Complete Mitogenome Sequence Research Articles

Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

BackgroundThe Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties.ResultsA total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species.ConclusionsThe recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.

The complete mitochondrial genome of the Acropora pruinosa

In this study, the complete mitogenome sequence of stony coral, Acropora pruinosa (Scleractinia), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome, consisting of 18,480 bp, has unique 13 protein-coding genes (PCGs), three transfer RNAs, and two ribosomal RNAs genes. The complete mitogenome of Acropora pruinosa showing 99% identities to Acropora nasuta. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analyses for coral phylogeny.

Sequencing and analysis of the complete mitochondrial genome of the Ussuri shrew (Sorex mirabilis) from China

The complete mitogenome sequence of the Ussuri shrew (Sorex mirabilis) was determined using long PCR. The genome was 17,315 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (32.6%), C (25.2%), T (28.8%), and G (13.4%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of the Ussuri shrew. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Sequencing and analysis of the complete mitochondrial genome of the slender shrew (Sorex gracillimus) from China

The complete mitogenome sequence of the slender shrew (Sorex gracillimus) was determined using long PCR. The genome was 17,002 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (32.5%), C (25.5%), T (28.5%), and G (13.5%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of the slender shrew. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Higher DNA insert fragment sizes improve mitogenomic assemblies from metagenomic pyrosequencing datasets: an example using Limenitidinae butterflies (Lepidoptera, Nymphalidae)

A large number of diverse mitogenomic sequences can be obtained more easily and affordably via mitochondrial metagenomics, which generates high-throughput sequences directly from sheared DNA extractions and assembles mitogenomic sequences using a few bioinformatic processing steps. However, following de novo assembly analysis, the optimal DNA fragment insert size is unclear. In this study, four extracted Limenitidinae butterfly DNA samples were sonically fragmented, and two fragment size ranges (200–400 and 400–600 bp) of each sample were tagged with different barcodes, producing pyrosequencing datasets. The results show that the datasets generated from longer DNA insert fragments result in better coverage and more complete mitogenomic sequences, and the phylogenetic analysis shows high support at nodes, revealing that Athyma butterflies do not represent a monophyletic group. Therefore, we recommend using longer insert DNA fragment sizes to generate high-throughput datasets for obtaining complete mitogenomic sequences which can improve phylogenetic studies.

Genome skimming yields the complete mitogenome of Chromodoris annae (Mollusca: Chromodorididae)

In this study, the complete mitogenome sequence of sea slug, Chromodoris annae (Mollusca: Chromodorididae), has been decoded for the first time by genome skimming method. The overall base composition of C. annae mitogenome is 30.6% for A, 14.5% for C, 17.8% for G, and 37.2% for T, and has GC content of 32.2%. The assembled mitogenome, consisting of 14,260 bp, has unique 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs genes. The C. annae has the common mitogenome gene organization and feature of Chromodorididae. The complete mitogenome of C. annae provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for sea slugs.

Revealing the complete mitogenome sequence of Hypsugo alaschanicus based on next generation sequencing

Hypsugo alaschanicus belong to Chiroptera, which is the only type of mammals with the real ability to fly. The complete mitochondrial genome of H. alaschanicus based on next generation sequencing data thus determined had 37 genes for 13 proteins, 22 tRNAs, and 2 rRNAs together with a major non-coding region in a typical gene arrangement of vertebrate mitogenomes. Phylogenetic analysis shows that Pipistrellini is multiline origin, Pipistrellus-like bats can be divided into three groups: Pipistrellini-Nyctalini, Vespertilionini-Eptesicini, and Asian Pipistrelles. Hypsugo alone become a clade, Vespertilio and Eptesicus phylogenetic relationship are closer, Pipistrellus and Nyctalus have a close phylogenetic relationship.

The complete mitochondrial genome sequence of Anthracoceros coronatus (Bucerotiformes: Bucerotidae)

Anthracoceros coronatus (Bucerotiformes: Bucerotidae) has been listed in near threatened category in the IUCN Red List of Threatened Species, due to population decline. Mitochondrial genome (mitogenome) sequence is informative and very useful for systematics and conservation biology studies. In this study, we first determined and characterized the complete mitogenome of A. coronatus using next-generation sequencing platform. The complete mitogenome of A. coronatus was 17,214 bp in length, with an AT ratio of 52.8%. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region or D-loop region, with an identical gene order to that of most other vertebrates. The complete mitogenome sequence of A. coronatus would not only provide additional molecular markers of choice for detecting illegal poaching and trafficking of this bird species, but also would contribute to phylogenomic study of hornbill birds.

The complete mitogenome of sea hares, Dolabella auricularia (Mollusca: Aplysiidae)

In this study, the complete mitogenome sequence of sea hares, Dolabella auricularia (Mollusca: Aplysiidae), has been decoded for the first time by low coverage whole genome sequencing method. The overall base composition of D. auricularia mitogenome is 31.5% for A, 14.0% for C, 16.4% for G, and 38.0% for T, and has low GC content of 30.5%. The assembled mitogenome, consisting of 14,598 bp, has unique 13 protein-coding genes (PCGs), 22 transfer RNAs, and two ribosomal RNAs genes. The D. auricularia has the common mitogenome gene organization and feature of Aplysiidae. The complete mitogenome of D. auricularia provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Aplysiidae.

The complete mitogenome of Acropora nana (Cnidarian: Acroporidae)

Acropora nana belongs to Cnidaria phylum, Anthozoa class, and staghorn coral groups. Like other corals, Acropora could be an indicator for environmental changes and with great conservational values. In this study, the complete mitogenome sequence of A. nana (Cnidarian: Acroporidae), has been decoded for the first time by low coverage whole genome sequencing method. The overall base composition of A. nana mitogenome is 25.0% for A, 13.8% for C, 24.4% for G, and 36.9% for T, and has low GC content of 38.2%. The assembled mitogenome, consisting of 18,480 bp, has unique 13 protein-coding genes (PCGs), three transfer RNAs, and two ribosomal RNAs genes. The A. nana has one big intron insert in ND5 gene. The complete mitogenome of A. nana provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony corals.

The complete mitogenome and phylogenetic analysis of Japanese firefly ‘Genji Botaru’ Luciola cruciata (Coleoptera: Lampyridae)

We performed mitogenome analysis of Japanese firefly Luciola cruciata (Coleoptera: Lampyridae), which is unique species in Japan. It is classified into six haplotypes based on the difference of COII sequence on mitochondrial DNA. The complete mitogenome sequence of Tohoku group has been registered so far, we newly analysed West Japan groups which belong to different haplotype. The total length of analysed mitogenome was 15,990 bp, being one base longer than the case of Tohoku’s firefly. The base substitution was found at 273 positions over the whole mitochondrial sequence, while amino acid substitution accompanying it was observed at only 11 positions.

The complete mitochondrial genome of Bombyx lemeepauli (Lepidoptera: Bombycidae) and its phylogenetic relationship

The complete mitochondrial genome (mitogenome) of Bombyx lemmepauli Lemée has been sequenced with 15,801 bp in length (Genbank no. KY620270), and has a base composition of A (43.17%), G (7.40%), C (11.90%), and T (37.86%). Similar to other bombyciod species, it contains a typically conserved structure including 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and an A + T-rich region. Excepting cox1 started with CGA, the start codons of the other 12 PCGs were ATN. Eleven of the 13 PCGs ended with TAA, expect for cox1 and cox2, which ended with a single T. The complete mitogenome sequence provided here would be useful for further understanding the evolutional position of B. lemeepauli, which is a key species to relate the famous resource insect B. mori and the important insect pest Rondotia menciana (Lepidoptera: Bombycidae).

The complete mitochondrial genome of the causative agent of the human cercarial dermatitis, the visceral bird schistosome species Trichobilharzia szidati (platyhelminthes: Trematoda: Schistosomatidae)

We report the first complete mitochondrial genome of visceral bird schistosome Trichobilharzia szidati (Platyhelminthes, Trematoda: Schistosomatidae). The circular genome is 14293 bp in length and contains 12 protein-coding genes, 12S and 16S rRNAs genes, 22 tRNAs and one non-coding region (202 bp) (accession number MF136777). Phylogenetic relationships based on 12 protein-coding gene sequences (PCG) of mitogenomes of a number of trematode and cestode species have shown that T. szidati is the closest genetic relative to nasal bird schistosome T. regenti. The complete mitogenome sequence of T. szidati may serve as a resource for comparative mitogenomics and trematode evolution studies.

The first complete mitochondrial genome sequence of an Australian raven (Corvus coronoides)

Here, we report the complete mitochondrial genome of an Australian raven (Corvus coronoides). The mitogenome of C. coronoides was characterised as a circular molecule of 16,925 bp in length encoding a typically conserved structure similar to those of other Corvidae. It consisted of 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes, with all protein-coding sequences commencing with methionine. The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 980 bp and 1600 bp, respectively, and were located between tRNA-Phe and tRNA-Leu. The overall base composition of the mitogenome of C. coronoides was slightly higher AT (56.0%) content than GC (44.0%). A phylogenetic tree using available complete mitogenome sequences of the family Corvidae revealed a close evolutionary relationship of C. coronoides with the now extinct Chatham raven (C. moriorum), a large songbird that was native to the Chatham Islands east of New Zealand.

The complete mitogenome of nereid worm, Neanthes glandicincta (Annelida: Nereididae)

In this study, the complete mitogenome sequence of nereid worm, Neanthes glandicincta (Annelida: Nereididae), has been decoded for the first time by PCR amplification and Sanger sequencing methods. The overall base composition of N. glandicincta mitogenome is 31.5% for A, 22.2% for C, 14.5% for G and 31.7% for T, and has GC content of 36.7%. The assembled mitogenome, consisting of 16,126 bp, has unique 13 protein-coding genes (PCGs), 22 transfer RNAs and 2 ribosomal RNAs genes. The complete mitogenome of N. glandicincta shows 65% identities to Namalycastis abiuma. All PCGs, tRNA and rRNA genes were encoded on H-strand. The potential D-loop is 1625 bp in length and located between tRNA-Gly and tRNA-Met. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for Annelida.

Sequencing and analysis of the complete mitochondrial genome of the masked shrew (Sorex caecutiens) from China

The complete mitogenome sequence of the masked shrew (Sorex caecutiens) was determined using long PCR. The genome was 17,096 bp in length and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, one origin of L strand replication, and one control region. The overall base composition of the heavy strand is A (32.9%), C (24.5%), T (29.3%), and G (13.3%). The base compositions present clearly the A–T skew, which is most obviously in the control region and protein-coding genes. The extended termination-associated sequence domain, the central conserved domain and the conserved sequence block domain are defined in the mitochondrial genome control region of the masked shrew. Mitochondrial genome analyses based on MP, ML, NJ, and Bayesian analyses yielded identical phylogenetic trees. The five Sorex species formed a monophyletic group with the high bootstrap value (100%) in all examinations.

Complete mitochondrial genome sequence of an Australian little penguin (Eudyptula minor novaehollandia, J.R. Forster, 1781)

In this paper, we report the complete mitochondrial genome of an Australian little penguin (Eudyptula minor novaehollandia). The mitogenome sequence has been found to be circular, and 17,608 bp in length. Similar to other Spheniscidae species, the genome encoded a typically conserved structure consisting of 13 protein-coding genes (PCGs), two rRNA genes, and 22 tRNA genes, as well as all protein coding sequences started with methionine. The lengths of 12S ribosomal RNA and 16S ribosomal RNA were 977 bp and 1612 bp, respectively, and were located between tRNA-Phe and tRNA-Leu. The overall base composition of the mitogenome of E. minor novaehollandia had slightly higher AT (55.5%) content than GC (45.5%). The complete mitogenome sequence determined in this study would be useful to track the deeper evolutionary history and conservation of E. minor novaehollandia.

Sequencing and analysis of the complete mitochondrial genome of Rana amurensis (Anura: Ranidae)

In this study, the complete mitogenome sequence of Rana amurensis (Anura: Ranidae) is determined using long PCR. It is a circular molecule of 20,571 bp in length (GenBank accession no. MF370348). The complete mtDNA sequence of R. amurensis contained 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, 13 protein-coding genes (PCGs) and 2 control regions (D-loops). The nucleotide composition was 28.6% A, 26.8% C, 14.0% G and 30.6% T. Mitochondrial genome analyses based on NJ method yield phylogenetic trees, including that 20 reported family Ranidae frogs. These molecular data presented here provide a useful tool for systematic analyses of genus Rana.

Next-generation sequencing yields the complete mitogenome of stony coral (Favites abdita)

In this study, the complete mitogenome sequence of stony coral, Favites abdita (Scleractinia), has been decoded for the first time by next-generation sequencing and genome assembly. The assembled mitogenome, consisting of 17,825 bp, has unique 13 protein-coding genes (PCGs), 2 transfer RNAs and 3 ribosomal RNAs genes. The complete mitogenome provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis for stony coral phylogeny.

The complete mitochondrial genome of Sympiezomias velatus (Coleoptera: Curculionidae)

Here, we determined the complete mitogenome sequence of Sympiezomias velatus (Coleoptera: Curculionidae: Entiminae). This mitogenome was 15,592 bp long with an A + T content of 74.1% and contains 13 protein-coding genes (PCGs), 21 transfer RNA genes (tRNAs), 2 ribosomal RNA unit genes and a large non-coding region (putative control region). The trnI gene was not found in the S. velatus mitogenome. The order and orientation of the mitochondrial genes were identical to the inferred ancestral arrangement of insects except for trnR which was changed to be adjacent the nad3 gene. All tRNAs had the typical cloverleaf structure, except for trnS1 which lacked the dihydrouridine arm. The Bayesian phylogenetic tree of 10 Entiminae species based on the concatenated nucleotide sequences of 13 PCGs strong supported a sister relationship of S. velatus and Barynotus obscures.