The complete mitochondrial genome of the longfin dragonfish <i>Tactostoma macropus</i> (Stomiiformes: Stomiidae)

Ijichi, Minoru; Takano, Tsuyoshi; Hasegawa, Masamitsu; Yashiki, Haruka; Kogure, Kazuhiro; Kojima, Soichi; Yoshizawa, Susumu

doi:10.1080/23802359.2018.1464411

Cited by 3 publications

(5 citation statements)

References 10 publications

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“…The mitogenome length (control region excluded) is 17,224 bp, within the observed size of other Stomiiformes mitogenomes (Miya et al 2001;Nishida 1999, 2000;Aguilar et al 2018;Ijichi et al 2018). Regarding gene content, as expected 13 PCGs and 2 ribosomal RNA genes are present.…”

supporting

confidence: 73%

“…Both BI and ML phylogenetic trees, rooted with Coregonus lavaretus (Linnaeus, 1758), Salmonidae (following Ijichi et al 2018), show the same topology (Figure 1). The phylogenetic analysis separates with high support, the group Stomiiformes from a cluster formed by families Synodontidae, Ateleopodidae, Myctophidae, and Trachipteridae.…”

mentioning

confidence: 89%

“… 2018 ; Ijichi et al. 2018 ). Regarding gene content, as expected 13 PCGs and 2 ribosomal RNA genes are present.…”

mentioning

confidence: 99%

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A new gene order in the mitochondrial genome of the deep-sea diaphanous hatchet fish Sternoptyx diaphana Hermann, 1781 (Stomiiformes: Sternoptychidae)

Vilas-Arrondo

Gomes‐dos‐Santos

Román-Marcote

et al. 2020

Mitochondrial DNA Part B

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Species of the Sternoptychidae teleost family display an impressive morphology, including their extreme reduced size. Here, we report the first mitochondrial genome of the diaphanous hatchet fish Sternoptyx diaphana. By using short-read sequencing Illumina HiSeq, we generated two mitochondrial contigs which were later physically assembled by PCR. The mitochondrial genome of S. diaphana was 17,224 bp in length (excluding the control region) and is composed of 13 PCGs and 2 ribosomal RNA genes. Strikingly, we could not identify the tRNA-Phe and two copies of tRNA-Met were differently positioned. Additionally, the mitogenome displays a completely new gene rearrangement among vertebrates. We expect that the study presented here will pave the way for further molecular studies with this underrepresented group of illusive teleost fish.

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supporting

confidence: 73%

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confidence: 89%

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A new gene order in the mitochondrial genome of the deep-sea diaphanous hatchet fish Sternoptyx diaphana Hermann, 1781 (Stomiiformes: Sternoptychidae)

Vilas-Arrondo

Gomes‐dos‐Santos

Román-Marcote

et al. 2020

Mitochondrial DNA Part B

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“…We next analysed the phylogenetic relationships between the various deep-sea hatchetfish species. The resulting phylogenetic inference, rooted with Coregonus lavaretus (Linnaeus, 1758) (following [ 16 , 30 ]), is split into two major groups, one composed of order Stomiiformes and the other composed of families Synodontidae, Ateleopodidae, Myctophidae and Trachipteridae ( figure 4 ). Stomiiformes' phylogenetic relationships are poorly resolved, with very low support in most of the nodes.…”

Section: Resultsmentioning

confidence: 99%

Mitochondrial replication's role in vertebrate mtDNA strand asymmetry

Gomes-dos-Santos,

Vilas-Arrondo,

Machado

et al. 2023

Open Biol.

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Mitogenomes are defined as compact and structurally stable over aeons. This perception results from a vertebrate-centric vision, where few types of mtDNA rearrangements are described. Here, we bring a new light to the involvement of mitochondrial replication in the strand asymmetry of the vertebrate mtDNA. Using several species of deep-sea hatchetfish (Sternoptychidae) displaying distinct mtDNA structural arrangements, we unravel the inversion of the coding direction of protein-coding genes (PCGs). This unexpected change is coupled with a strand asymmetry nucleotide composition reversal and is shown to be directly related to the strand location of the Control Region (CR). An analysis of the fourfold redundant sites of the PCGs (greater than 6000 vertebrates), revealed the rarity of this phenomenon, found in nine fish species (five deep-sea hatchetfish). Curiously, in Antarctic notothenioid fishes (Trematominae), where a single PCG inversion (the only other record in fish) is coupled with the inversion of the CR, the standard asymmetry is disrupted for the remaining PCGs but not yet reversed, suggesting a transitory state. Our results hint that a relaxation of the classic vertebrate mitochondrial structural stasis promotes disruption of the natural balance of asymmetry of the mtDNA. These findings support the long-lasting hypothesis that replication is the main molecular mechanism promoting the strand-specific compositional bias of this unique and indispensable molecule.

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“…We next analysed the phylogenetic relationships between the various deep-sea hatchetfish species. The resulting phylogenetic inference, rooted with Coregonus lavaretus (Linnaeus, 1758) (following (Ijichi et al 2018;Arrondo et al 2020)), is split into two major groups, one composed of order Stomiiformes and the other composed of families Synodontidae, Ateleopodidae, Myctophidae and Trachipteridae (fig. 4).…”

Section: Phylogenetic Analysis Shows Poorly Resolved Deep-sea Hatchet...mentioning

confidence: 99%

Rare but not absent: the Inverted Mitogenomes of Deep-Sea Hatchetfish

Gomes‐dos‐Santos

Vilas-Arrondo

Machado

et al. 2023

Preprint

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Mitochondrial genomes are by definition compact and structurally stable over aeons. This generalized perception results from a vertebrate-centric vision, as very few types of mtDNA rearrangements have been described in vertebrates. By combining a panel of sequencing approaches, including short- and long-reads, we show that species from a group of illusive marine teleosts, the deep-sea hatchetfish (Stomiiforms: Sternoptychidae), display a myriad of new mtDNA structural arrangements. We show a never reported inversion of the coding direction of protein-coding genes (PGG) coupled with a strand asymmetry nucleotide composition reversal directly related to the strand location of the Control Region (which includes the heavy strand replication origin). An analysis of the 4-fold redundant sites of the PCGs, in thousands of vertebrate mtDNAs, revealed the rarity of this phenomenon, only found in 9 fish species, five of which are deep-sea hatchetfish. Curiously, in Antarctic notothenioid fishes (Trematominae), where a single PCG inversion (the only other record in fish) is coupled with the inversion of the Control Region, the standard asymmetry is disrupted for the remaining PCG but not yet reversed, suggesting a transitory state in this species mtDNA. Together, our findings hint that a relaxation of the classic vertebrate mitochondrial structural stasis, observed in Sternoptychidae and Trematominae, promotes disruption of the natural balance of asymmetry of the mtDNA. Our findings support the long-lasting hypothesis that replication is the main molecular mechanism promoting the strand-specific compositional bias of this unique and indispensable molecule.

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The complete mitochondrial genome of the longfin dragonfish Tactostoma macropus (Stomiiformes: Stomiidae)

Cited by 3 publications

References 10 publications

A new gene order in the mitochondrial genome of the deep-sea diaphanous hatchet fish Sternoptyx diaphana Hermann, 1781 (Stomiiformes: Sternoptychidae)

A new gene order in the mitochondrial genome of the deep-sea diaphanous hatchet fish Sternoptyx diaphana Hermann, 1781 (Stomiiformes: Sternoptychidae)

Mitochondrial replication's role in vertebrate mtDNA strand asymmetry

Rare but not absent: the Inverted Mitogenomes of Deep-Sea Hatchetfish

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