Mitochondrial Gene Arrangement Research Articles

Characterization of the complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus (Spariformes, Nemipteridae) and phylogenetic analysis

The complete mitochondrial genome of the fork-tailed threadfin bream, Nemipterus furcosus, which belongs to the family Nemipteridae was first determined. The complete mitochondrial genome was 16,882 bp in size and encoded of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. Nemipterus furcosus has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that N. furcosus formed a well-supported monophyletic group with the other Nemipteridae species. This mitochondrial genome provides a useful information for addressing taxonomic issues.

Complete mitochondrial genome of the double-lined fusileer, Pterocaesio digramma (Perciformes, Caesionidae): mitogenome characterization and phylogenetic analysis

The complete mitochondrial genome of the double-lined fusileer, Pterocaesio digramma, which belongs to the family Caesionidae was determined. The complete mitochondrial genome has a length of 16,504 bp and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. P. digramma has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 15 related species revealed that P. digramma formed a well-supported monophyletic group with the other Caesionidae and Lutjanidae species.

Complete mitochondrial genome of the orange-spotted trevally, Carangoides bajad (Perciformes, Carangidae) and a comparative analysis with other Carangidae species

The complete mitochondrial genome of the orange-spotted trevally, Carangoides bajad, which belongs to the family Carangidae was determined. The complete mitochondrial genome has a length of 16,556 bp and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Carangoides bajad has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 13 related species revealed that C. bajad formed a well-supported monophyletic group with the other Carangidae species.

Characterization and comparison of mitogenomes of three ‘eyed’ turtles Sacalia spp

In this paper, we characterized the mitogenomes of three ‘eyed’ turtles, the Beal’s Eyed turtle (Sacalia bealei), the Four Eye-spotted turtle (S. quadriocellata), and the Hainan Four Eye-spotted turtle which was a unique lineage in the four-eyed turtle and considered as an independent species S. insulensis recently. The full lengths of the S. bealei and S. quadriocellata mitogenomes are 16,564 bp, and 16,555 bp, respectively, while the length of partial mitochondrial genome of S. insulensis is 16,433 bp without tailed part of D-loop. All the genes exhibit the typical mitochondrial gene arrangement and transcribing directions of turtles. Phylogenetic analysis indicating that a deep divergence about 7.8% p distance was found between S. bealei and (S. quadriocellata + S. insulensis), and the divergence (2.8% in patristic distance) between S. quadriocellata and S. insulensis is comparable with other closely related species in turtles.

The complete mitochondrial genome of Xanthomantis bimaculata (Mantodea: Iridopterygidae) and its phylogeny

The mitochondrial genome sequence of Xanthomantis bimaculata (Mantodea: Iridopterygidae) from Yunnan, China is a circular molecule with the typical insect mitochondrial gene arrangement, which is 15,941 bp in length and contains 22 tRNAs, two rRNAs, 13 protein-coding genes, and one control region. The overall AT content of the mitogenome is 73.12% (A = 37.58%, T = 35.54%, C = 16.54%, G = 10.34%). In BI and ML phylogenetic analyses, X. bimaculata was a sister clade to Sceptuchus simplex. The monophyly of the families Iridopterygidae, Thespidae and Liturgusidae were supported.

The complete mitochondrial genome of the hydrozoan jellyfish Spirocodon saltatrix (Cnidaria; Hydrozoa; Anthoathecata) with phylogeny analysis

In the present study, we sequenced and analyzed the complete mitochondrial genome of the hydrozoan jellyfish Spirocodon saltatrix. The mitochondrial genome was a linear form (15,752 bp long, 70.4% AT), consisting of 13 protein coding genes (cox1, cox2, atp8, atp6, cox3, nad2, nad5, nad6, nad3, nad4L, nad1, nad4, and cytB), two tRNAs (tRNA-Met and tRNA-Trp), and two rRNAs (12S and 16S). Mitochondrial gene arrangement of the S. saltatrix was completely identical to already-known mitochondrial genomes of hydrozoans. Molecular phylogenetic analysis using 13 protein-coding genes showed that S. saltatrix was closely related to the hydrozoan Clava multicornis.

Characterization and phylogenetic position of two sympatric sister species of toxic flatworms Planocera multitentaculata and Planocera reticulata (Platyhelminthes: Acotylea)

The complete mitochondrial genomes of two toxic flatworm species of the genus Planocera were determined. The total length of mitochondrial DNA (mtDNA) was 15,657 bp in Planocera multitentaculata and 15,486 bp in Planocera reticulata and included 12 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 4 non-coding regions. The mitochondrial gene arrangement of these planocerid species was identical to that of previously described acotylean species, Hoploplana elisabelloi, and also to those of other polyclads. Maximum likelihood analysis against 14 Platyhelminthes showed that a tree was robustly constructed using 12 protein-coding genes than COI gene.

Evolution of mitochondrial gene arrangements in Arcidae (Bivalvia: Arcida) and their phylogenetic implications

Arcidae is a diverse group of ark shells with over 260 described species. The phylogenetic relationships and the evolution of the mitochondrial genomes in this family were poorly understood. Comparisons of mitogenomes have been widely used to explore the phylogenetic relationship among animal taxa. We described the complete mitogenomes of Arca navicularis, Scapharca gubernaculum and one nearly complete mitogenome of Anadara consociata. The mitogenome of A. navicularis (18,103 bp) is currently the smallest known Arcidae mitogenome, while the mitogenomes of S. gubernaculum (45,697 bp) and A. consociata (44,034 bp) are relatively large. The mitochondrial gene orders of the three taxa were substantially different from each other, as well as the patterns found in other ark shells. The relationships among Arcidae species recovered from different mitochondrial characters (nucleotide sequence versus gene order) were in disagreement. The phylogeny based on nucleotide sequences did not support the monophyly of Arcidae, as Cucullaea labiata (Cucullaeidae) appeared as a subgroup within Arcinae, rather than sister group to the family Arcidae. In addition, we presented the first time-calibrated evolutionary tree of Arcidae based on mitochondrial DNA (mtDNA) sequences, which placed the deepest divergence within Arcidae at 342.36 million years ago (Mya), around the Carboniferous (360–300 Mya).

Characterization of the complete mitochondrial genome of the white grouper Epinephelus aeneus (Perciformes, Serranidae) and a comparative analysis with other Serranidae species

The complete mitochondrial genome of the white grouper Epinephelus aeneus, which belongs to the family Serranidae, was determined. The complete mitochondrial genome measured 16,578 bp in length and consisted of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. The mitochondrial gene arrangement of E. aeneus was typical of vertebrates. Phylogenetic analysis conducted using the mitochondrial genomes of 13 related species showed that E. aeneus clustered with other Serranidae species. This mitochondrial genome provides an important resource for addressing taxonomic issues and developing conservation strategies.

Characterization of the complete mitochondrial genome of Oriental reed warbler, Acrocephalus orientalis (Aves: Passeriformes), and a comparative analysis with other Sylviidae species

The complete mitochondrial genome of the Oriental reed warbler, Acrocephalus orientalis, which belongs to the family Sylviidae was determined. The complete mitochondrial genome has a length of 16,971 bp and consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. A. orientalis has a mitochondrial gene arrangement that is typical of vertebrates. Phylogenetic analysis using mitochondrial genomes of 11 related species revealed that A. orientalis is clustered with Acrocephalus scirpaceus and rooted with the other Sylviidae species. This mitochondrial genome provides an important resource for addressing taxonomic issues and studying molecular evolution.

A distinct mitogenome of peanut worm Sipunculus nudus (Sipuncula, Sipunculidae) from Beibu Gulf

Peanut worm, Sipunculus nudus is a cosmopolitan species found in inter-tidal sands. In this article, based on the samples collected from the Beibu Gulf, China, a mitochondrial DNA sequence by Illumina high throughput sequencing, was carried out on muscle and determined the complete mitogenome. This mitogenome of peanut worm is 15,331 base pairs in length (Accession number: MN481531) and comprises of 37 genes as in the typical mitochondrial gene arrangement of Sipunculus. Moreover, the phylogenetic analysis shows that our sample is a novel type in China and has a distantly genetic relationship with the known populations in South China Sea. This mitogenome will serve as the foundation for the molecular genetic studies of peanut worm.

The complete mitochondrial genome of the jellyfish Aurelia coerulea (Cnidaria and Scyphozoa) with phylogenetic analysis

In this study, we sequenced the complete mitochondrial genome of the jellyfish Aurelia coerulea (A. coerulea). The mitochondrial genome was a linear form (16,748 bp long, 65.7% AT), consisting of 13 protein coding genes (PCGs) (cox1, cox2, atp8, atp6, cox3, nad2, nad5, nad6, nad3, nad4L, nad1, nad4, and cytB), 2 rRNAs (12S and 16S), and 2 tRNAs (trnM and trnW). Mitochondrial gene arrangement of the A. coerulea was identical when compared to already-known mitochondrial genomes of Aurelia species. The maximum-likelihood (ML) phylogenetic tree using of 13 mitochondrial proteins showed that A. coerulea collected from Korea waters was closely related to A. limbata.

Particular gene order and complete mitochondrial genome of Parupeneus chrysopleuron (Perciformes, Mullidae)

Parupeneus chrysopleuron were under threat of climate change and unregulated fishing. For protecting the fish, complete mitochondrial genome (mitogenome) of P. chrysopleuron was firstly determined. The mitogenome is 17,397 nucleotides, including 38 genes. The gene arrangement of the P. chrysopleuron mitogenome is different from most of bony fishes. Investigating the mitochondrial gene arrangement pattern found that the tRNAIle and tRNAGln, followed by tRNAMe. Observing four notable non-coding regions, a non-coding region of 814 bp was identified as control region based on its location and central conserved sequence blocks (CSB-1 and CSB-2) were recognized.

The complete mitochondrial genome of Gouldian Finch (Erythrura gouldiae) and its phylogenetic analysis

In this paper, we reported the complete mitogenome of Erythrura gouldiae. E. gouldiae mitogenome is 16,830bp base pairs long. The overall base compositions of complete mitogenomes of E. gouldiae is 30.87% A, 22.77% T, 32.07% C, 14.28% G. All genes exhibit the typical mitochondrial gene arrangement and transcribing directions. The phylogenetic analysis based on 15 mitochondrial sequence data suggested that E. gouldiae are closely related to the same family specie Taeniopygia guttata. The results obtained here would be useful for the conservation and phylogeny of E. gouldiae.

The complete mitochondrial genome sequence of Centropus bengalensis (Lesser Coucal)

We first reported the mitochondrial genome of Centropus bengalensis. The mitogenome of C. bengalensis contains 17,117 base pairs. The overall base composition of complete mitogenome is 28.15% A, 27.95% T, 21.86% C, and 22.04% G, with 43.90% of the GC content. All genes exhibit the typical mitochondrial gene arrangement and transcribing directions. Phylogenetic analysis of 4 Centropus species was performed based on the sequence of cytochrome b gene using the neighbor-joining method and the Kimura 2-parameter model in MEGA 7.0.

Complete mitochondrial genome of the Ruff, Calidris pugnax (Aves, Scolopacidae)

This paper reports the mitochondrial genome of Calidris pugnax, which is a closed circular molecule of 16,902 bp. The overall base composition of this species is 25.2% T, 30.6% C, 32.0% A, and 12.2% G, with an A + T content of 55.2%. The structure of the mitogenome is a typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis of complete mitochondrial genome concatenated sequences from 13 species from 6 genera was conducted using the maximum-likelihood (ML) model. The topology demonstrated that the mitogenome of this species was genetically closest to that of Calidris tenuirostris. Calidris pugnax mitogenome can contribute to our understanding of the phylogeny and evolution of this species.

Characterization of the complete mitochondrial genome of Dactylopterus volitans (Syngnathiformes, Dactylopteridae)

The complete mitochondrial genome was determined for the flying gurnard Dactylopterus volitans belonging to the family Dactylopteridae. The total length of the D. volitans mitochondrial genome is 16,632 bp, which consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 20 species showed that D. volitans formed a well-supported monophyletic group with other Dactylopteridae species.

Next-generation sequencing yields the first complete mitochondrial genome of the ruby dragonet Synchiropus sycorax (Syngnathiformes, Callionymidae)

The complete mitogenome sequence of the ruby dragonet Synchiropus sycorax was first determined using next-generation sequencing strategy in this study. The circle genome was 16,656 bp in length and consisted of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 1 control region. The mitochondrial gene arrangement of S. sycorax is similar to those of most other fish species. Results from neighbor-joining phylogenetic analysis showed that S. sycorax clustered with S. splendidus and other species of the family Callionymidae. This study will be valuable for phylogenetic analysis of the genus Synchiropus and the other genera of the order Syngnathiformes.

The mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) from Fujian and the phylogeny of Caenidae within Ephemeroptera

The phylogenetic relationship of Caenidae remains hotly debated within the Ephemeroptera. We sequenced the complete mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) to discuss the phylogenetic relationships among the Caenidae. The mitochondrial genome of Caenis sp. collected from Jian’ou, Fujian province, China is a circular molecule of 15,392 bp in length containing 37 genes (13 protein-coding genes, 22 tRNAs, and two rRNAs), which showed the typical insect mitochondrial gene arrangement. In BI and ML phylogenetic trees using 23 species from 13 families, the monophyly of the families Caenidae, Heptageniidae, Isonychiidae, and Vietnamellidae was strongly supported. The clade of Caenidae is a sister clade to the clade of Teloganodidae and Baetidae.

Syntenies Between Cohosted Mitochondrial, Chloroplast, and Phycodnavirus Genomes: Functional Mimicry and/or Common Ancestry?

Recent analyses suggest bacterial and/or mitochondrion-like ancestry for giant viruses (Megavirales sensu latu): amoeban mitochondrial gene arrangements resemble those of their candidate homologs in megaviral genomes. This presumed ancestral synteny decreases with genome size across megaviral families at large and within Poxviridae. In this study, analyses focus on Phycodnaviridae, a polyphyletic group of giant viruses infecting Haplophyta, Stramenopiles, and other algae, using syntenies between algal mitogene arrangements and chloroplast genomes and Rickettsia prowazekii as positive controls. Mitogene alignment qualities with Rickettsia are much higher than with viral genomes. Mitogenome synteny with some viruses is higher, for others lower than with Rickettsia, despite lower alignments qualities. In some algae, syntenies among cohosted chloroplast, virus, and mitochondrion are higher, in others lower than expected. This suggests gene order coevolution in cohosted genomes, different coregulations of organelle metabolisms for different algae, and viral mitogenome mimicry, to hijack organelle-committed cellular resources and/or escape cellular defenses/genetic immunity systems. This principle might explain high synteny between human mitochondria and the pathogenic endocellular alphaproteobacterium R. prowazekii beyond common ancestry. Results indicate that putative bacteria/mitochondrion-like genomic ancestors of Phycodnaviridae originated before or at the mitochondrion-bacteria split, and ulterior functional constraints on gene arrangements of cohosted genomes.