The complete mitochondrial genome sequence of <Emphasis Type="Italic">Buceros bicornis</Emphasis> (Bucerotiformes: Bucerotidae)

Buceros bicornis (Bucerotiformes: Bucerotidae) has been listed as a near threatened species by the International Union for Conservation of Nature and Natural Resources (IUCN) due to over-hunting and habitat loss. Thus, it is a great challenge for us to efficiently protect the Buceros bicornis resource from extinct. Molecular biology research can provide the scientific basis for the conservation of key endangered species. In this work, we first reported the complete mitochondrial genome (mitogenome) sequence of Buceros bicornis by next-generation sequencing (NGS). The total length of the complete mitogenome was 17,117 bp and its overall base composition was estimated to be 30.2% for A, 23.5% for T, 32.3% for C and 14.0% for G, indicating an A?+?T (53.7%)-rich feature in the Buceros bicornis complete mitogenome. In addition, it contained the typical structure of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes (tRNAs) and a non-coding control region (D-loop region). The newly obtained mitogenome sequence seems to be useful for conservation biology and evolutionary studies on hornbill bird species, which would contribute to enrich the Buceros bicornis mitogenome resource and promote its biological research.     

The complete mitogenome of the winged argonaut <Emphasis Type="Italic">Argonauta hians</Emphasis> and its phylogenetic relationships in Octopoda

The mitogenome of the winged argonaut Argonauta hians (Argonautidae) was decoded using next generation sequencing. The de novo assembled mitogenome consists of 16,130 bp, including 13 protein coding genes, 2 ribosomal RNAs and 22 transfer RNA genes. The gene arrangement is identical to the other available Octopodidae octopus sequences submitted to NCBI. The overall base composition of the A. hians mitogenome is 29.1% A, 6.9% C, 13.2% G and 40.9% T. The phylogenetic analysis of the A. hians mitogenome suggests an ancestral position in the order Octopoda, compared to species in the Amphioctopus, Cistopus and Octopus (Octopodidae) genera. The decoding of the A. hians mitogenome provides insight into the evolutionary history and rises the concern of conservation on this uncommon and ancestral Octopoda species.     

Characterization of the complete mitochondrial genome sequence of the Asiatic toad <Emphasis Type="Italic">Bufo gargarizans</Emphasis> (Amphibia,Anura, Bufonidae) with phylogenetic analysis

The Asiatic toad Bufo gargarizans belongs to Bufonidae. This species is known from the Russian Far East, central, northern and north-eastern China, the Democratic People’s Republic of Korea and Japan. In this study, the complete mitochondrial genome of B. gargarizans was sequenced. The mitogenome was 17,407 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the B. gargarizans is 28.9% A, 28.2% T, 27.5% C and 15.3% G. Phylogenetic analysis showed B. gargarizans was closely related to B. bankorensis and B. tuberculatus. The complete mitogenome of B. gargarizans can provide an important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.     

The complete mitochondrial genome of the scaleshell <Emphasis Type="Italic">Leptodea leptodon</Emphasis> (Bivalvia: Unionidae)

The Leptodea leptodon (Bivalvia: Unionidae) is native to the United States, it is threatened by human activities and habitat destruction. In the present study, it’s complete mitochondrial genome was reconstructed from whole-genome Illumina sequencing data with an average coverage of 1213X. The total length of mitogenome is 16,133 bp, which consists of 37 typical animal mitochondrial genes, including 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs) and two ribosomal RNAs. The putative control region (329 bp) is located between ND5 and tRNA-Gln, with an A + T content of 67.4 %. The base composition of the genome is A (38.7 %), C (26.7 %), G (10.8 %) and C (26.7 %) with an overall GC content of 37.5 %. Phylogenetic analysis suggests that L. leptodon is closely related to its confamilial counterparts than to the other taxa.     

Characterization of the complete mitochondrial genome for the <Emphasis Type="Italic">Euphractus sexcinctus flavimanus</Emphasis> (Mammalia,Xenarthra) subspecies

We are reporting the complete mitochondrial genome for the Euphractus sexcinctus flavimanus, a subspecies from South America, who is also known as yellow armadillo and six-banded armadillo. The de novo short read assembly was obtained from a west-central Brazil specimen. A typical mammalian mitogenome, containing 37 genes and one non-coding region (D-loop) was found. The total length was 16,805 base pairs and differences were observed among the E. s. flavimanus mitogenome described here and that previously reported for an E. sexcinctus unknown subspecies. Such difference was mainly due to the variation in the non-coding region. The complete mitochondrial genome described for the E. s. flavimanus is an important data source for comparative approaches, including genetic diversity studies among armadillo species and subspecies.     

The complete mitochondrial genome of Chinese Shrew, <Emphasis Type="Italic">Sorex sinalis</Emphasis> (Soricidae)

The complete mitogenome sequence of Chinese Shrew (Sorex sinalis) was determined in this study. The mitogenome is a circular molecule of 17,216 bp in length, containing 13 protein-coding genes, two ribosome RNA genes, 22 transfer RNA genes and two non-coding regions. Recently, Chinese Shrew has been listed as Data Deficient by the IUCN red list of threatened animals and Near Threatened by the red list of China’s vertebrates. The new sequenced complete mitogenome of S. sinalis would provide useful information for application in conservation genetics and evolution for the endemic species of China.     

The complete mitochondrial genome sequence of <Emphasis Type="Italic">Rusa unicolor dejeani</Emphasis> (Artiodactyla: Cervidae)

Rusa unicolor has been listed as a vulnerable species by the International Union for Conservation of Nature and Natural Resources (IUCN) because of overexploitation for subsistence and markets in meat and antlers. Mitochondrial DNA has been used to differentiate R. unicolor from other ungulates and sympatric species. In this study, we determined the complete mitochondrial DNA genome of Rusa unicolor dejeani. The circle genome (16,437 bp in length) contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and one D-loop region. All the PCGs in R. u. dejeani were distributed on the H-strand, except for the ND6 gene and eight tRNA genes which were encoded on the L-strand. We expect that the complete mitogenome of R. u. dejeani could provide a molecular data for species identification, phylogeography analysis, population genetics research and evolutionary studies.     

The complete mitochondrial genome of <Emphasis Type="Italic">Indirana semipalmata</Emphasis> (Amphibia: Anura)

The complete mitochondrial genome of the endemic frog Indirana semipalmata was sequenced. The mitogenome is a circular molecule of 17,052 bp in length, containing 13 protein-coding genes (PCGs), two ribosomal RNA (r RNA) genes, 21 transfer RNA (tRNA) genes and a non-coding D-loop region (control region). Its gene arrangements are similar to the typical neobatrachian-type except for the loss of tRNA ^Asn gene. Our data, which represent the first mitogenome for the genus, will serve as a reference for further studies on the conservation genetics of the endemic amphibian fauna of the Western Ghats.     

Characterization of an endangered marine strombid gastropod <Emphasis Type="Italic">Strombus luhuanus</Emphasis> complete mitochondrial genome

In this study, we first determined the complete mitochondrial genome of the endangered marine strombid gastropod Strombus luhuanus, an important shellfish traditionally distributed around Hainan island of China and parts of Papua New Guinea. The complete mitogenome sequence was 15,799 bp in length containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one non-coding control region (D-loop). We further compared the mtDNA sequences of S. luhuanus and S. gigas, and calculated the moderate sequence variations in their protein coding regions, which would further provide valuable genome variation information for conservative studies of S. luhuanus.     

The complete mitochondrial genome sequence of the sea urchin <Emphasis Type="Italic">Glyptocidaris crenularis</Emphasis> and its phylogenetic analysis

We have sequenced and characterized the complete mtDNA nucleotide sequence of the sea urchin Glyptocidaris crenularis on Illumina’ HiSeq platform. The genome is 15,760 bp in size and contains 12 protein genes, 22 transfer RNAs, 2 ribosomal RNAs and 1 control region. ATP synthase subunit 8 was missing. ND6 and 5 tRNAs are on the L-strand and the others are on the H-strand, which was consistent with other sea urchins. Gene arrangement and size were conserved with other sea urchins. The phylogenetic relationships of 13 sea urchin species from seven families was analysised based on COI sequence. G. crenularis shares a closer relationship with Echinocarsium ordatum, which provides us a new sight on the origin traceability of G. crenularis.     

The complete mitochondrial genome of <Emphasis Type="Italic">Etheostoma okaloosae</Emphasis> (Perciformes: Percidae)

The threatened Okaloosa darter (Etheostoma okaloosae) is found almost exclusively in the Choctawhatchee Bay of Florida, and its habitat is threatened by natural disasters and water pollution. In this study, the complete mitochondrial genome of E. okaloosae has been determined by polymerase chain reaction method for the first time. The overall base composition of E. okaloosae mitogenome is 26.1% for A, 28.2% for C, 18.2% for G and 27.5% for T. The percentage of G+C content is 45.7%. The mitogenome is a circular DNA molecule of 16,616 bp in length with a D-loop region and contains 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and 13 protein-coding genes (PGCs). Phylogenetic analysis suggests that E. okaloosae is closely related to Etheostoma nigrum and Etheostoma radiosum. The mitochondrial genome sequencing of E. okaloosae in this study provides important molecular data for conservation genetic studies.     

The complete mitochondrial genome of <Emphasis Type="Italic">Ovis ammon darwini</Emphasis> (Artiodactyla: Bovidae)

Ovis ammon darwini: has been listed as a near-threatened species by IUCN-World Conservation Union due to over-hunting and poaching, competition with domestic livestock, and habitat destruction. Study on molecular biology research provides the scientific basis for the protection and sustainable utilization of key endangered species. Mitochondrial genome is very useful for researches in ecology, systematics and conservation biology. In this study, the complete mitochondrial genome sequence of O. a. darwini was determined by next-generation sequencing data, which is 16,618 bp in length and contains 13 protein-coding genes(PCGs), 2 rRNAs genes, 22 tRNAs genes and a non-coding control region. Base composition of genome is A(33.7?%), C(25.8?%), G(13.1?%), T(27.4?%) with an A?+?T content of 61.1?%. Phylogenetic analysis suggested that the systematic status of O. a. darwini was more closed related to O. a. hodgsoni clustered with O. ammon. The mitogenome of O. a. darwini offered significant information for molecular genetic research of O. ammon.     

Complete mitochondrial genome sequence of the tiny dragonfly, <Emphasis Type="Italic">Nannophya pygmaea</Emphasis> (Odonata: Libellulidae)

The tiny dragonfly, Nannophya pygmaea (Odonata: Libellulidae), has been listed as an endangered insect in South Korea. We sequenced the complete 15,112-bp-long mitochondrial genome (mitogenome) of the species. The genome included a typical set of genes (13 protein-coding genes [PCGs], two rRNA genes, and 22 tRNA genes) and one non-coding region with an arrangement identical to that found in most insects. Among the 13 PCGs, only ND1 started with the atypical TTG. The 441-bp-long A+T-rich region possessed the highest A/T content (84.6%) in the genome. N. pygmaea was placed as the sister to Orthetrum species belonging to Libellulidae. Unlike conventional phylogenetic results, the suborders Anisozygoptera and Zygoptera formed a strong sister group in both Bayesian inference (BI) and maximum likelihood (ML) methods (BI, BPP?=?1 and ML, 88–94%), justifying the use of different types of molecular markers for phylogenetic analysis.     

The complete mitochondrial genome of goby <Emphasis Type="Italic">Acentrogobius viridipunctatus</Emphasis>

In this study, we first determined and described the complete mitochondrial genome of Acentrogobius viridipunctatus, a member of the Family Gobiidae. The complete mitogenome sequence was 16,507 bp in length containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, one non-coding control region (D-loop). We identified genome-wide variations among mitochondrial genomes of different Acentrogobius species and found that the D-loop regions harbored most of the sequence variations, which would further provide valuable genome variation information for the conservation and utilization of A. viridipunctatus.     

The complete mitochondrial genome of the long-lived Greenland shark (<Emphasis Type="Italic">Somniosus microcephalus</Emphasis>): characterization and phylogenetic position

The Greenland shark (Somniosus microcephalus) has recently been identified as the world’s longest-living vertebrate animal, which raises conservational concern in light of recently high bycatch. We report the complete mitochondrial genome of S. microcephalus to be 16,730 bp and composed by 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and a control region. The overall nucleotide composition was 30.8% A, 29.9% T, 14.5% G, and 24.9% C, with a total of 39.4% GC content. Phylogenetic analysis confirmed the position of S. microcephalus in the traditional tree of sharks. The availability of the S. microcephalus mitogenome will contribute to further conservational genetic studies of a unique species, listed as ‘data deficient’ on the Norwegian Red List and ‘near threatened’ on the IUCN Red list.     

The complete mitochondrial genome sequence of spotted linsang (<Emphasis Type="Italic">Prionodon pardicolor pardicolor</Emphasis>)

In this study, the complete mitochondrial genome sequence of Prionodon pardicolor pardicolor has been reported for the first time in China. The total length of the mitogenome was 16,689 bp. It contained the typical structure, including 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and 1 control region (D-loop). tRNA^Ser lost the stem of DHC loop and failed to form a typical cloverleaf secondary structure. Mitochondrial control region of P. p. pardicolor was 1242 bp long, laying between the tRNA^Pro and tRNA^Phe genes. Based on the 13 PCG sequences, homology and single-nucleotide mutation loci were performed between P. p. pardicolor and P. pardicolor. As a result, the homology between two species was 99.6% on average, and Nucleotide mutation loci was 41. Also, in view of their mitochondrial control region comparison, P. p. pardicolor drop 28 bp nucleotides.     

The complete mitochondrial genome characterization of <Emphasis Type="Italic">Thunnus obesus</Emphasis> (Scombriformes: Scombridae) and phylogenetic analyses of <Emphasis Type="Italic">Thunnus</Emphasis>

Thunnu obesus is important in commercial fisheries around the world. Due to human overfishing, climate change and ocean acidification, it was listed as Vulnerable (VU) under the International Union for the Conservation of Nature. In the present study, the complete mitogenome of T. obesus was determined. It is 16,524 bp in length and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes, one origin of replication on the light-strand (O_L) and a control region (CR). The overall base composition is 28.5, 25.4, 29.4 and 16.7% for A, T, C and G, respectively. The 13 PCGs encode 3797 amino acids in total, most of which use the initiation codon ATG except COI use GTG, and TAA or TAG as the stop codon, except COII, ND4 and Cyt b use an incomplete stop codon T. Additionally, a phylogenetic tree was constructed to explore the taxonomic status of T. obesus, which expects for phylogenetic relationship within Thunnu and further conservation strategies for this species.     

Variation in the whole mitogenome of reef-building <Emphasis Type="Italic">Porites</Emphasis> corals

The study of complete mitochondrial genomes (mitogenomes) revealed different gene rearrangements, highly variable markers, and delineated clades that have aided the understanding of the evolutionary history in corals. In this study, we examined mitogenomic variation of reef-building Porites corals and designed 34 primer pairs to target high diversity regions and to amplify the complete mitogenome of a widely-distributed Indo-Pacific species of Porites (P. lobata) and two endemic species of the Eastern Pacific (P. sverdrupi and P. panamensis). All primer pairs amplified for each species and the mitogenomes assembled yielded the same gene order as obtained from next-generation sequencing. Mitogenomic variation in Porites corals was three to ten times higher than in Acropora or Pocillopora, two other major reef builders. In contrast to these corals, the nucleotide variation in Porites species was distributed evenly along the mitogenome. Primers designed here are useful to amplify regions with the highest variation possible as well as to assemble the whole mitogenomes of different Porites species. The resulting mitogenomes should improve our understanding of evolutionary relationships, delimitation of species, and conservation within the genus Porites.     

The complete mitochondrial genome of Myanmar warty newt <Emphasis Type="Italic">Tylototriton shanorum</Emphasis> (Salamandridae: <Emphasis Type="Italic">Tylototriton</Emphasis>)

Tylototriton shanorum, an endemic species of Myanmar, is threatened by illegal capture and environmental destruction. Here, the complete mitochondrial genome (mitogenome) of T. shanorum is described. The entire mitogenome sequence of T. shanorum is 17,096 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region. In addition, two additional 3′ Cytb like sequences and two complete tRNA^Thr genes, one pseudo tRNA^Thr, and three noncoding sequences (NC1, NC1′ and NC2) were situated between Cytb and tRNA^Pro genes. The new complete mitogenome sequence of T. shanorum will be useful for conservation genetics, evolutionary biology, phylogeography, as well as phylogenetic relationships studies of this threatened species.     

The complete mitochondrial genome of <Emphasis Type="Italic">Budorcas taxicolor bedfordi</Emphasis> (Artiodactyla: Bovidae) and phylogenetic studies of Caprinae

Budorcas taxicolor bedfordi is uniquely distributed in Qinling Mountains in China. It is classified as vulnerable under International Union for the Conservation of Nature and is a first-class national protected animal in China. Here, the complete mitogenome of B. t. bedfordi was described, which is 16,660 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, one origin of replication on the light-strand and a putative control region. Most of the protein-coding genes use the initiation codon ATG except ATP6 uses ATT, ND2, ND3 and ND5 use ATA, which is quite uncommon in vertebrate mtDNA. Most of them have TAA or TAG as the stop codon, except ND6 and Cytb use AGA, COIII, ND3 and ND4 use an incomplete stop codon TA or T. A phylogenetic tree involving 18 Caprinae species was constructed, which will contribute to phylogenetic studies of Bovidae and further conservation strategies for this species.