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.     

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 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 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.     

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.     

Characterization of the whole chloroplast genome of a rare and endangered species <Emphasis Type="Italic">Aconitum reclinatum</Emphasis> (Ranunculaceae) in the United States

The complete chloroplast genome (cp genome) of Aconitum reclinatum (Ranunculaceae) was characterized through Illumina paired-end sequencing. The cp genome is circle and 157,354 bp in length, consisting of a pair of 26,061 bp inverted repeat regions (IRs) which are separated by a large single copy region (LSC) of 88,269 bp and a small single copy region (SSC) of 16,963 bp. The cp genome contains 135 genes, including 87 protein-coding genes (PCGs), 40 tRNA genes (tRNA) and eight ribosomal RNA genes (rRNA). Among these, seven PCGs, eight tRNA and four rRNA are duplicated. The overall GC content of the A. reclinatum cp genome is 38.00%, while the corresponding values of the LSC, SSC and IRs regions are 36.00, 32.80 and 43.00%, respectively. The phylogenetic analysis suggested that A. reclinatum is closely related to A. barbatum var. hispidum and A. barbatum var. puberulum with high bootstrap support of 100%.     

Characterization of the whole chloroplast genome of a rare candelabra primrose <Emphasis Type="Italic">Primula chrysochlora</Emphasis> (Primulaceae)

The complete chloroplast genome (plastome) of Primula chrysochlora is a circular molecule of 151,944 bp and contains a pair of inverted repeats of 25,460 bp which is separated by a large single copy region of 83,953 bp and a small single copy region of 17,801 bp. The plastome encodes 131 genes, including 86 protein-coding genes (PCGs), 37 tRNA genes and eight ribosomal RNA genes. Of these, seven PCGs, seven tRNA genes and four rRNA genes are duplicated in inverted repeats region and 18 genes harbor one or two introns. Based on the SSR analysis, a total of 36 microsatellites with a length of at least 10 bp were detected in the P. chrysochlora genome. A phylogenetic analysis showed that section Proliferae is a monophyletic with high support, and P. chrysochlora is sister to P. poissonii.     

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 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 of <Emphasis Type="Italic">Indirana semipalmata</Emphasis> (Amphibia: Anura)

The complete mitochondrial genome of the endemic frog Indirana semipalmata was sequenced. The mitogenome is a circular molecule of 17,052 bp in length, containing 13 protein-coding genes (PCGs), two ribosomal RNA (r RNA) genes, 21 transfer RNA (tRNA) genes and a non-coding D-loop region (control region). Its gene arrangements are similar to the typical neobatrachian-type except for the loss of tRNA ^Asn gene. Our data, which represent the first mitogenome for the genus, will serve as a reference for further studies on the conservation genetics of the endemic amphibian fauna of the Western Ghats.     

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 chloroplast genome of <Emphasis Type="Italic">Primula persimilis</Emphasis> (Primulaceae)

Using an Illumina platform, we sequenced the complete chloroplast genome of Primula persimilis. The total length of the plastome is 152,756 bp, and the overall AT content is 62.8%. A pair of 25,753 bp inverted repeats (IRs) is separated by large and small single copy regions (LSC and SSC) of 83,537 bp and 17,713 bp, respectively, and the AT contents of the LSC, SSC and IR are 64.8%, 69.4% and 57.2%, respectively. The plastome encodes 130 genes, including 85 protein-coding genes (PCGs), 37 tRNA genes and eight ribosomal RNA genes. Of these, seven PCGs, seven tRNA genes and four rRNA genes are duplicated in inverted repeats, and 18 genes harbor one or two introns. The phylogenetic analysis suggested that the Primula species formed a monophyletic clade, and P. persimilis is closely related to P. kwangtungensis.     

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 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 goby <Emphasis Type="Italic">Acentrogobius viridipunctatus</Emphasis>

In this study, we first determined and described the complete mitochondrial genome of Acentrogobius viridipunctatus, a member of the Family Gobiidae. The complete mitogenome sequence was 16,507 bp in length containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, one non-coding control region (D-loop). We identified genome-wide variations among mitochondrial genomes of different Acentrogobius species and found that the D-loop regions harbored most of the sequence variations, which would further provide valuable genome variation information for the conservation and utilization of A. viridipunctatus.     

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 chloroplast genomes of two <Emphasis Type="Italic">Sinalliaria</Emphasis> species and species delimitation (Brassicaceae)

Sinalliaria is a new small genus of Brassicaceae with only two species (S. grandifolia and S. limprichtiana) endemic in eastern China. Because of their limited distribution, identifying the species and sources of S. grandifolia and S. limprichtiana are important for biodiversity conservation and ecological preservation. The chloroplast genome sizes of Sinalliaria grandifolia and S. limprichtiana were 154,113 and 154,060 bp in length. Both genomes contain a large single copy region of 83 k bp and a small single copy region of 17 k bp, which were separated by a pair of 26,253 bp (S. grandifolia) and 26,275 bp (S. limprichtiana) inverted repeat regions. They both contained 129 genes, including 85 protein-coding genes (78 PCG species), seven ribosomal RNA genes (four rRNA species) and 37 tRNA genes (30 tRNA species). Phylogenetic analyses of five chloroplast genome sequences clustered two Sinalliaria grandifolia individuals and three S. limprichtiana individuals into two highly supported monophyletic groups. These complete chloroplast genomes laid a good foundation for biodiversity conservation, population genomics, molecular and ecological studies of Sinalliaria.     

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.     

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.