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">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 of a vulnerable species <Emphasis Type="Italic">Champereia manillana</Emphasis> (Opiliaceae)

Champereia manillana (Bl.) Merr. is a vulnerable plant from the family Opiliaceae. The complete chloroplast genome (plastome) of Opiliaceae family was sequenced for the first time. The plastome of C. manillana was 147,461 bp in length. It was consisted of a large single copy (LSC) region (83,505 bp) and a small single copy (SSC) region (7,806 bp), which were separated by two inverted repeats (IRs, 28,075 bp). This plastome contained 101 different genes, including 67 protein-coding genes (PCGs), 30 tRNA genes and four rRNA genes. The overall GC content was 37.4%. Furthermore, phylogenetics analysis of 4 species in the Santalales was also conducted. The whole chloroplast genome of this species will be useful for the future plant evolutionary, phylogeny and genomic studies in the family Opiliaceae.     

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 chloroplast genome of <Emphasis Type="Italic">Anemoclema glaucifolium</Emphasis> (Ranunculaceae), a vulnerable and threatened species endemic to the Hengduan Mountains

Anemoclema glaucifolium is a vulnerable and threatened species endemic to the Hengduan Mountains. In this study, we reported a complete plastome of A. glaucifolium, which was de novo assembled using Next-generation Sequencing data. The plastome of A. glaucifolium was quadripartite and 160,400 bp in size, including two inverted repeats (31,256 bp for each) that separate one large single copy (80,251 bp) and one small single copy (17,637 bp) regions. The plastome contained 113 unique genes (with 80 protein-coding, 4 ribosomal RNA and 29 tRNA genes), and 24 entire genes, and partial rps12 (799 bp), rps36 (3 bp) and ycf1 (1097 bp) duplicated in the IR regions. The trnT-UGU tRNA was lost in A. glaucifolium. A maximum likelihood tree using the plastome data recovered A. glaucifolium sister to Clematis spp.     

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.     

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.     

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.     

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 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 <Emphasis Type="Italic">Cortusa matthioli</Emphasis> subsp. <Emphasis Type="Italic">pekinensis</Emphasis> (Primulaceae)

The complete chloroplast genome sequence of Cortusa matthioli subsp. pekinensis has been characterized using Illumina pair-end sequencing. The circular genome is 152,239 bp in length, containing a pair of inverted repeats (IRs) of 25,677 bp, separated by a large single copy (LSC) and a small single copy (SSC) region of 83,026 and 17,859 bp, respectively. It contains 131 genes, including 85 protein-coding genes (78 PCG species), 37 transfer RNA genes (28 tRNA species) and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 18 genes are duplicated. The nucleotide composition is asymmetric (31.1% A, 19.0% C, 18.2% G and 31.7% T) with an overall AT content of 62.8%. The corresponding values for the LSC, SSC and IR regions are 64.7, 69.8 and 57.2%, respectively. Phylogenetic analysis suggested that C. matthioli subsp. pekinensis is closely related to Primula species.     

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 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.     

The complete chloroplast genome sequence of an economically important plant, <Emphasis Type="Italic">Zanthoxylum bungeanum</Emphasis> (Rutaceae)

The complete chloroplast genome (cp genome) sequence of Zanthoxylum bungeanum has been assembled from Illumina pair-end sequencing. This genome was 158,401 bp in length, consisting of a pair of inverted repeats (IRs) of 27,446 bp which separated by a large single copy (LSC) region and a small single copy (SSC) region (85,898 and 17,611 bp in length, respectively). There are 132 genes, including 87 protein-coding genes (78 PCG species), 37 rRNA genes (30 rRNA species) and eight tRNA genes (four tRNA species) in the cp genome. The overall GC content of the whole genome is 38.6?%, while the corresponding values of the LSC, SSC, and IR regions are 36.87, 33.51 and 42.54?%, respectively. Phylogenetic analysis indicated that the cp genome of Z. bungeanum is closely related to that of congeneric Zanthoxylum piperitum.     

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">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).     

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.     

Characterization of the complete chloroplast genome of <Emphasis Type="Italic">Acer miaotaiense</Emphasis> (Sapindales: Aceraceae), a rare and vulnerable tree species endemic to China

Acer miaotaiense (Sapindales: Aceraceae) is a rare and vulnerable tree species endemic to China’s Mts. Qinling and Mts. Bashan. In this study, its complete chloroplast genome was assembled and characterized from the high-throughput Illumina sequencing data. The circular genome is 156,595 bp long, and contains a pair of inverted repeat (IR) regions of 26,100 bp each, separated by a large single-copy (LSC) region of 86,327 bp and a small single-copy (SSC) region of 18,068 bp. It harbors 137 genes, including 89 protein-coding genes (80 PCG species), 40 tRNA genes (30 tRNA species) and eight rRNA genes (four rRNA species). Its nucleotide composition is asymmetric (30.69 % A, 19.32 % C, 18.57 % G & 31.42 % T) with an overall A+T content of 62.12 %. Phylogenetic analysis indicates that A. miaotaiense is closely related to the congeneric A. morrisonense and A. buergerianum, and strongly supports that Acer and Dipteronia are sister taxa.     

Complete chloroplast genome sequences of <Emphasis Type="Italic">Rehmannia chingii</Emphasis>, an endemic and endangered herb

The complete chloroplast genome (cpDNA) sequence of a rare herbaceous species, Rehmannia chingii, was determined by Illumina pair-end sequencing in this study. The cpDNA is 154,055 bp long, and includes a pair of inverted repeat (IR) regions (25,707 bp), one large single copy (LSC) region (84,966 bp), and one small single copy (SSC) region (17,675 bp). The chloroplast genome contains 133 unique genes, including 88 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes, 17 of which are duplicated within the IRs, including 6 protein-coding genes, 7 tRNA genes, and 4 rRNA genes. The overall A+T content of the whole genome is 62.0 %, while the corresponding values of the LSC, SSC and IR regions are 64.0, 67.7 and 56.8 %, respectively. A phylogenetic analysis based on chloroplast genomes indicates that R. chingii is closely related to Lindenbergia philippensis.     

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.