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.     

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.     

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.     

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.     

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 invasive semi-aquatic mammal,nutria <Emphasis Type="Italic">Myocastor coypus</Emphasis> (Rodentia; Myocastoridae)

The nutria or coypu (Myocastor coypus, Molina, 1782) is one of the world’s worst invasive alien species. Nutria have significant harmful effects on natural ecosystems and agricultural industries on a global scale, including in South Korea. Herein, we report the complete mitochondrial genome of M. coypus. The 16,874 bp sequenced genome exhibited a typical rodential mitochondrial gene arrangement, and consisted of the typical set of 37 genes, one replication origin, and a D-loop. The mitogenome of nutria displayed the highest similarity with that of Cuvier’s spiny rat, Proechimys cuvieri, and was distinct from that of the house mouse, Mus musculus. Multigene phylogenetic analysis also revealed that M. coypus was well clustered with other species in Myocastorini, and the overall tree topology accorded well with recent molecular phylogenetic analysis of South American spiny rats. The results will provide information fundamental for the scientific management of the nutria populations in South Korea.     

The complete mitogenome of <Emphasis Type="Italic">Pelochelys cantorii</Emphasis> (<Emphasis Type="Italic">Guangning</Emphasis>) and the comparative analysis of different habitats

Pelochelys cantorii has become one of the most critically endangered species in the world. The complete mitochondrial DNA (mtDNA) genome of P. cantorii (Guangning) was generated by polymerase chain reaction (PCR) amplification, primer-walking sequencing and fragment cloning. The mitochondrial genome is 17,424 base pairs (bp) and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one control region. Comparative analyses of complete mitochondrial genome sequences from different habitats, we found that the P. cantorii (unknown) may be wrong identified. And the phylogenetic position of P. cantorii also support this result, maximum likelihood (ML) and Bayesian (BI) analyses were conducted based on 12 heavy-strand PCGs and 2 rRNAs from 18 taxa. P. cantorii (unknown) is not closely related to other P. cantorii, but formed a clade with Apalone spinifera and Apalone ferox.     

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.     

The complete maternal mitochondrial genome sequence of <Emphasis Type="Italic">Cuneopsis heudei</Emphasis> (Bivalvia: Unionoida: Unionidae)

The freshwater mussel Cuneopsis heudei is an endemic species in China. The population size has been declining dramatically due to water pollution, overfishing and habitat destruction. In this study, the complete maternal mitochondrial genome of C. heudei was determined (GenBank accession no. MF687348) for the first time. The circle genome is 15,981 bp in length. There are 14 protein-coding genes (cox1-3, nad1-6, nad4L, cob, atp6, atp8 and female ORF), 22 tRNA genes, two rRNA genes and a control region. Pylogenetic analyses reveal that C. heudei genome is inside of Unionidae and close related to C. pisciculus.     

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.     

Characterization of the complete maternal mitochondrial genome of <Emphasis Type="Italic">Ptychorhynchus pfisteri</Emphasis> (Bivalvia: Unionidae: Gonideinae)

The freshwater mussel Ptychorhynchus pfisteri is a threatened and endemic species in China. In this study, the complete maternal mitochondrial genome of P. pfisteri was firstly determined (GenBank accession no. KY067440). The circle genome is 16,040 bp in length. It consists of 14 protein-coding genes (cox1-3, nad1-6, nad4L, cob, atp6, atp8 and FORF), 22 tRNA genes, two rRNA genes and a putative control region. The gene order of P. pfisteri is not identical to other unionoid bivalves except Gonideinae species. Maximum likelihood analyses reveal that P. pfisteri belongs to the subfamily Gonideinae.     

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 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.     

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.     

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 chloroplast genome of <Emphasis Type="Italic">Lilium taliense</Emphasis>, an endangered species endemic to China

The complete chloroplast genome of Lilium taliense which is a rare and endangered species native to China was determined in this study. The chloroplast genome is 153,055 bp long and consists of a pair of inverted repeat regions (26,543 bp), one large single copy region (82,458 bp), and one small single copy region (17,511 bp). The genome contains 132 genes, including 86 protein-coding genes, 38 transfer RNA gens and eight ribosomal RNA genes. In addition, 188 simple sequence repeats (SSRs) were identified in the L. taliense chloroplast genome. Maximum likelihood phylogenetic analysis with the reported chloroplast genomes revealed that L. taliense was closely related to L. fargesii and L. superbum.     

Complete plastid genome of <Emphasis Type="Italic">Larix potaninii</Emphasis> var. <Emphasis Type="Italic">macrocarpa</Emphasis>, an endangered conifer endemic to China

Larix potaninii var. macrocarpa Y. W. Law. belongs to the genus Larix within family Pinaceae, is an endangered conifer species endemic to western China. In this study, the complete plastid genome sequence of L. potaninii var. macrocarpa was characterized using next generation Illumina pair-end sequencing data. The chloroplast DNA is 122,642 bp in length, and contains a pair of 436 bp inverted repeat (IR) region, one large single copy (LSC) region of 65,733 bp, and one small single copy (SSC) region of 56,037 bp. The genome contains 110 genes, including 72 protein-coding genes (72 PCG species), 4 ribosomal RNA genes (4 RNA species) and 34 transfer RNA genes (33 tRNA species). The overall G+C content of the whole genome is 38.8%, and the corresponding values of the LSC, SSC and IR regions are 38.0, 39.7 and 37.4%, respectively. Phylogenetic analysis based on 36 chloroplast genomes indicated that L. potaninii var. macrocarpa is closely related to L. potaninii var. chinensis.     

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.     

Characterization of the complete mitochondrial genome of the ecotoxicity indicator insect <Emphasis Type="Italic">Aiolopus thalassinus</Emphasis> (Orthoptera; Acrididae; Oedipodinae)

The grasshopper Aiolopus thalassinus has long been used as an ecotoxicity indicator species of heavy metal pollution. The rapid molecular identification and genetic resource determination of this species would be of great helpful for the application in environmental monitoring. Mitochondrial DNA sequences are the widely applied molecular markers in insect taxonomic identification. In this study, we reported the complete mitochondrial genome of A. thalassinus. The whole genome was 15,753 bp in size and encoded 37 typical mitochondrial genes. The nucleotide composition was asymmetric, with an obvious bias towards A and T (75.3% combined). The typical ATN start codons were exhibited in the initiation of all protein-coding genes (PCGs). The typical TAA/TAG codons or the incomplete T(aa) codon were the terminal codons. The control region was determined by its remarkably high A+T content of 83.3%. This mitochondrial genome data for A. thalassinus will provide a useful resource for environmental monitoring.