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.     

The complete chloroplast genome of <Emphasis Type="Italic">Lilium taliense</Emphasis>, an endangered species endemic to China

The complete chloroplast genome of Lilium taliense which is a rare and endangered species native to China was determined in this study. The chloroplast genome is 153,055 bp long and consists of a pair of inverted repeat regions (26,543 bp), one large single copy region (82,458 bp), and one small single copy region (17,511 bp). The genome contains 132 genes, including 86 protein-coding genes, 38 transfer RNA gens and eight ribosomal RNA genes. In addition, 188 simple sequence repeats (SSRs) were identified in the L. taliense chloroplast genome. Maximum likelihood phylogenetic analysis with the reported chloroplast genomes revealed that L. taliense was closely related to L. fargesii and L. superbum.     

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 <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.     

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.     

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 of <Emphasis Type="Italic">Caryopteris mongholica</Emphasis> and phylogenetic implications in Lamiaceae

Caryopteris mongholica, which belongs to the mint subfamily Ajugoideae (Lamiaceae), has high ornamental and medicinal value. Previously published phylogenetic studies strongly support the monophyly of Lamiaceae, but some major relationships within the family still remain unclear. In this study, we report the chloroplast (cp) genome of C. mongholica and take advantage of several previously reported cp genomes from related taxa to infer phylogeny in Lamiaceae. The cp genome of C. mongholica is 151,707 bp in length, comprising a pair of inverted repeat regions (25,634 bp) separated by a large single-copy region (83,203 bp) and a small single-copy region (17,236 bp). The genome encodes 114 unique genes consisting of 80 different protein-coding genes, 30 transfer RNA and four ribosomal RNA genes, with 19 duplicated genes in the inverted repeats. The phylogeny reconstruction based on the complete genome sequences of 20 mint species strongly supports the placement of Ajugoideae as sister to (Lamioideae?+?Scutellarioideae), as well as the sister relationship between Premnoideae and Tectona.     

The complete chloroplast genome sequence of <Emphasis Type="Italic">Phyllostachys heterocycla</Emphasis>, a fast-growing non-timber bamboo (Poaceae: Bambusoideae)

Moso bamboo (Phyllostachys heterocycla var. pubescens) is one of the fastest growing lignocellulose abundant plants on Earth. Here, we report the complete nucleotide sequence of the Phyllostachys heterocycla chloroplast genome using next-generation sequencing technology. The genome size is 139,682 bp in length, containing a pair of inverted repeats (IRs) of 21,797 bp separated by a large single-copy region and a small single-copy region of 83,217 and 12,871 bp, respectively. A total of 130 genes were annotated, of which 111 were unigenes (77 protein-coding genes, 4 rRNA genes, and 30 tRNA genes) and 19 are duplicated in the IRs. A phylogenomic analysis showed that P. heterocycla is closely related to P. edulis that belongs to the same genus Phyllostachys of Subfamily Bambusoideae in the grass family. The newly sequenced complete chloroplast genome of P. heterocycla will enhance our knowledge of the evolution and diversification of the bamboo species and potentially help to conserve the bamboo biodiversity.     

Characterization of the complete chloroplast genome of the golden crane butterfly, <Emphasis Type="Italic">Euonymus schensianus</Emphasis> (Celastraceae)

The golden crane butterfly, Euonymus schensianus, is an important forest tree species with dramatically fragmented and declined populations. Here we characterized the complete chloroplast (cp) genome of this plant using Illumina pair-end sequencing data. The E. schensianus cp genome was 157,702 bp in length, containing a pair of inverted repeats (IRs) of 26,574 bp which separated a large single copy region (LSC) of 86,026 bp and a small single copy region (SSC) of 18,528 bp. The genome contained 131 genes, including 86 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Most of genes occurred as single-copy in the LSC or SSC, while 18 gene species had two copies in the IRs. The GC content of E. schensianus cp genome, LSC, SSC and IR regions were 37.2, 35.0, 31.8 and 42.5%, respectively. Further, phylogenomic analysis strongly supported the close relationship of E. schensianus and E. japonicus in Celastrales.     

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 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 Purple Feathergrass <Emphasis Type="Italic">Stipa purpurea</Emphasis> (Poales: Poaceae)

The complete chloroplast genome of the Purple Feathergrass Stipa purpurea (Poales: Poaceae: Stipeae) has been assembled from the whole-genome Illumina sequencing data. The circular genome is 137,370 bp in size, and comprises a pair of inverted repeat regions of 21,663 bp each, a large single-copy region of 81,202 bp and a small single-copy region of 12,842 bp. It harbors 130 genes, including 84 protein-coding genes (78 PCG species), eight ribosomal RNA genes (four rRNA species) and 38 transfer RNA genes (30 tRNA species). The base composition is asymmetric (30.7 % A, 19.3 % C, 19.5 % G, 30.5 % T) with an overall A+T content of 61.2 %. Phylogenetic analysis indicated that S. purpurea is more phylogenetically related to its contribal counterparts than to those from other tribes, except for the case of Ampelodesmos mauritanicus (tribe Ampelodesmeae) probably due to its identity as an ancient hybrid between parents from Stipeae and Phaenospermateae.     

Characterization of the complete chloroplast genome of an endangered species dwarf birch (<Emphasis Type="Italic">Betula nana</Emphasis> L.)

Betula nana L. is a deciduous shrub belonging to the Betulaceae family, which is recorded as endangered species in the Red List. The complete chloroplast genome of B. nana was reported in this study. The size of the B. nana chloroplast genome is 160,579 bp, with an average GC content of 36.1?%. This circular molecule has a typical quadripartite structure containing a large single copy region of 89,492 bp, a small single copy region of 19,343 bp, and two inverted repeat regions of 25,872 bp. It encodes an identical set of 114 unique genes, including 79 protein coding, 31 transfer RNA and 4 ribosomal RNA genes. The total of 20 genes were duplicated in the inverted repeats. A maximum likelihood phylogenetic tree supported that the chloroplast genome of B. nana is closely related to that of Ostrya rehderiana.     

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 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.     

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.     

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.     

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 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.     

Characterization of the complete chloroplast genome of <Emphasis Type="Italic">Koelreuteria paniculata</Emphasis> (Sapindaceae)

In this study, the complete chloroplast (cp) genome sequence of Koelreuteria paniculata was determined using next-generation sequencing. The entire cp genome was determined to be 163,258 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 90,236 of 18,268 bp, respectively, which were separated by a pair of 27,377 bp inverted repeat (IR) regions. The genome contained 131 genes, including 85 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene. The overall GC content of the K. paniculata cp genome was 37.3%, whereas the corresponding values for the LSC, SSC, and IR regions were 35.3, 31.3, and 42.6%, respectively. The phylogenetic analysis demonstrated a close relationship between K. paniculata and Sapindus mukorossi.