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 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.     

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.     

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 complete mitochondrial genomes of <Emphasis Type="Italic">Mastacembelus erythrotaenia</Emphasis> and <Emphasis Type="Italic">Mastacembelus armatus</Emphasis> (Synbranchiformes: Mastacembelidae) and phylogenetic studies of Mastacembelidae

Mastacembelus erythrotaenia and Mastacembelus armatus, are economically and ecologically important freshwater fishes and distribute mainly in tropical and subtropical zone. In this study, the complete mitochondrial genomes of M. erythrotaenia and M. armatus were determined. The circle genomes are 16493 and 16487 bp in length, respectively. They contain 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and one control region. All the protein-coding genes use ATG as start codon except COI uses GTG. Most of them have TAA or TA as the stop codon, while COII, ND3, ND4 and Cyt b use T. Phylogenetic trees involving all the available Mastacembelidae species were also constructed, contributing to phylogenetic studies and conservation of these spiny eels.     

The complete chloroplast genome of endangered <Emphasis Type="Italic">Manglietia insignis</Emphasis>, a rare landscaping tree with red lotus-like flowers

Manglietia insignis, a rare and endangered evergreen tree endemic to South Asia, is of great importance for landscaping because of its graceful appearance and red lotus-like flowers. In this study, the complete chloroplast (cp) genome of M. insignis was assembled based on the Illumina sequences. The cp genome of M. insignis was 160,117 bp in length and contained a pair of inverted regions (IR, 26,575 bp) which were separated by the small single copy (SSC, 18,660 bp) and the large single copy (LSC, 88,307 bp) regions. It encoded 131 genes including 86 protein-coding genes, 37 tRNA genes, and eight rRNA ribosomal genes. The overall AT content of M. insignis cp genome is 60.8%. The maximum likelihood phylogenetic analysis revealed that M. insignis was closely related to Michelia odora. This result will be helpful for the conservation, taxonomy, and phylogeny programs of the genus Manglietia.     

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.     

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 chloroplast genome sequence of <Emphasis Type="Italic">Pinus dabeshanensis</Emphasis>

The complete chloroplast genome sequence of Pinus dabeshanensis was mapped and determined based on the Illumina data. The length of the complete cp genome is 117,058 bp, that contains 38.8 % G+C base pairs. The cp genome displayed the typical quadripartite structure that consists of a pair of inverted repeat (IRs, 473 bp) separated by the large single-copy (LSC, 64,098 bp) and small single-copy (SSC, 52,014 bp) regions. It encodes an identical set of 111 unique genes, including 72 protein coding, 35 transfer RNA and 4 ribosomal RNA genes, respectively. The phylogenetic analysis indicated that the cp genome of P. dabeshanensis is closely related to that of congeneric P. armandii.     

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 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 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">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 chloroplast genome of threatened <Emphasis Type="Italic">Magnolia laevifolia</Emphasis>, a rare ornamental shrub with strong aromatic flowers

In this study, we assembled the complete chloroplast (cp) genome of Magnolia laevifolia Y.W. Law & Y. F. Figlar endemic to Yunnan, China. The species is a rare and threatened evergreen shrub with great important for horticulture because of its attractive strong aromatic flowers. The cp genome of M. laevifolia was 160,120 bp in length and contained a pair of inverted repeat (IR, 26,588 bp) regions, which were separated by the small single copy (SSC, 18,799 bp) and the large single copy (LSC, 88,145 bp) regions. The cp genome encoded 131 genes including 86 protein-coding genes, 37 tRNA genes, and eight rRNA ribosomal genes. The overall AT content of M. laevifolia cp genome is 60.8%. The maximum likelihood phylogenetic analysis revealed that M. laevifolia was closely related to M. odora. This result will be helpful for the conservation, taxonomy, and phylogeny programs of the genus Magnolia.     

The complete chloroplast genome of the long blooming and critically endangered <Emphasis Type="Italic">Camellia azalea</Emphasis>

Camellia azalea, a rare and critically endangered plant endemic to South China, can bloom throughout the year and is thus of great interest for camellia breeders. In this study, the complete chloroplast (cp) genome of C. azalea was assembled based on sequencies obtained with Illumina HiSEq. The cp genome of C. azalea was 157,039 bp in length and contained a pair of inverted repeat regions (IR, 25,992 bp) separated by the small single copy (SSC, 18,169 bp) and large single copy (LSC, 86,886 bp) regions. It encoded 135 genes including 87 protein-coding genes, 37 tRNA genes and eight ribosomal RNA genes. The overall AT content of C. azalea cp genome is 62.7%. The maximum likelihood phylogenetic analysis revealed that C. azalea was most closely related to the congeneric C. crapnelliana and C. oleifera. This result will be helpful for the taxonomy, conservation, and breeding programs of the genus Camellia.     

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.     

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 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.     

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.