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 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 whole chloroplast genome of a rare and endangered species <Emphasis Type="Italic">Aconitum reclinatum</Emphasis> (Ranunculaceae) in the United States

The complete chloroplast genome (cp genome) of Aconitum reclinatum (Ranunculaceae) was characterized through Illumina paired-end sequencing. The cp genome is circle and 157,354 bp in length, consisting of a pair of 26,061 bp inverted repeat regions (IRs) which are separated by a large single copy region (LSC) of 88,269 bp and a small single copy region (SSC) of 16,963 bp. The cp genome contains 135 genes, including 87 protein-coding genes (PCGs), 40 tRNA genes (tRNA) and eight ribosomal RNA genes (rRNA). Among these, seven PCGs, eight tRNA and four rRNA are duplicated. The overall GC content of the A. reclinatum cp genome is 38.00%, while the corresponding values of the LSC, SSC and IRs regions are 36.00, 32.80 and 43.00%, respectively. The phylogenetic analysis suggested that A. reclinatum is closely related to A. barbatum var. hispidum and A. barbatum var. puberulum with high bootstrap support of 100%.     

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">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">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">Xanthoceras sorbifolium</Emphasis>, an endangered oil tree

Xanthoceras sorbifolium is an important biodiesel tree in northern China, but its natural population is now very fragmented and in decline. Here we assembled and characterized the complete chloroplast (cp) genome of X. sorbifolium using Illumina pair-end sequencing data. The X. sorbifolium cp genome was 161,231 bp in size, containing a large single copy region (LSC) of 85,299 bp and a small single copy region (SSC) of 18,692 bp separated by a pair of inverted repeats (IRs) of 28,620 bp. The genome had 132 genes, including 86 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the X. sorbifolium cp genome was 37.7%, with the corresponding values of LSC, SSC and IR regions being 36.0, 31.7 and 42.3%, respectively. The phylogenomic analysis strongly supported that X. sorbifolium diverged firstly in Sapindaceae. This complete cp genome will be useful for further studies of this endangered plant.     

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.     

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.     

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.     

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.     

Characterization of the whole chloroplast genome sequence of <Emphasis Type="Italic">Acer davidii</Emphasis> Franch (Aceraceae)

The whole chloroplast genome (cp DNA) sequence of Acer davidii Franch has been characterized from Illumina pair-end sequencing. The complete cpDNA was 157,044 bp in length, containing a large single copy region (LSC) of 85,410 bp and a small single copy region (SSC) of 18,112 bp, which were separated by a pair of 26,761 bp inverted repeat regions (IRs). The cpDNA contained 134 genes, including 86 protein-coding genes (78 PCG species), forty tRNA genes (31 tRNA species) and eight ribosomal RNA genes (four rRNA species). The most of gene species occur as a single copy, while 21 gene species occur in double copies. The overall AT content of A. davidii cpDNA is 62.1 %, while the corresponding values of the LSC, SSC and IR regions are 63.9, 67.7 and 57.3 %, respectively. The phylogenetic analysis suggested that the sampled Acer species formed a monophyletic clade, and the cpDNA of A. davidii is closely related to that of congeneric A. morrisonense.     

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.     

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 genome of vulnerable <Emphasis Type="Italic">Aesculus wangii</Emphasis> (<Emphasis Type="Italic">Sapindaceae</Emphasis>), a narrowly endemic tree in Yunnan,China

In this study, we assembled the complete chloroplast (cp) genome of Aesculus wangii Hu (Sapindaceae), a rare and vulnerable deciduous tree native to Southeast Yunnan of China. The cp genome of A. wangii was 155,871 bp in length and contained a pair of inverted repeat (IR, 26,390 bp) regions, which were separated by the small single copy (SSC, 18,209 bp) and the large single copy (LSC, 84,882 bp) regions. The cp genome encoded 135 genes including 84 protein-coding genes, 40 tRNA genes, and eight rRNA ribosomal genes. The overall AT content of A. wangii cp genome is 62.0%. The maximum likelihood phylogenetic analysis revealed that A. wangii is sister to maples of tribe Acereae and the Acereae-Aesculus clade is sister to all other sampled Sapindaceae. The cp genome of A. wangii will be useful for future studies on the conservation, taxonomy, and phylogeny of the genus Aesculus.     

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.     

The complete chloroplast genome of <Emphasis Type="Italic">Littledalea przevalskii</Emphasis> Tzvelev (Poaceae: Bromeae), an endemic of the Qinghai–Tibetan Plateau

Littledalea przevalskii is an alpine endemic species distributed in the Qinghai–Tibetan Plateau. In this study, we performed the sequencing and analysis of the complete chloroplast (cp) genome of L. przevalskii on the Illumina HiSeq platform. The cp genome sequence was 136,862 bp in length with high A?+?T content of 61.5%, and had a standard quadripartite structure with the large (LSC, 81,053 bp) and small (SSC, 12,857 bp) single copy regions separated by two copies of an inverted repeat region (IRs, 21,476 bp each). It encoded 143 genes including 97 protein-coding genes, 38 tRNAs genes and eight rRNAs genes. The majority of genes occurred within the single copy regions. The gene type, number and A?+?T content were similar with L. racemosa reported. The maximum likelihood phylogenetic analysis based on 38 cp genomes suggested that L. przevalskii is sister to the clade of species in Triticeae of Pooideae.     

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.     

The complete chloroplast genome of threatened <Emphasis Type="Italic">Magnolia laevifolia</Emphasis>, a rare ornamental shrub with strong aromatic flowers

In this study, we assembled the complete chloroplast (cp) genome of Magnolia laevifolia Y.W. Law & Y. F. Figlar endemic to Yunnan, China. The species is a rare and threatened evergreen shrub with great important for horticulture because of its attractive strong aromatic flowers. The cp genome of M. laevifolia was 160,120 bp in length and contained a pair of inverted repeat (IR, 26,588 bp) regions, which were separated by the small single copy (SSC, 18,799 bp) and the large single copy (LSC, 88,145 bp) regions. The cp genome encoded 131 genes including 86 protein-coding genes, 37 tRNA genes, and eight rRNA ribosomal genes. The overall AT content of M. laevifolia cp genome is 60.8%. The maximum likelihood phylogenetic analysis revealed that M. laevifolia was closely related to M. odora. This result will be helpful for the conservation, taxonomy, and phylogeny programs of the genus Magnolia.     

The complete chloroplast genome of endangered <Emphasis Type="Italic">Manglietia insignis</Emphasis>, a rare landscaping tree with red lotus-like flowers

Manglietia insignis, a rare and endangered evergreen tree endemic to South Asia, is of great importance for landscaping because of its graceful appearance and red lotus-like flowers. In this study, the complete chloroplast (cp) genome of M. insignis was assembled based on the Illumina sequences. The cp genome of M. insignis was 160,117 bp in length and contained a pair of inverted regions (IR, 26,575 bp) which were separated by the small single copy (SSC, 18,660 bp) and the large single copy (LSC, 88,307 bp) regions. It encoded 131 genes including 86 protein-coding genes, 37 tRNA genes, and eight rRNA ribosomal genes. The overall AT content of M. insignis cp genome is 60.8%. The maximum likelihood phylogenetic analysis revealed that M. insignis was closely related to Michelia odora. This result will be helpful for the conservation, taxonomy, and phylogeny programs of the genus Manglietia.