The complete chloroplast genome of <Emphasis Type="Italic">Sinowilsonia henryi</Emphasis> (Saxifragales: Hamamelidaceae), an endangered relict species

Sinowilsonia henryi Hemsl. (Hamamelidaceae) is a living fossil and an endangered relict species endemic to China. The complete chloroplast (cp) genome was sequenced and assembled by using Illumina paired-end reads data. The circular chloroplast genome consists of 158,741 bp, including a pair of inverted repeat (IR) regions of 26,233 bp each, a large single copy (LSC) region of 87,507 bp and a small single copy (SSC) region of 18,768 bp. The nucleotides consists of 30.5% A, 19.5% C, 18.7% G and 31.3% T. In total, the genome contained 135 genes, of which 87 are protein-coding genes (80 unique), 40 transfer RNAs (33 unique), and 8 ribosomal RNAs (4 unique). Phylogenetic analysis based on chloroplast genome sequences shows that S. henryi is closely related to Liquidambar formosana Hance.     

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 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.     

Development of chloroplast genomic resources for <Emphasis Type="Italic">Akebia quinata</Emphasis> (Lardizabalaceae)

Akebia quinata is an over-harvesting shrub which faces an urgent need for reasonable conservation strategies. In this study, we report its complete chloroplast genome by Illumina pair-end sequencing. The total cp genome size was 157,817 bp in length, containing a pair of inverted repeats of 26,143 bp, separated by large single copy and small single copy of 86,543 bp and 18,988 bp, respectively. The chloroplast genome of A. quinata encodes 113 different genes, including 79 protein-coding genes, 30 transfer RNAs and 4 ribosomal RNAs. A total of 47 perfect cp microsatellites were analyzed in the A. quinata. The majority of the SSRs in this cp genome are mononucleotides (74.47 %). Regions of the highest variability were sought out by comparing with A. trifoliate. There are only 385 nucleotide substitutions and 141 indels between the two genomes. Six highly variable regions were identified including four intergenic regions and two coding regions.     

Characterization of the complete mitochondrial genome of the Yunnan endemic grasshopper <Emphasis Type="Italic">Yunnanacris yunnaneus</Emphasis> (Insecta: Orthoptera: Acrididae)

Yunnanacris yunnaneus (Y. yunnaneus) was once a destructive grasshopper in the Yunnan province (People’s Republic of China) that jeopardized tobacco cultivation. However, its population has severely declined because of extensive pesticide use. Identifying the species and sources of Y. yunnaneus is important for biodiversity conservation and ecological/environmental preservation. In this study, the complete mitochondrial genome of Y. yunnaneus was assembled from high-coverage (35.5×) Illumina MiSeq sequencing data. The circular genome is 15,475 bp in length, harboring 37 typical mitochondrial genes and one control region. The nucleotide composition is highly asymmetric (42.6 % A, 14.4 % C, 10.6 % G, and 32.4 % T), with an overall A + T content of 75.1 %. All the protein-coding genes are initiated with typical ATN start codons and terminated with a TAA codon. The control region has a remarkably high A + T content (85.1 %) and is located between genes rrnS and trnV.     

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 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 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">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.     

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 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.     

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">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.     

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.     

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 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">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.     

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.     

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 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.