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 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 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.     

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.     

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.     

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 <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 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 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.     

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">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 chloroplast genome of <Emphasis Type="Italic">Ranzania japonica</Emphasis>, an endangered species native to Japan

Ranzania japonica, which has high ornamental value, is an endangered species native to Japan. To better understand its genetic background, here we report the first chloroplast (cp) genome of R. japonica. The complete chloroplast genome is 169,224 bp in length and shares the common feature of comprising two copies of inverted repeats (IRs 37,924 bp) that divide the genome into two single-copy (LSC 74,477 bp and SSC 18,899 bp) regions. The genome contains 113 unique genes, including 68 protein coding gene, 37 tRNA genes, and eight rRNA genes. By comparing cp genomes of R. japonica, Mahonia bealei, Berberis amurensis and B. koreana, an expansion of IRs at their junction with LSC was revealed in Ranzania.     

The complete chloroplast genome of the dove tree <Emphasis Type="Italic">Davidia involucrata</Emphasis> (Nyssaceae), a relict species endemic to China

The dove tree, Davidia involucrate, with its distinguishing pair of white bracts, is endemic to China. Here, we reported the complete chloroplast (cp) genome sequence and the cp genomic features of D. involucrata. The D. involucrata cp genome was 169,196 bp long, with 129 genes comprising 83 protein-coding genes (PCG), 40 tRNA genes, and six rRNA genes. The majority of the gene species occurred as a single-copy, while 18 gene species occurred in double copies, including six PCG species (ndhB, rpl2, rpl23, rps7, rps15, and ycf2), eight tRNA species (trnH-GTG, trnL-CAA, trnI-CAT, trnV-GAC, trnL-GAV, trnA-UGC, trnN-GTT, and trnR-ACG) and all four rRNA species (rrn4.5, rrn5, rrn16, and rrn23). A neighbor-joining (NJ) phylogenetic tree was reconstructed with sequences of complete cp, revealing that D. involucrata belongs to the asterids. The complete cp genome of D. involucrata will be useful for further investigations and the conservation of this endemic relict woody plant.     

Characterization of the complete chloroplast genome of <Emphasis Type="Italic">Oxyria sinensis</Emphasis>

In this study, the whole chloroplast genome of Oxyria sinensis is determined by using re-sequencing reads and de novo assembly. The genome size of O. sinensis is 160,404 bp in length. The genome comprises a large single copy region of 83.5 K bp and a small single copy region of 12.8 K bp, which were separated by a pair of 30,885 bp inverted repeat regions. The complete chloroplast genome contained 131 genes, including 83 protein-coding genes (83 PCG species), 37 tRNA genes (28 tRNA species), 8 ribosomal RNA genes (4 rRNA species) and 3 pseudogenes. Based on Bayesian dating analysis, O. sinensis diverged from its relative species Rheum palmtuam 27 million years ago. The whole chloroplast genome is useful for plant evolutionary and genomic studies within this species endemic to Himalaya-Hengduan Mountians, which give important insight into the conservation and maintenance of genetic resource in a global biodiversity “hotspot” region.     

The complete chloroplast genome of <Emphasis Type="Italic">Populus rotundifolia</Emphasis> (Salicaceae)

Populus rotundifolia, which is an endemic of the Himilayas and adjacent regions, is the species that occupy the highest habitat in the Populus genus. In this study, we assembled its complete chloroplast genome. The total genome size of P. rotundifolia is 155,373 bp in length, containing a large single-copy region of 84,603 bp, a small single-copy region of 16,806 bp and a pair of inverted repeat regions of 26,982 bp. We annotated 131 genes in the genome, including 86 protein-coding genes (78 PCG species), 8 rRNA genes (4 rRNA species), and 37 tRNA genes (30 tRNA species). Among these, 19 genes were duplicated in the inverted repeats. Phylogenetic analysis suggested that, among all reported poplar chloroplast genomes, P. rotundifolia is most closely related to the common aspen (P. tremula).     

Characterization of the complete chloroplast genome sequence of <Emphasis Type="Italic">Cardamine macrophylla</Emphasis> (Brassicaceae)

Cardamine macrophylla is a perennial herb with short-lived seeds. Here, the complete chloroplast genome (plastome) of C.macrophylla was obtained by Illumina sequencing technology. The plastome is 155,393 bp in length, including a large single copy (LSC) region of 84,492 bp, a small single copy (SSC) region of 17,957 bp and a pair of inverted repeats (IRs) of 26,472 bp. The genome contained 131 genes, including 85 protein-coding genes (78 PCG species), 37 tRNA genes (30 tRNA species), eight rRNA genes (four rRNA species) and one pseudogene. Among these genes, 15 genes harbored a single intron and three genes harbored two introns. Seven tRNA, five protein-coding and all four rRNA genes were completely duplicated in the IR regions. The GC content of C. macrophylla plastome is 36.4%. A total of 26,470 codons were detected in 85 protein-coding genes of C. macrophylla plastome. Phylogenetic analysis demonstrated that the all Cardamine species formed a monophyletic clade, and C. macrophylla was closely related to C. impatiens.     

Characterization of the complete plastid genome of <Emphasis Type="Italic">Quercus tarokoensis</Emphasis>

Quercus tarokoensis is an endemic species to Taiwan, China. The complete plastid genome of Q. tarokoensis was assembled from Illumina pair-end sequence reads. The whole plastome was 161,355 bp in length and presented a quadripartite structure consisting of two copies of inverted repeat (IR) regions (25,860) separated by a large single copy region (90,602 bp) and a small single copy region (19,033 bp). The plastome of Q. tarokoensis encoded a total of 134 genes, including 86 protein-coding genes (79 PCG species), 40 tRNA genes (33 tRNA species), and 8 rRNA genes (4 rRNA species). The overall GC content of Q. tarokoensis plastome is 36.8%. A maximum likelihood phylogenetic analysis based on 33 complete plastomes revealed that Q. tarokoensis was collectively sister to a clade of (Quercus variabilis, (Quercus dolicholepis, Quercus baronii)) with high support.     

The complete chloroplast genome of <Emphasis Type="Italic">Lagerstroemia intermedia</Emphasis> (Lythraceae), a threatened species endemic to southwestern Yunnan province,China

Lagerstroemia intermedia: is a threatened species endemic to southwestern Yunnan province, China. It has high-value light purple-blue petals. Not much is known about the ecological and genetic characteristics of the species. Chloroplast genome sequencing is an efficient tool for understanding enigmatic and basal phylogenetic relationships at different taxonomic levels. Here, we report the chloroplast genome of L. intermedia. The L. intermedia chloroplast genome is 152,330 bp long, with 129 coding genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among the 129 genes, 6 coding genes (ndhB, rpl2, rpl23, rps7, rps12, and ycf2), 7 tRNA genes (trnA-UGC, trnI-CAU, trnI-GAU, trnL-CAA, trnN-GUU, trnR-ACG, and trnV-GAC) and 4 rRNA genes (rrn4.5, rrn5, rrn16, and rrn23) occur in the two IR regions. A neighbour-joining (NJ) phylogenetic tree was constructed to show the relationships between species in Myrtales. This complete chloroplast genome of L. intermedia will supply more genetic information about the Lagerstroemia chloroplast and will be useful for further research and conservation of this endemic endangered plant.