Characterization of the complete mitochondrial genome of the Yunnan endemic grasshopper <Emphasis Type="Italic">Yunnanacris yunnaneus</Emphasis> (Insecta: Orthoptera: Acrididae)

Yunnanacris yunnaneus (Y. yunnaneus) was once a destructive grasshopper in the Yunnan province (People’s Republic of China) that jeopardized tobacco cultivation. However, its population has severely declined because of extensive pesticide use. Identifying the species and sources of Y. yunnaneus is important for biodiversity conservation and ecological/environmental preservation. In this study, the complete mitochondrial genome of Y. yunnaneus was assembled from high-coverage (35.5×) Illumina MiSeq sequencing data. The circular genome is 15,475 bp in length, harboring 37 typical mitochondrial genes and one control region. The nucleotide composition is highly asymmetric (42.6 % A, 14.4 % C, 10.6 % G, and 32.4 % T), with an overall A + T content of 75.1 %. All the protein-coding genes are initiated with typical ATN start codons and terminated with a TAA codon. The control region has a remarkably high A + T content (85.1 %) and is located between genes rrnS and trnV.     

The complete mitochondrial genome of <Emphasis Type="Italic">Carabus (Damaster) lafossei</Emphasis> (Coleoptera: Carabidae)

Carabus (Damaster) lafossei: (Coleoptera, Carabidae) is an endangered beetle endemic to China; it was listed as National Second Class Protected Animal in China. Here, we provide the first report of the complete mitochondrial genome sequence of Carabus lafossei. The sequence contains 16,793 bp, with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and 1 control region. All of the protein-coding genes use the typical ATN as the initiation codon, except for ND1, which uses TTG. Only COX2 employs a single T as a termination signal, while others have the typical termination codons (TAA or TAG). The average A+T content of the mitochondrial genome is 79.7%. Phylogenetic analyses revealed that C. lafossei has a closer relationship with Carabus mirabilissimus than with other Carabus species. These molecular biology data provide a scientific basis for the protection and sustainable utilization of this key endangered Carabid beetle.     

Characterization of the complete mitochondrial genome of the giant black Himalayan honeybee (<Emphasis Type="Italic">Apis laboriosa</Emphasis>) from Nepal

The giant black honeybee, Apis laboriosa, has been applied to the highlands of Southeast Asia, where the number of nests has been drastically decreasing. In this study, we first analyzed the complete mitochondrial genome of A. laboriosa from Nepal using Next sequencing technology. The mitochondrial genome is a circular molecule of approximately 1.5 kb, and includes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content of the A. laboriosa mitochondrial genome is 84.7%. Start codons ATG and ATT were found in three and ten genes, respectively, while stop codons TAA and TAG were observed in 12 and 1 gene, respectively. All tRNA genes formed typical cloverleaf secondary structures, except for Ser (AGN) and Gln (Q). The heavy strand (H-strand) was predicted to have 9 PCGs and 14 tRNA genes, while the light strand (L-strand) was predicted to contain four protein-coding, eight tRNA, and two rRNA genes. The 1858 mutation sites that differ between A. laboriosa and Apis dorsata were evenly distributed throughout the mitochondrial genome. The phylogenetic relationship, inferred using 13 PCGs (based on maximum likelihood) was consistent with several previous studies that predicted a sister relationship between A. laboriosa and A. dorsata. A phylogenetic analysis inferred from the 13 mitochondrial PCGs, based on maximum likelihood, indicates that A. laboriosa and A. dorsata are very closely related. We found that the genetic distance between A. laboriosa and A. dorsata is 0.197, indicating that, while they are genetically similar enough to be considered sister species, they are indeed two distinct species.     

Characterization of the complete mitochondrial genome of an endangered alpine toad, <Emphasis Type="Italic">Scutiger ningshanensis</Emphasis> (Amphibia: Anura: Megophryidae)

Scutiger ningshanensis has been listed as an endangered species by the International Union for Conservation of Nature and Natural Resources. Here we report the complete mitochondrial genome of S. ningshanensis, which we hope will be useful for species identification and will contribute to further phylogenetic studies. The circular genome is 17,265 bp in length and encodes the same typical 37 mitochondrial genes. Most of these genes are located on the heavy strand, except for ND6 and eight tRNA genes. The nucleotide composition is particularly rich in A and T, with an overall A?+?T content of 61.8?%. All the protein-coding genes have the standard ATG initiation codon, except for COX1 and ATP8, which initiate translation at GTG. All protein-coding genes are terminated by either TAA or incomplete T(aa) stop codons. A typical set of 22 tRNA genes are present, but their arrangement is unique, with three (tRNA-Ile, tRNA-Phe and tRNA-Trp) found at inverted locations. Because of this gene rearrangement, the control region is located between tRNA-Pro and tRNA-Ile instead of between tRNA-Pro and tRNA-Phe.     

The mitochondrial genome of a stonefly species, <Emphasis Type="Italic">Cerconychia sapa</Emphasis> (Plecoptera: Styloperlidae)

The nearly complete sequence of the mitochondrial DNA (mtDNA) of the stonefly, Cerconychia sapa, has been completed and annotated in this study. The circular genome is 15,188 bp in length with an A+T content of 71.2%, and contains 13 PCGs, 22 tRNA genes and 2 rRNA subunit genes. The control region can only be assembled partially. All PCGs use normal start codon ATN, while ND1 and ND5 use TTG and GTG as start codon, respectively. Meanwhile, 12 PCGs use the typical termination codons TAN, except ND5, which stopped with the incomplete terminaton signal T. Phylogenetic analysis suggests that C. sapa is closely related to Styloperla sp. and S. spinicercia. Our results provide basic data for further study of phylogeny in Plecoptera.     

The complete mitochondrial genome of <Emphasis Type="Italic">Triplophysa brevibarba</Emphasis> with phylogenetic consideration

Triplophysa brevibarba is distributed in the upstream of Ya-lung River. The conservation status of this fish has been assessed as near threatened due to overfishing and habitat destruction. In the present study, we determined the first complete mitochondrial genome of T. brevibarba. This genome was 16,570 bp in size and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a typical control region. The overall nucleotide composition was: 28.2% A, 28.5% T, 25.3% C, and 18.0% G, with a total A?+?T content of 56.7%. The genome size, gene arrangement, and composition were similar to those of other Triplophysa species. Phylogenetic analysis of all 42 Nemacheilidae species showed that Triplophysa is a monophyletic group and T. brevibarba was clustered with Triplophysa minxiannesis and Triplophysa robusta located in the basal clade of Triplophysa.     

The complete mitochondrial genome of an endangered reef gastropods <Emphasis Type="Italic">Trochus pyramis</Emphasis>

In this study, we determined and described the complete mitochondrial genome of an endangered reef gastropods Trochus pyramis for the first time. T. pyramis belongs to the family Trochidae, its natural populations were originally distributed in the Indo-West Pacific Ocean which have now reduced to near extinction because of commercial over-exploitation. The complete mitochondrial genome sequence is 18,439 bp in length containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes and one non-coding region (D-loop). Phylogenetic analysis employing a data set of six sequenced mitochondrial genomes in the superfamily Trochoidea suggests that T. pyramis has a close relationship with Stomatella planulata. Our results are expected to provide useful information for molecular identification of the endangered species T. pyramis and for further phylogenetic studies of the family Trochidae.     

The complete mitochondrial genome and genetic distinction of the Taiwanese honeybee, <Emphasis Type="Italic">Apis cerana</Emphasis> (Hymenoptera: Apidae)

The Asian cavity-nesting honeybee, Apis cerana is widely distributed across Asia and nearby islands, showing interesting patterns of genetic differences caused by repeated isolation and re-unification of populations owing to repeated changes in sea levels. In the present study, we analyzed the complete mitochondrial genome of A. cerana from Taiwan and eastern China for the first time. The mitochondrial genomes of these honeybee populations were circular 15,251- and 15,332-bp molecules, respectively, and included 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one AT-rich control region. The average AT content in mitochondrial genome of Taiwanese and Chinese honeybees was 83.50 and 83.54%, respectively. The heavy strand encoded nine PCGs and 14 tRNA genes and the light strand encoded four PCGs, eight tRNA genes, and two rRNA genes. The ATP6 and ATP8 genes shared 19 nucleotides. Eight PCGs of the A. cerana mitochondrial genome started with ATT, ATP6, COIII, and Cytb genes with ATG, ATP8 gene with ATC, and ND4 gene with ATA. All tRNA genes formed typical cloverleaf secondary structures, except for tRNA-Ser (AGN). The phylogenetic analysis inferred from the 13 mitochondrial PCGs, based on maximum likelihood, indicated that the Taiwanese and eastern Chinese populations of A. cerana are closely related taxa. The 272 sites that differed between A. cerana from Taiwan and eastern China were evenly distributed throughout the mitochondrial genome. We found that the genetic distance between the two population was 0.025, indicating that they are genetically different enough to be considered different subspecies or local populations.     

Complete mitochondrial genome of the Pacific white-sided dolphin <Emphasis Type="Italic">Lagenorhynchus obliquidens</Emphasis> (Cetacea: Delphinidae)

The Pacific white-sided dolphin (Lagenorhynchus obliquidens Gill, 1865) is one of the most abundant, widely distributed delphinids in the North Pacific Ocean, whose existence is threatened by fisheries and environmental contamination. Herein, we report the first complete mitochondrial genome of L. obliquidens. The 16,392-bp sequenced genome exhibited typical cetacean mitochondrial gene arrangement, consisted of the typical set of 37 genes, one replication origin, and a D-loop. As expected, the genome displayed the highest similarity with that of Cephalorhynchus heavisidii and was distinct from that of L. albirostris. Multigene phylogeny also revealed that L. obliquidens was closely related to C. heavisidii, thus suggesting that the genus Lagenorhynchus is polyphyletic, in accordance with the results of recent molecular phylogenetic studies. The results provide information fundamental for genetic and conservation studies for L. obliquidens.     

The complete mitochondrial genome of Chinese <Emphasis Type="Italic">Sarcocheilichthys kiangsiensis</Emphasis> (Cypriniformes: Cyprinidae: <Emphasis Type="Italic">Sarcocheilichthys</Emphasis>)

Sarcocheilichthys kiangsiensis: is a threatened (IUCN: Least Concern) and native fish in China. This study deals with the complete mitochondrial genome of Sarcocheilichthys kiangsiensis by using next-generation sequencing. The full length of the circular genome is 16,672 bp. It consists of 37 typical animal mitochondrial genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and 2 ribosomal RNA (rRNA) genes and a control region. The overall nucleotide composition is: 29.7% A, 25.7% T, 27.4% C, and 17.2% G, with a total A?+?T content of 55.4%.     

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.     

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.     

Complete mitochondrial genome of the honeybee <Emphasis Type="Italic">Apis cerana</Emphasis> native to two remote islands in Japan

The honeybee species native to two remote islands (Amami-Oshima and Tsushima) in Japan were previously reported to be morphologically distinct from the Japanese honeybee Apis cerana japonica. To our knowledge, this is the first study to analyze the complete mitochondrial genome of the honeybee species from the two islands. The mitochondrial genome was a circular and approximately 1.5 kbp molecule that included 13 protein-cording genes (PCGs), 22 tRNA genes, 2 rRNA genes, and 1 AT-rich control region. The average AT content of the mitochondrial genome was 84%. The genetic distance suggested that the honeybee species from the two remote islands were more closely related to A. cerana japonica, among the A. cerana subspecies. Although the mitochondrial genome of the honeybee species from the two remote islands showed genetic variation distinct from those found in the A. cerana group, they were classified as the Japanese honeybee A. cerana japonica.     

The complete mitochondrial genome of a threatened loach (<Emphasis Type="Italic">Beaufortia kweichowensis)</Emphasis> and its phylogeny

The Beaufortia kweichowensis is a threatened and native fish in China. In present study, the complete mitochondrial genome of B. kweichowensis was determined using the next-generation sequencing. The circular mitochondrial genome was 16543 bp in length, and contained 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, a putative displacement loop locus and an origin of replication on the light-strand. The overall nucleotide composition was 29.1% A, 25.0% T, 28.7% C, 17.2% G, with 54.1% AT, respectively. Phylogenetic analyses using a nucleotide dataset of cytochrome c oxidase subunit I gene with two different methods (Maximum likelihood and Bayesian analysis) both highly supported the close relationship of B. kweichowensis, Beaufortia szechuanensis and Beaufortia liui, consistent with previous classifications based on morphological and molecular studies. Furthermore, the topology demonstrated that the Balitoridae can be classified into two subfamilies, and the B. kweichowensis belongs to the subfamily Gastromyzoninae. These data provide useful information for a better understanding of the mitochondrial genomic diversities and evolution in fish as well as novel genetic markers for studying population genetics and species identification.     

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 chloroplast genome of the endangered <Emphasis Type="Italic">Przewalskia tangutica</Emphasis> Maxim

Przewalskia tangutica Maxim., an endangered medicinal species, is endemic to the Qinghai-Tibetan Plateau of China. In this study, we sequenced and characterized the chloroplast genome of P. tangutica for the first time. The P. tangutica chloroplast genome is 155,569 bp in length, exhibits a typical quadripartite structural organization, consisting of a LSC region of 86,707 bp, two IR regions of 25,287 bp and a SSC region of 18,288 bp. The genome contains 138 complete genes, including 85 protein-coding genes (85 PCG species), 44 tRNA genes (21 tRNA species) and eight rRNA genes (four rRNA species, rrn16S, rrn23S, rrn4.5 S, rrn5S). The most of gene species occur as a single copy, while 18 gene species occur in double copies including eight PCG species, six tRNA species (trnN, trnR, trnA, trnI, trnV, trnL) and all of rRNA species. Further, phylogenetic analysis indicated that P. tangutica clustered together with Scopolia parviflora, and formed a clade with Hyoscyamus niger in the Solanaceae. The whole chloroplast genome of P. tangutica not only provides important insight into conservation and restoration efforts for P. tangutica, but also plays a critical role in phylogenetic and evolution studies of the Solanaceae family. More importantly, it will contribute to the ongoing efforts for maintenance of existing genetic resource in the Qinghai-Tibet Plateau.     

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 <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.     

Complete mitochondrial genome and phylogenetic analysis of <Emphasis Type="Italic">Anabarilius grahami</Emphasis> (Teleostei,Cyprinidae, Cultrinae)

The complete mitochondrial DNA genome of Anabarilius grahami was determined by the primer walking sequence method. The entire mitochondrial genome is 16,612 bp in length and contains 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and one control region (CR). As in other teleosts, 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 nucleotide composition was 28.9% A, 24.8% T, 27.9% C, and 18.3% G, respectively, with a slight A+T bias (53.7%). Phylogenetic analysis based on 12 concatenated protein-coding genes of the heavy strand shows the evolutionary position of A. grahami is more closely related to two species of the genus Hemiculter within the subfamily Cultrinae.     

The complete mitochondrial genomes of two globally invasive ants,the Argentine ant <Emphasis Type="Italic">Linepithema</Emphasis><Emphasis Type="Italic">humile</Emphasis> and the little fire ant <Emphasis Type="Italic">Wasmannia auropunctata</Emphasis>

Ants are among the most widespread and damaging of invasive alien species. Here, we report the complete mitochondrial genomes for two globally invasive ants: the Argentine ant Linepithema humile and the little fire ant Wasmannia auropunctata. The circular genomes of L. humile and W. auropunctata are 15,929 and 16,362 bp in length, respectively, and encode the same typical set of 37 mitochondrial genes (i.e. 13 PCGs, 22 tRNAs and two rRNAs) and one control region. The mitochondrial genome of W. auropunctata harbors a unique gene arrangement (‘rrnS-trnV-CR-trnM-trnI-trnQ-nad2-trnW-trnC-trnY’; the underlines indicate inverted genes) between rrnL and cox1. Phylogenetic analysis largely corroborated the traditional taxonomy, except for L. humile which was found to be more related to those taxa of the subfamilies Formicinae and Myrmicinae than to the consubfamilial Leptomyrmex pallens. Our genomic data can be readily used for genetic assays of these two globally invasive ants.