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.     

Development and characterization of 23 microsatellite markers for the endangered beetle <Emphasis Type="Italic">Carabus lafossei</Emphasis> (Coleoptera,Carabidae)

Carabus lafossei Feisthamel (Coleoptera, Carabidae) is an endemic species and an endangered beetle of China. In this study, the novel 23 microsatellite markers were developed by method of Fast Isolation by AFLP of Sequence COntaining Repeats (FIASCO). The number of alleles ranged from 2 to 14 (mean 7.3) and the value of polymorphism information content (PIC) ranged from 0.364 to 0.844 (mean 0.691), suggesting a high level of polymorphism in the tested population. The expected and observed heterozygosities ranged from 0.488 to 0.875 (mean 0.745) and from 0.500 to 0.875 (mean 0.668), respectively. All loci were in Hardy–Weinberg equilibrium. These markers will be effective to help the future studies of genetic diversity and population structure in C. lafossei and to develop the conservation and management strategies.     

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.     

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 sequence of an endangered traditional Chinese medicine plant <Emphasis Type="Italic">Dendrobium candidum</Emphasis> (Orchidaceae)

Dendrobium candidum Lindl. is an endangered lithophytic orchid distrubuted in the subtropical regions of China which was listed in the category of the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Here, we reported the complete chloroplast (cp) genome sequence and the cp genomic features of D. candidum. The genome was 152,094 bp long with 129 genes comprising 83 protein-coding genes, 40 tRNA genes, and six rRNA genes. Most of the genes occurred as a single-copy, while 18 occurred in two copies. Phylogenetic analysis of a data set of cp genomes indicated that D. candidum is closely related to that of other species in Dendrobium.     

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 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%.     

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 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.     

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 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.     

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 complete mitochondrial genome sequence of a wild forest musk deer (<Emphasis Type="Italic">Moschus berezovskii</Emphasis>)

Forest musk deer (FMD) is an endangered species, and its population size has dropped dramatically. In this study, we determined the complete mitochondrial genome of a FMD. The genome was 16,353 bp long, and contained 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes, and one control region. Most PCGs were distributed on the heavy strand except ND6 and eight tRNA genes, which were encoded on the light strand. The nucleotide composition was asymmetric, with an overall A+T content of 62.1%. Comparison with one previously described mitochondrial genome revealed 94.4% sequence homology and 1128 nucleotide mutation sites, which represents a substantial difference. A phylogenetic tree based on Cytb genes of eight closely related musk deer species showed that our sample clustered with two FMD subspecies from Yunnan, China. These results provide novel molecular information that can potentially be used for genetic diversity conservation of this species.     

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.     

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.     

The complete chloroplast genome of a staple food of the giant panda, <Emphasis Type="Italic">Fargesia denudata</Emphasis> (Poaceae)

Fargesia denudata: T. P. Yi (Poaceae), endemic to China, is the most important food for the giant panda. Here we reported the complete chloroplast (cp) genome sequence for the F. denudate using Illumina high-throughput sequencing technology. The F. denudata cp genome is 133,784 bp long, and the overall GC content is 39.69%. The F. denudata cp genome encodes 129 unique genes, including 82 protein-coding genes (PCG), 39 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The majority of the genes occur as single-copy sequences, and 19 genes are duplicated in the inverted repeats (IRs). Further, phylogenetic analysis suggests that F. denudata is close to Fargesia nitida.     

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 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">Naemorhedus griseus</Emphasis> (Artiodactyla: Bovidae) and its phylogenetic implications

The Chinese goral (Naemorhedus griseus) has been categorized as vulnerable species by the World Conservation Union and listed as a Class I protected species in China for its over-hunting for meat, fur and medicines. In order to provide efficient genetic resources for the conservation and preservation of the endangered species, the complete mitochondrial genome of this species was determined and analyzed. It is 16,446 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, one origin of replication on the light-strand (O_L) and a control region. Most of the PCGs use ATG as the common initiation codon, while ND2, ATP6 and ND3 use ATA and ND5 uses ATC as the initiation codon. Most of them have TAA or TAG as the stop codon, except COIII, ND3 and ND4 use an incomplete stop codon T or TA and Cyt b uses an uncommon AGA. An ML tree involving 19 Caprinae species was constructed, which will contribute to phylogenetic studies of Caprinae and further conservation strategies for the Chinese goral.     

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.