ◽  
Gene Rearrangement ◽  
Mitochondrial Genomes ◽  
Primary Mechanism ◽  
Intramolecular Recombination

scholarly journals Vertebrate Mitochondrial Genome Organization: Evidence of Convergent Evolution

2021 ◽  
Author(s):  
Maria Paula Montaña Lozano ◽  
Manuela Alejandra MorenoCarmona ◽  
Jesus Mauricio Ochoa Capera ◽  
Natalia Sofía Medina Camacho ◽  
Jeffrey L. Boore ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Genome Organization ◽  
Gene Rearrangement ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Mitochondrial Genomes ◽  
Comparative Genomic ◽  
Sequencing Technology ◽  
Taxonomic Class ◽  
Evolutionary Studies

Abstract The evolution of the vertebrate mitochondrial genome has been the focus of numerous genetic and evolutionary studies over the last several decades. Initially, sampling was heavily biased toward taxonomic orders of greatest economic or health importance, but recent advances in DNA sequencing technology have facilitated a much broader phylogenetic sampling from which we can clarify general evolutionary trends such as patterns of gene rearrangement. Toward this end, we performed a comparative genomic analysis of the 2,831 vertebrate mitochondrial genomes representing 12 classes that are available in the NCBI database. Using a combination of bioinformatics methods, we determined that there is a great variation in the proportion of rearrangement by gene and by taxonomic class, with higher rates being observed in Reptilia, Amphibia, Petromyzonti, Mammalia, and Actinopteri. Further, within each class, there is large variation in proportion of reorganization among different orders or even taxonomic families. Eleven events of convergence in the genic order among different taxonomic orders were determined, most of them not previously reported.

Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology'

2002 ◽  
Vol 16 (3) ◽  
pp. 345 ◽  
Author(s):  
M. Dowton ◽  
L. R. Castro ◽  
A. D. Austin
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Gene Rearrangement ◽  
Mitochondrial Gene ◽  
Molecular Data ◽  
Mitochondrial Genomes ◽  
Gene Rearrangements ◽  
Genome Organisation ◽  
Rearrangement Mechanism ◽  
Molecular Characters

Mitochondrial gene rearrangements are the latest tool in the arsenal of phylogeneticists for investigating historical relationships. They are complex molecular characters that may provide more reliable evidence of ancestry than comparative molecular data. Here we review the phylogenetic utility of mitochondrial gene rearrangements, and find that despite isolated incidences of convergence, derived gene order appears highly congruent with phylogenies produced from other sources of data. We calculate that the chance of two mitochondrial genomes sharing the same derived genome organisation is only 1/2664, but caution that this ignores the possibility that the (as yet uncharacterised) gene rearrangement mechanism may greatly increase the chance of convergence. Broader taxonomic surveys of mitochondrial genome organisation will lead to a more realistic indication of the historical incidence of convergence in genome organisation.

The complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae) indicates extensive independent evolutionary events

Genome ◽  
2009 ◽  
Vol 52 (4) ◽  
pp. 308-319 ◽  
Author(s):  
Shu-jun Wei ◽  
Min Shi ◽  
Jun-hua He ◽  
M. Sharkey ◽  
Xue-xin Chen
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeat ◽  
Gene Rearrangement ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Genomes ◽  
Repeat Region ◽  
Diadegma Semiclausum ◽  
Repeat Elements ◽  
Tandem Repeat Region ◽  
Variable Loops

Few complete mitochondrial genomes representing limited families in the order Hymenoptera have been sequenced. Here, we sequenced the complete mitochondrial genome of Diadegma semiclausum (Hymenoptera: Ichneumonidae). This genome is 18 728 bp long, the second largest hexapod mitochondrial genome sequenced in its entirety and that with the highest A+T content at 87.4%. Four tRNAs are rearranged compared with the ancestral arrangement. Gene rearrangement mechanisms are different among all three rearranged regions. Six tRNAs have a large variable loop, which is not found in other metazoan mitochondrial genomes. trnS(AGY) uses the abnormal anticodon TCT but trnK uses the normal CTT. The A+T-rich region is very long (2161 bp). An extremely A+T-rich (99.1%) 1515 bp tandem repeat region with three types of repeat elements is located between cox1 and cox2, and the most likely ancestral element originated from the 3′ end of cox1. Independent tandem duplications followed by mutation–insertion–deletion is the best model to explain the formation of this region. These results indicate that independent evolutionary events occurred extensively, such as gene rearrangement events, gene rearrangement mechanisms, derivation of tRNA variable loops, and tandem repeat region evolutionary processes, all of which likely contribute to the diversified features of hymenopteran mitochondrial genomes.

scholarly journals Mitochondrial genome evolution in pelagophyte algae

2021 ◽  
Author(s):  
Shannon J Sibbald ◽  
Maggie Lawton ◽  
John M Archibald
Keyword(s):  
Mitochondrial Genome ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
23S Rrna ◽  
Mitochondrial Genomes ◽  
Trna Genes ◽  
Unique Region ◽  
Long Read ◽  
Genomic Studies ◽  
Aureoumbra Lagunensis

Abstract The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756) and five strains of A. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984 and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 base-pairs (bp) (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five A. anophagefferens strains varied slightly in length (42,401 bp—42,621 bp) and were 99.4%-100.0% identical. Gene content and order was highly conserved between the A. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in A. anophagefferens containing DNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. While the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five A. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to non-bloom-forming species.

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 Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1134
Author(s):  
Fei Ye ◽  
Hu Li ◽  
Qiang Xie
Keyword(s):  
Gene Rearrangement ◽  
Hot Spot ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Deep Understanding ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Current View ◽  
Novel Gene ◽  
Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

The mitochondrial genome organization of a maize fertile cmsT revertant line is generated through recombination between two sets of repeats.

Genetics ◽  
1990 ◽  
Vol 124 (2) ◽  
pp. 423-428 ◽  
Author(s):  
C M Fauron ◽  
M Havlik ◽  
R I Brettell
Keyword(s):  
Mitochondrial Genome ◽  
Genome Organization ◽  
Callus Tissue ◽  
Mitochondrial Genomes ◽  
Normal Type ◽  
Male Sterile ◽  
Sequence Complexity ◽  
Mtdna Organization ◽  
Callus Tissue Culture ◽  
Fertile Revertant

Abstract The mitochondrial genome (mtDNA) organization from a fertile revertant line (V3) derived from the maize cytoplasmic male sterile type T (cmsT) callus tissue culture has been determined. We report that the sequence complexity can be mapped on to a circular "master chromosome" of 705 kb which includes a duplication of 165 kb of DNA when compared to its male sterile progenitor. Associated with this event is also a 0.423-kb deletion, which removed the cmsT-associated urf13 gene. As found for the maize normal type (N) and cmsT mitochondrial genomes, the V3 master chromosome also exists as a multipartite structure generated by recombination through repeated sequences.

Mitochondrial genome assembly v1

2020 ◽  
Author(s):  
Graham Etherington
Keyword(s):  
Mitochondrial Genome ◽  
Genome Assembly ◽  
De Novo Assembly ◽  
De Novo ◽  
Mitochondrial Genomes

De novo assembly of 49 mustelid whole mitochondrial genomes

scholarly journals Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9309
Author(s):  
Viktoria Yu Shtratnikova ◽  
Mikhail I. Schelkunov ◽  
Aleksey A. Penin ◽  
Maria D. Logacheva
Keyword(s):  
Mitochondrial Genome ◽  
Rna Editing ◽  
Transcriptome Sequencing ◽  
Unique Feature ◽  
Genetic Material ◽  
Mitochondrial Genes ◽  
Vaccinium Macrocarpon ◽  
Mitochondrial Genomes ◽  
Plastid Genomes ◽  
Trans Splicing

Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.

scholarly journals Revealing the high variability on nonconserved core and mobile elements of Austropuccinia psidii and other rust mitochondrial genomes

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0248054
Author(s):  
Jaqueline Raquel de Almeida ◽  
Diego Mauricio Riaño Pachón ◽  
Livia Maria Franceschini ◽  
Isaneli Batista dos Santos ◽  
Jessica Aparecida Ferrarezi ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Transmembrane Protein ◽  
Genome Structure ◽  
Rust Fungi ◽  
Mitochondrial Genomes ◽  
Phylogenomic Analysis ◽  
The Core ◽  
Mtdna Sequence ◽  
Austropuccinia Psidii

Mitochondrial genomes are highly conserved in many fungal groups, and they can help characterize the phylogenetic relationships and evolutionary biology of plant pathogenic fungi. Rust fungi are among the most devastating diseases for economically important crops around the world. Here, we report the complete sequence and annotation of the mitochondrial genome of Austropuccinia psidii (syn. Puccinia psidii), the causal agent of myrtle rust. We performed a phylogenomic analysis including the complete mitochondrial sequences from other rust fungi. The genome composed of 93.299 bp has 73 predicted genes, 33 of which encoded nonconserved proteins (ncORFs), representing almost 45% of all predicted genes. A. psidii mtDNA is one of the largest rust mtDNA sequenced to date, most likely due to the abundance of ncORFs. Among them, 33% were within intronic regions of diverse intron groups. Mobile genetic elements invading intron sequences may have played significant roles in size but not shaping of the rust mitochondrial genome structure. The mtDNAs from rust fungi are highly syntenic. Phylogenetic inferences with 14 concatenated mitochondrial proteins encoded by the core genes placed A. psidii according to phylogenetic analysis based on 18S rDNA. Interestingly, cox1, the gene with the greatest number of introns, provided phylogenies not congruent with the core set. For the first time, we identified the proteins encoded by three A. psidii ncORFs using proteomics analyses. Also, the orf208 encoded a transmembrane protein repressed during in vitro morphogenesis. To the best of our knowledge, we presented the first report of a complete mtDNA sequence of a member of the family Sphaerophragmiacea.

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