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.     

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 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 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.     

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.     

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.     

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 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.     

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 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 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.     

The complete mitochondrial genome of Myanmar warty newt <Emphasis Type="Italic">Tylototriton shanorum</Emphasis> (Salamandridae: <Emphasis Type="Italic">Tylototriton</Emphasis>)

Tylototriton shanorum, an endemic species of Myanmar, is threatened by illegal capture and environmental destruction. Here, the complete mitochondrial genome (mitogenome) of T. shanorum is described. The entire mitogenome sequence of T. shanorum is 17,096 bp long, containing 13 protein coding genes, two ribosomal RNA, 22 transfer RNA genes, one control region. In addition, two additional 3′ Cytb like sequences and two complete tRNA^Thr genes, one pseudo tRNA^Thr, and three noncoding sequences (NC1, NC1′ and NC2) were situated between Cytb and tRNA^Pro genes. The new complete mitogenome sequence of T. shanorum will be useful for conservation genetics, evolutionary biology, phylogeography, as well as phylogenetic relationships studies of this threatened species.     

The complete chloroplast genome sequence of the endangered Chinese endemic tree <Emphasis Type="Italic">Corylus fargesii</Emphasis>

The complete chloroplast genome sequence of a Betulaceae species, Corylus fargesii, was mapped and determined based on Illumina sequencing data. The complete chloroplast genome was shown to be 159,856 bp, and comprises a pair of inverted repeat regions of 26,602 bp each, a large single-copy region of 88,313 bp, and a small single-copy region of 18,339 bp. It harbors 131 genes, including 94 protein-coding genes, 8 ribosomal RNA genes, and 29 transfer RNA genes. The A+T content of the entire genome is 63.49%. Phylogenetic analysis based on chloroplast genomes indicates that C. fargesii is closely related to Ostrya rehderiana.     

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.     

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 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.     

Characterization of the complete chloroplast genome sequence of <Emphasis Type="Italic">Gynostemma compressum</Emphasis> (Cucurbitaceae), an endemic plant in China

Gynostemma compressum is an endemic herbaceous species distributed in northwestern China. Here, we report the complete chloroplast (cp) genome sequence of G. compressum using Illumina pair-end sequencing. The circular complete cp genome of G. compressum was 157,959 bp in length and contained a large single copy region (86,809 bp), a small single copy region (18,560 bp) and two short inverted repeat (IRa and IRb) regions (26,295 bp). The cp genome encodes 133 genes including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, 8 ribosomal RNA (rRNA) genes and 1 pseudogene. The maximum likelihood phylogenetic analysis showed that all the species of G. compressum formed a monophyletic clade and Gynostemma pentaphyllum was closely related to the genus Citrullus with strong bootstrap values.     

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 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 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.