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.     

Characterization of the complete chloroplast genome of the relict Chinese false tupelo, <Emphasis Type="Italic">Camptotheca acuminata</Emphasis>

The Chinese false tupelo, Camptotheca acuminata, is a Tertiary relict species with dramatically fragmented and declined populations. Here we characterized the complete chloroplast (cp) genome of C. acuminata using Illumina pair-end sequencing data. The C. acuminata cp genome was 157,806 bp in length, containing a pair of inverted repeats (IRs) of 25,771 bp which separated a large single copy region (LSC) of 87,504 bp and a small single copy region (SSC) of 18,760 bp. The genome contained 134 genes, including 88 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Most of genes occurred as single-copy in the LSC or SSC, while 18 genes had two copies in the IRs. The GC content of C. acuminata cp genome is 37.8%. Phylogenomic analysis strongly supported the close relationship of C. acuminata and Davidia involucrata. This complete cp genome will be useful for further conservation genomics studies of C. acuminata.     

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 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.     

Characterization of the whole chloroplast genome of <Emphasis Type="Italic">Caragana microphylla</Emphasis> Lam (Fabaceae)

The complete chloroplast (cp) genome of Caragana microphylla (Fabaceae) has been characterized from Illumina pair-end sequencing. The whole cp genome is relatively short (130,029 bp) because it lacks an inverted repeat (IR) region. It comprises 110 genes, including four unique rRNAs, 30 tRNAs, and 76 protein-coding genes. Similar to other closely related plastomes, rpl22 and rps16 are absent. The overall GC content of C. microphylla cp genome is 34.3 %. The phylogenetic analysis suggested that C. microphylla is closely related to the genera of Astragalus.     

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.     

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 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.     

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.     

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.     

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 chloroplast genome sequence of <Emphasis Type="Italic">Sophora japonica</Emphasis> var. <Emphasis Type="Italic">violacea</Emphasis>: gene organization and genomic resources

Sophora japonica var. violacea is an important ornamental plant, but its wild populations are now in danger, and need urgent conservation. In the present study, we sequenced the complete chloroplast genome of S. japonica var. violacea and used these data to assess genomic resources. The S. japonica var. violacea chloroplast genome is 158,837 bp in length, and includes a pair of inverted repeats of 25,398 bp that are separated by small and large single copy regions of 19,058 and 88,983 bp, respectively. The chloroplast genome of S. japonica var. violacea encodes 112 different genes, including 78 protein-coding genes, 30 transfer RNAs (tRNA) and 4 ribosomal RNAs (rRNA). We identified a total of 171 simple sequence repeat markers in the chloroplast genome. A phylogenetic tree constructed based on 78 protein-coding genes of 42 angiosperms showed that the position of S. japonica var. violacea is on the base of Papilionoideae. Overall, the results of this study will contribute to better support of the evolution, molecular biology and genetic improvement of S. japonica var. violacea.     

The complete chloroplast genome of <Emphasis Type="Italic">Cupressus chengiana</Emphasis>

The whole chloroplast (cp) genome sequence of Cupressus chengiana has been characterized from Illumina pair-end sequencing. The circular genome is 128,151 bp in length with 115 single copy genes and two duplicated genes (trnl-CAU, trnQ-UUG). This genome contains 82 protein-coding genes, 31 tRNA genes and four ribosomal RNA genes (four rRNA species). In these genes, eight genes (atpF, ndhA, ndhB, rpoC1, petD, petB, rpl16 and rpl2) harbor a single intron and two genes (rps12 and ycf3) harbor two introns. This cp genome does not contain canonical IRs, and the overall GC content is 34.7%. Further, phylogenetic analysis suggested that C. chengiana is closely related to the species of C. gigantea.     

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.     

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 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 <Emphasis Type="Italic">Pinus uliginosa</Emphasis> (Neumann) from the <Emphasis Type="Italic">Pinus mugo</Emphasis> complex

Taxonomic status of endangered peat-bog pine, Pinus uliginosa (Neumann) classified within the Pinus mugo complex, still remains to be elucidated. Here we present a complete chloroplast genome of P. uliginosa, to aid resolve its complex systematical position. The total genome size was 119,877 bp in length and contained a total of 112 genes, including 73 protein-coding genes, 35 tRNAs, and four rRNAs. The most of genes occur as a single copy. Five tRNA genes were duplicated from two to four times. Eighteen genes contain one intron, with a single gene containing two introns. No large inverted repeats were identified. The overall G?+?C content of P. uliginosa chloroplast genome is 38.5%.     

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.     

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.     

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.