A linear mitochondrial genome of Cyclospora cayetanensis (Eimeriidae, Eucoccidiorida, Coccidiasina, Apicomplexa) suggests the ancestral start position within mitochondrial genomes of eimeriid coccidia

Sequences and structural attributes of mitochondrial genomes have played a key role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic groups in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both ceriantharian species studied, the mitochondrial gene sequences could not be assembled into a circular genome. Instead, our analyses suggest both species have fragmented mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The number of fragments and the variation in gene order between species is much greater in Ceriantharia than among Medusozoa. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other anthozoan groups.

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Revisiting Ceriantharian (Anthozoa) Mitochondrial Genomes: Casting Doubts about Their Structure and Size

Genome Biology and Evolution ◽

10.1093/gbe/evaa130 ◽

2020 ◽

Vol 12 (8) ◽

pp. 1440-1443

Author(s):

David Roy Smith

Keyword(s):

Mitochondrial Genome ◽

News Media ◽

Chromosome Numbers ◽

Mitochondrial Genomes ◽

Mitochondrial Dnas ◽

Linear Mitochondrial Genome ◽

Significant Attention

Abstract Recently, Stampar et al. (2019. Linear mitochondrial genome in Anthozoa (Cnidaria): a case study in. Sci Rep. 9(1):6094.) uncovered highly atypical mitochondrial genome structures in the cnidarian species Pachycerianthus magnus and Isarachnanthus nocturnus (Anthozoa, Ceriantharia). These two mitochondrial DNAs assembled as linear fragmented genomes, comprising eight and five chromosomes, respectively—architectures unlike any other anthozoan mitogenome described to date. What’s more, they have cumulative lengths of 77.8 (P. magnus) and 80.9 kb (I. nocturnus), making them the largest animal mitochondrial DNAs on record, a finding which garnered significant attention by various news media. Here, I take a closer look at the work of Stampar et al. and question their key results. I provide evidence that the currently available mitogenome sequences for I. nocturnus and P. magnus, including their structures, sizes, and chromosome numbers, should be treated with caution. More work must be done on these genomes before one can say with any certainty that they are linear, fragmented, or the largest animal mitogenomes observed to date.

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Linear Mitochondrial genome in Anthozoa (Cnidaria): A case study in Ceriantharia

10.7287/peerj.preprints.27042v1 ◽

2018 ◽

Author(s):

Sergio N Stampar ◽

Michael B Broe ◽

Jason Macrander ◽

Adam M Reitzel ◽

Marymegan Daly

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Mitochondrial Gene ◽

Phylogenetic Position ◽

Mitochondrial Genomes ◽

Gene Sequences ◽

Phylogenetic Placement ◽

Organellar Genome ◽

Linear Mitochondrial Genome

Sequences and structural attributes of mitochondrial genomes have played a key role in the clarification of relationships among Cnidaria, a key phylum of early-diverging animals. Among the major lineages of Cnidaria, Ceriantharia ("tube anemones") remains one of the most enigmatic groups in terms of its phylogenetic position. We sequenced the mitochondrial genomes of two ceriantharians to see whether the complete organellar genome would provide more support for the phylogenetic placement of Ceriantharia. For both ceriantharian species studied, the mitochondrial gene sequences could not be assembled into a circular genome. Instead, our analyses suggest both species have fragmented mitochondrial genomes consisting of multiple linear fragments. Linear mitogenomes are characteristic of members of Medusozoa, one of the major lineages of Cnidaria, but are unreported for Anthozoa, which includes the Ceriantharia. The number of fragments and the variation in gene order between species is much greater in Ceriantharia than among Medusozoa. The novelty of the mitogenomic structure in Ceriantharia highlights the distinctiveness of this lineage but, because it appears to be both unique to and diverse within Ceriantharia, it is uninformative about the phylogenetic position of Ceriantharia relative to other anthozoan groups.

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Mitochondrial genome evolution in pelagophyte algae

Genome Biology and Evolution ◽

10.1093/gbe/evab018 ◽

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.

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The linear mitochondrial genome of commensal hydroid Eutima japonica (Cnidaria, Hydrozoa, Eirenidae)

Mitochondrial DNA Part B ◽

10.1080/23802359.2021.1899869 ◽

2021 ◽

Vol 6 (3) ◽

pp. 1082-1084

Author(s):

Jung Soo Seo ◽

Hey-Jin Eom ◽

Jae-Kwon Cho ◽

Hyun-Sil Kang ◽

Jae-Sung Rhee

Keyword(s):

Mitochondrial Genome ◽

Linear Mitochondrial Genome

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

Genetics ◽

10.1093/genetics/124.2.423 ◽

1990 ◽

Vol 124 (2) ◽

pp. 423-428 ◽

Cited By ~ 1

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.

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Mitochondrial genome assembly v1

10.17504/protocols.io.bqzbmx2n ◽

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

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

PeerJ ◽

10.7717/peerj.9309 ◽

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.

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

PLoS ONE ◽

10.1371/journal.pone.0248054 ◽

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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Complete mitochondrial genome of Glomeridesmus spelaeus (Diplopoda), a troglobitic species from Carajás iron-ore caves (Pará, Brazil)

10.1101/228882 ◽

2017 ◽

Author(s):

Gisele Lopes Nunes ◽

Renato Renison Moreira Oliveira ◽

Eder Soares Pires ◽

Santelmo Vasconcelos ◽

Thadeu Pietrobon ◽

...

Keyword(s):

Mitochondrial Genome ◽

Base Composition ◽

Iron Ore ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Significant Advance ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Rich Region ◽

The Public

AbstractWe report the complete mitochondrial genome sequence of Glomeridesmus spelaeus, the first sequenced genome of the order Gomeridesmida. The genome is 14,825 pb in length and encodes 37 mitochondrial (13 PCGs, 2 rRNA genes, 22 tRNA) genes and contains a typical AT-rich region. The base composition of the genome was A (40.1%), T (36.4%), C (15.8%), and G (7.6%), with an AT content of 76.5%. Our results indicated that Glomeridesmus spelaeus only distantly related to the other Diplopoda species with available mitochondrial genomes in the public databases. The publication of the mitogenome of G. spelaeus will contribute to the identification of troglobitic invertebrates, a very significant advance for the conservation of the troglofauna.

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