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.     

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 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.     

The complete chloroplast genome of <Emphasis Type="Italic">Pleione bulbocodioides</Emphasis> (Orchidaceae)

Pleione bulbocodioides is an endangered terrestrial orchid with significant medicinal and ornamental values. Here, we report on the first complete chloroplast (cp) genome of P. bulbocodioides. The circular genome was 159,269 bp in length and consisted of a pair of inverted repeats (IR 26,716 bp), which were separated by a large single-copy region (LSC 87,125 bp) and a small single-copy region (SSC 18,712 bp). It contained 115 unique genes, including 81 protein-coding genes, 30 tRNAs and 4 rRNAs. The maximum likelihood phylogenetic analysis indicated that P. bulbocodioides was closely related to the genera Cymbidium and Bletilla. The complete cp genome will useful for further studies of the endangered orchid.     

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 chloroplast genome of the Chinese yew <Emphasis Type="Italic">Taxus chinensis</Emphasis> (Taxaceae), an endangered and medicinally important tree species in China

The Chinese yew Taxus chinensis (Taxaceae) is an endangered tree species native to China, and possesses high medicinal values. To facilitate its conservation genetics studies, its complete chloroplast genome was characterized using Illumina high-throughput sequencing technology in this study. The circular genome is 127,743 bp in length with an asymmetric base composition (32.6% A, 17.7% C, 17.0% G and 32.7% T). It harbors a total of 113 genes, including 82 protein-coding genes (PCGs), 27 tRNAs and four rRNAs. Gene duplication was detected for a couple of genes (trnG-UCC and trnQ-UUG). Besides, seven genes (atpF, ndhA, ndhB, ropC1, rpl2, trnK-UUU and trnL-UAA) harbor a single intron, and another gene (ycf3) possesses a couple of introns. Phylogenetic analysis suggests that T. chinensis and T. mairei are closely related to each other.     

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 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.     

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 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">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 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 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.     

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 chloroplast genome of an endangered species dwarf birch (<Emphasis Type="Italic">Betula nana</Emphasis> L.)

Betula nana L. is a deciduous shrub belonging to the Betulaceae family, which is recorded as endangered species in the Red List. The complete chloroplast genome of B. nana was reported in this study. The size of the B. nana chloroplast genome is 160,579 bp, with an average GC content of 36.1?%. This circular molecule has a typical quadripartite structure containing a large single copy region of 89,492 bp, a small single copy region of 19,343 bp, and two inverted repeat regions of 25,872 bp. It encodes an identical set of 114 unique genes, including 79 protein coding, 31 transfer RNA and 4 ribosomal RNA genes. The total of 20 genes were duplicated in the inverted repeats. A maximum likelihood phylogenetic tree supported that the chloroplast genome of B. nana is closely related to that of Ostrya rehderiana.     

Chloroplast genome sequence of the endangered Orchidaceae species <Emphasis Type="Italic">Dendrobium hancockii</Emphasis>

Dendrobium hancockii Rolfe is an endangered Orchidaceae species distributed in Southwest China. Here, we reported the complete chloroplast (cp) genome sequence and the cp genomic features of D. hancockii. The genome was 152,159 bp long with 129 genes comprising 83 protein-coding genes, 40 tRNA genes, and 6 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. hancockii is closely related to that of other species in Dendrobium.     

The complete chloroplast genome of <Emphasis Type="Italic">Sinojackia xylocarpa</Emphasis> (Ericales: Styracaceae), an endangered plant species endemic to China

Sinojackia xylocarpa is an endangered plant species endemic to China. Here, we assembled its complete chloroplast genome from Illumina sequencing reads. The circular genome is 158,725 bp long, and contains a pair of inverted repeat regions of 26,090 bp each, a large single-copy region of 87,994 bp and a small single-copy region of 18,551 bp. It encodes 137 genes, including 91 protein-coding genes (82 PCG species), 38 tRNA genes (31 tRNA species) and eight rRNA genes (four rRNA species). Fifteen gene species harbor a single intron, while another two gene species have a couple of introns. The base composition is asymmetric (31.1% A, 19.0% C, 18.2% G & 31.7% T) with an overall A+T content of 62.8%. Phylogenetic analysis corroborated the traditional family-level taxonomy of the order Ericales, and suggested that S. xylocarpa is closely related to Alniphyllum eberhardtii and Bruinsmia polysperma within the family Styracaceae.     

Mitochondrial genome of the sand goby <Emphasis Type="Italic">Acentrogobius caninus</Emphasis> (<Emphasis Type="Italic">Acentrogobius</Emphasis>, Gobiidae)

In this study, we first determined and described the complete mitochondrial genome of Acentrogobius caninus, a member of the Family Gobiidae. The complete mitogenome sequence is 16,616 bp in length containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (OL). Phylogenetic analysis suggests that A. caninus boasts a close relationship with other two species of the genus Acentrogobius. Our results are expected to provide useful molecular information for species identification and further phylogenetic studies of the Gobiiformes family.     

The complete chloroplast genome of the endangered Chinese paperbark maple, <Emphasis Type="Italic">Acer griseum</Emphasis> (Sapindaceae)

The paperbark maple, Acer griseum, is an excellent landscape and ornamental species endemic to China, but its populations are now very fragmented and in decline. Here we characterized the complete chloroplast (cp) genome of A. griseum using genome skimming sequencing. The A. griseum cp genome was 156,857 bp in size, with a large single copy region of 85,227 bp and a small single copy region of 18,134 bp separated by a pair of inverted repeats of 26,748 bp. The genome encoded a total of 134 genes, of which 113 were unique, including 78 protein-coding genes, 4 rRNA genes and 31 tRNA genes. The overall GC content of the cp genome was 37.9%. The phylogenomic analysis strongly supported the monophyly of Acer and placed A. griseum as the basal-most species in Acer lineage. This complete cp genome will be useful for further studies of the endangered maple tree.