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.     

The complete chloroplast genome sequence of <Emphasis Type="Italic">Lilium fargesii</Emphasis> (<Emphasis Type="Italic">Lilium</Emphasis>, Liliaceae)

Lilium fargesii Franchet is an endangered species endemic to China. In this study, the complete chloroplast genome has been generated from the Next Generation Sequencing. The whole genome is 153,235 bp in length, and includes one large single copy region of 82,217 bp, one small single copy region of 17,038 bp and a pair of inverted repeat region of 26,990 bp. It contains 132 genes, comprising 86 protein-coding genes (78 PCG species), 38 transfer RNA (30 tRNA species) and eight ribosomal RNA genes (four rRNA species). In the maximum likelihood tree, all species of Lilium were clustered into two monophyletic groups with 100 % bootstrap value.     

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%.     

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 sequence of Chinese wild grape <Emphasis Type="Italic">Vitis amurensis</Emphasis> (Vitaceae: <Emphasis Type="Italic">Vitis</Emphasis> L.)

Vitis amurensis is a species of wild grape with high ecological, medicinal, and economic values. Here, the complete chloroplast genome of this plant was assembled from whole-genome high-throughput sequencing data. The circular double-stranded DNA molecule is 160,953 bp in size, including a pair of inverted repeats (26,354 bp each) separated by large (89,187 bp) and small (19,058 bp) single-copy regions. The chloroplast genome contains 133 genes, including 88 protein-coding genes (80 PCG species), 37 transfer RNA genes (29 tRNA species) and eight ribosomal RNA genes (four rRNA species), 20 of which are duplicated, including eight protein-coding, eight tRNA, and four rRNA genes. The base composition is asymmetric (30.93?% A, 19.07?% C, 18.33?% G, 31.67?% T) with an overall A?+?T content of 62.60?%. A phylogenetic analysis based on complete chloroplast genome sequences showed that V. amurensis is closely related to V. vinifera, V. aestivalis, and V. rotundifolia.     

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 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 of <Emphasis Type="Italic">Populus ilicifolia</Emphasis>

The whole chloroplast (cp) genome sequence of Populus ilicifolia has been characterized from Illumina pair-end sequencing. The complete cp genome was 158,017 bp in length, containing a large single copy region (LSC) of 85,926 bp and a small single copy region (SSC) of 16,533 bp, which were separated by a pair of 27,780 and 27,778 bp inverted repeat regions (IRs). The genome contained 126 genes, including 82 protein-coding genes (75 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. The overall AT content of P. ilicifolia cp genome is 63.5 %, while the corresponding values of the LSC, SSC and IR regions are 65.7, 69.4 and 58.2 %, respectively. Further, phylogenetic analysis suggested that P. ilicifolia is closely related to P. euphratica.     

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.     

Characterization of the complete chloroplast genome of <Emphasis Type="Italic">Camptotheca acuminata</Emphasis>

The whole chloroplast (cp) genome sequence of Camptotheca acuminata has been characterized from Illumina pair-end sequencing. The complete cp genome was 162,382 bp in length, containing a large single copy region (LSC) of 89,493 bp and a small single copy region (SSC) of 16,540 bp, which were separated by two inverted repeat (IR) regions of 56,648 bp. The genome contained 129 genes, including 83 protein-coding genes, 38 tRNA genes and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 18 gene species occur in double copies. The overall GC content of C. acuminata cp genome is 38%, while the corresponding values of the LSC, SSC and IR regions are 36.2, 32.7 and 42.3%, respectively. Further, phylogenetic analysis suggested that C. acuminata is closely related to the species of Davidia involucrata.     

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.     

Characterization of the complete chloroplast genome of <Emphasis Type="Italic">Idesia polycarpa</Emphasis>

The whole chloroplast (cp) genome sequence of Idesia polycarpa has been characterized from Illumina pair-end sequencing. The complete cp genome was 157,017 bp in length, containing a large single copy region (LSC) of 84,787 bp and a small single copy region (SSC) of 16,512 bp, which were separated by a pair of 27,859 bp inverted repeat regions (IRs). The genome contained 130 genes, including 86 protein-coding genes (77 PCG species), 36 tRNA genes (29 tRNA species) and 8 ribosomal RNA genes (4 rRNA species). The most of gene species occur as a single copy, while 20 gene species occur in double copies. The overall AT content of I. polycarpa cp genome is 63.3 %, while the corresponding values of the LSC, SSC and IR regions are 65.5, 69.4 and 58.1 %, respectively. Further, phylogenetic analysis suggested that I. polycarpa is closely related to the genera of Salix and Populus.     

Characterization of the complete chloroplast genome of <Emphasis Type="Italic">Cycas panzhihuaensis</Emphasis>

The whole chloroplast (cp) genome sequence of Cycas panzhihuaensis has been characterized from Illumina pair-end sequencing. The complete cp genome was 162,470 bp in length, containing a large single copy region (LSC) of 88,932 bp and a small single copy region (SSC) of 23,448 bp, which were separated by a pair of 25,045 bp inverted repeat regions (IRs). The genome contained 156 genes, including 109 protein-coding genes (98 PCG species), 39 tRNA genes (32 tRNA species) and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 22 gene species occur in double copies. The overall AT content of C. panzhihuaensis cp genome is 60.6?%, while the corresponding values of the LSC, SSC and IR regions are 61.3, 63.5 and 58.0?%, respectively. Further, phylogenetic analysis suggested that C. panzhihuaensis is closely related to the species of C. revoluta.     

The complete chloroplast genome of <Emphasis Type="Italic">Lilium cernuum</Emphasis>: genome structure and evolution

Lilium cernuum is endangered and was listed in the category of key protected wild plants in China. In this study, we report the complete chloroplast genome of L. cernuum using Illumina paired-end sequencing. The entire chloroplast genome maps as a circular molecule of 152,604 bp built with a quadripartite organization: two inverted repeats (IRs) of 26,481 bp separated by a large single copy (LSC) sequence of 82,058 bp and a small single copy (SSC) sequence of 17,584 bp. The chloroplast genome contains the conservative structure present in most Liliaceae chloroplasts composing of 79 protein-coding genes, 30 tRNAs and 4 rRNAs. Among these genes, 15 harbor a single intron, and 2 contain a couple of introns. A maximum likelihood phylogenomic analysis showed that L. cernuum was closely related to L. tsingtauense and L. hansonii that belonged to the family Liliaceae.     

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.     

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

Lepidium meyenii (Maca), is an important medical plant, only located in a rather restricted ecological zone in the Andes at a high altitude. Here, the complete chloroplast (cp) genome of L. meyenii (Brassicaceae) was assembled based on the Illumina sequencing reads. The complete cp genome of L. meyenii was 154,624 bp in length and contained two short inverted repeat (IRa and IRb) regions (26,330 bp) which were separated by a small single copy (SSC) region (17,963 bp) and a large single copy (LSC) region (83,998 bp). The L. meyenii chloroplast encoded 130 genes including 85 protein-coding genes (80 PCG species), 37 tRNAs (30 tRNA species), eight rRNA operons (four rRNA species). The overall GC content of L. meyenii chloroplast genome is 36.4% and the corresponding values in LSC, SSC and IR regions are 34.2%, 29.3% and 42.4%, respectively. The maximum likelihood (ML) phylogenetic analysis based on 18 chloroplast genomes demonstrated a close phylogenetic relationship between L. meyenii and L. virginicum.     

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 sequence of the wild Chinese chestnut (<Emphasis Type="Italic">Castanea mollissima</Emphasis>)

The complete chloroplast genome sequence of a wild chestnut species, Castanea mollissima Blume, was determined and mapped based on Illumina sequencing data. The complete chloroplast genome is 160,869 bp and comprises a pair of inverted repeat regions of 25,701 bp each, a large single-copy region of 90,497 bp, and a small single-copy region of 18,970 bp. The genome harbors 131 genes, including 86 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analysis based on chloroplast genomes indicates that wild C. mollissima is closely related to Castanopsis echinocarpa and dissimilar to cultivated C. mollissima.     

Characterization of the complete chloroplast genome sequence of <Emphasis Type="Italic">Lysionotus pauciflorus</Emphasis> (Gesneriaceae)

Lysionotus pauciflorus, an evergreen subshrub with high medicinal and ecological values, mainly distributed in subtropical montane regions of China. In this study, we reported its complete chloroplast (cp) genome from Next Generation Sequencing data. The whole genome was 153,856 bp in length, containing a pair of inverted repeat region (IRs) of 25,465 bp, a large single copy (LSC) region of 85,087 bp and a small single copy (SSC) region of 17,839. The genome contained 133 genes, including 88 protein-coding genes (80 PCG species), 37 tRNA genes (28 tRNA species) and 8 rRNA genes (4 rRNA species). Among these genes, 12 genes harbored a single intron and 3 genes harbored 2 introns. The majority of gene species occurred as a single copy and one tRNA gene occurred as three copies. The overall AT content of L. pauciflorus cp genome is 62.5%. A maximum parsimony (MP) phylogenetic analysis demonstrated a close relationship between L. pauciflorus and Boea hygrometrica.     

The complete chloroplast genome sequence of wild service tree <Emphasis Type="Italic">Sorbus torminalis</Emphasis> (L.) Crantz

Sorbus torminalis is widely distributed tree species across Europe which shows interesting features from the genetic point of view and has high ecological values. Based on the whole genomic DNA we have assembled the complete 160,390 bp circular chloroplast genome of the species. The nucleotide share: 31.35% A, 18.61% C, 17.87% G, 32.12% T and 36.48% GC content is similar to those found in the Pyrus and Malus species. The genome is a standard quadripartite structure build from four subunits: large (88,029 bp) and small (19,547 bp) single copy unit and two inverted repeats (26,407 bp each). The genome contains 127 genes including: 83 protein-coding genes (77 unique), 36 tRNA genes (29 unique), and 8 rRNA genes (4 unique). Phylogenetic position of S. torminalis based on the whole chloroplast genome indicated that the species is phylogenetically closer to genus Malus than Pyrus.