LSC Regions Research Articles

The complete chloroplast genome sequence of Ziziphus incurva

The first complete chloroplast genome sequences of Ziziphus incurva were reported in this study. The complete chloroplast genome (cpDNA) sequence of Z. incurva was determined from Illumina HiSeq pair-end sequencing data. The cpDNA is 160,920 bp in length, contains a large single-copy region (LSC) of 88,778 bp and a small single-copy region (SSC) of 19,172 bp, which were separated by a pair of inverted repeat (IR) regions of 26,477 bp. The genome contains 129 genes, including 84 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 36.8% and the corresponding values of the LSC, SSC, and IR regions are 34.6, 30.8, and 42.7%, respectively. Further, the phylogenomic analysis showed that Z. incurva clustered together with Z. jujube, Z. mauritiana, and Z. spina-christi.

Characterization and phylogenetic analysis of the complete chloroplast genome of Curcuma longa (Zingiberaceae)

Curcuma longa, a well-known traditional medicinal plant in China, belongs to the genus Curcuma family Zingiberaceae. In this study, we firstly assembled the complete chloroplast genome of C. longa based on sequences from Illumina and PacBio sequencing platforms. We obtained the complete chloroplast genome with the total length of 162,176 bp. It consisted of a large single-copy region (LSC, 86,984 bp), a small single-copy region (SSC, 15,694 bp), and a pair of inverted repeats (IRs, 29,749 bp each). Sequence analyses indicated that the chloroplast genome contained 111 distinct genes including 79 protein-coding genes, 28 tRNA genes, and four rRNA genes. The nucleotide composition was asymmetric (31.62% A, 18.42% C, 17.79% G, 32.18% T) with an overall AT content of 63.80%. The AT contents of the LSC, SSC and IR regions were 66.00%, 70.35% and 58.85%, respectively. Sixteen genes owned a single intron, while another two genes had two introns. The phylogenetic analysis indicated that C. longa was closely related to species Curcuma roscoeana within the genus Curcuma in family Zingiberaceae.

Characterization of the complete chloroplast genome of Euphorbia helioscopia Linn. (Euphorbiaceae), a traditional Chinese medicine

Euphorbia helioscopia Linn. known as a traditional Chinese medicine of Euphorbiaceae, which contains terpenes, steroids, flavonoids, acetophenones, tannins, phenylpropanoids, cerebrosides and so on. Euphorbia helioscopia L. was used to treat malignant tumors and chronic obstructive pulmonary diseases such as cough, phlegm-turbidity, asthma, and chronic bronchitis. The complete chloroplast genome was assembled by Illumina paired-end reads data. The length of circular cp genome distribution in 160,041 bp, containing a large single-copy region (LSC) of 88,832 bp, a small single-copy region (SSC) of 17,145 bp and a pair of inverted repeat (IR) regions of 27,032 bp. In addition, 11 genes possess a single intron, while the other two genes (ycf3, clpP) have a couple of introns. The GC content of entire Euphorbia helioscopia L. cp genome, LSC, SSC and IR regions are 35.9, 33.1, 30.3, and 42.3%, respectively. From the NJ phylogenetic tree analysis showed that Euphorbia helioscopia L. and Euphorbia esula are closely related to each other within the family Euphorbiaceae.

The complete chloroplast genome sequence of Pellacalyx yunnanensis: an endangered species in China

Pellacalyx yunnanensis is an endangered plant species occurring in Yunnan province of China. The first complete chloroplast genome (cpDNA) sequence of P. yunnanensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 163,743 bp in length, contains a large single-copy region (LSC) of 91,075 bp and a small single-copy region (SSC) of 18,668 bp, which were separated by a pair of inverted repeats (IR) regions of 27,000 bp. The genome contains 128 genes, including 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 35.7%, and the corresponding values of the LSC, SSC, and IR regions are 33.0%, 29.6%, and 42.3%, respectively. Further phylogenomic analysis showed that P. yunnanensis clustered in a unique clade in family Rhizophoraceae.

Characterization of complete chloroplast genome of traditional Chinese medical plants Paris Mairei and its phylogenetic positions

The genus Paris (Liliaceae) has been used for traditional medicine in China. The wild Paris was on the verge of exhaustion due to illegal and immoderate exploitation coupled with environmental pollution. In order to alleviate resource pressure, Paris mairei can be considered as alternative sources. Here, we report the complete chloroplast genome of Paris mairei. The genome is 162,736 bp in length including a small single-copy region (SSC, 12,908 bp) and a large single-copy region (LSC, 84,286 bp) separated by a pair of inverted repeats (IRs; 32,771 bp). The genome contained 113 genes, including 79 protein-coding genes, 4 ribosomal RNA genes, and 30 tRNA genes. Among these genes, 16 harboured a single intron, and 2 contained a couple of introns. The overall G + C content of the cpDNA is 37.1%, while the corresponding values of the LSC, SSC, and IR regions are 35.7, 32.1, and 39.9%, respectively. The complete chloroplast genome sequence of Paris mairei will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for the genus Paris.

The complete chloroplast genome of Parnassia wightiana (Celastraceae)

The infrageneric relationships of the genus Parnassia were not clearly identified due to limited available genetic data. In this study, we presented the complete chloroplast genome of Parnassia wightiana for future phylogenetic study. The plastome of P. wightiana was 152,043 bp in length, with a large single-copy region (LSC) of 82,737 bp and a small single-copy region (SSC) of 19,030 bp, separated by a pair of inverted repeat regions (IRs) of 25,138 bp. It contained 134 genes, including 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 2 pseudogenes. The overall GC content was 37.1%, while the corresponding values in the LSC, SSC, and IR region were 35.0%, 30.8%, and 42.9%, respectively. The phylogenetic analysis supported the monophyly of Parnassia.

The complete chloroplast genome sequence of Pericampylus glaucus

The first complete chloroplast genome (cpDNA) sequence of Pericampylus glaucus was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 162,450 bp in length, contains a large single-copy region (LSC) of 90,871 bp and a small single-copy region (SSC) of 21,137 bp, which were separated by a pair of inverted repeats (IR) regions of 25,221 bp. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 38.0%, and the corresponding values of the LSC, SSC, and IR regions are 36.2, 32.1, and 43.5%, respectively. Further, phylogenomic analysis showed that P. glaucus and Stephania japonica clustered in a clade in family Menispermaceae.

The complete chloroplast genome sequence of Populus tremuloides (Salicaceae)

The complete chloroplast genome sequence of Populus tremuloides was characterized from Illumina pair-end sequencing. The chloroplast genome of P. tremuloides was 155,816 bp in length, containing a large single-copy region (LSC) of 85,804 bp, a small single-copy region (SSC) of 16,489 bp, and two inverted repeat (IR) regions of 26,962 bp. The overall GC content is 36.71%, while the correponding values of the LSC, SSC, and IR regions are 64.9%, 69.2%, and 60.3%, respectively. The genome contains 167 complete genes, including 86 protein-coding genes (77 protein-coding gene species), 73 tRNA genes (29 tRNA species) and 8 rRNA genes(4 rRNA species). The Neighbour-joining phylogenetic analysis showed that P. tremuloides and Populus tremula clustered together as sisters to other Populus species.

The complete chloroplast genome of a gynodioecious deciduous orchid Satyrium ciliatum (Orchidaceae) female

The chloroplast (cp) genome sequence of a gynodioecious Satyrium ciliatum female type has been characterized using Illumina pair-end sequencing. The complete cp genome was 154,418 bp in length, containing a large single copy region (LSC) of 83,475 bp and a small single copy region (SSC) of 17,513 bp, which were separated by a pair of 26,715 bp inverted repeat regions (IRs). The genome contained 132 genes, with 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 37.18% with the values of the LSC, SSC, and IR regions are 34.90%, 30.15%, and 43.06%, respectively. Phylogenetic analysis suggested that the S. ciliatum is close to Platanthera japonica (MG925368) in subfamily Orchidoideae.

The complete chloroplast genome sequence of Pinus kesiya var. langbianensis

Pinus kesiya var. langbianensis is an important oleoresin resource tree species in Yunnan province, China. In this study, the complete chloroplast genome (cpDNA) sequence of P. kesiya var. langbianensis was determined from Illumina HiSeq pair-end sequencing data. The cpDNA is 119,780 bp in length, contains a large single copy region (LSC) of 65,863 bp and a small single copy region (SSC) of 53,117 bp, which were separated by a pair of inverted repeat (IR) regions of 400 bp. The genome contains 113 genes, including 73 protein-coding genes, 4 ribosomal RNA genes, and 36 transfer RNA genes. The overall GC content of the whole genome is 38.5%, and the corresponding values of the LSC, SSC, and IR regions are 37.9, 39.4, and 35.5%, respectively. Further phylogenomic analysis showed that P. kesiya var. langbianensis clustered together with Pinus kesiya, Pinus densata, and Pinus taiwanensis.

The complete chloroplast genome of Vitis amurensis Rupr., an economic plant to China

The chloroplast (cp) genome sequence of Vitis amurensis has been characterized from Illumina pair-end sequencing. The complete cp genome was 161,014 bp in length, containing a large single-copy region (LSC) of 89,239 bp and a small single-copy region (SSC) of 19,067 bp, which were separated by a pair of 26,354 bp inverted repeat regions (IRs). The genome contained 133 genes, including 88 protein coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 37.4%, while the corresponding values of the LSC, SSC, and IR regions are 35.3%, 31.7%, and 43.0%, respectively. Further, phylogenetic analysis suggested that the V. amurensis was sister to Vitis coignetiae.

The complete chloroplast genome of a Cymbidium Tortisepalum (Orchidaceae) male mutant

The chloroplast (cp) genome of natural male mutant Cymbidium tortisepalum ‘Guanshihe’ has been characterized using Illumina pair-end sequencing technology. The complete cp genome was 149,830 bp in length, containing a large single-copy region (LSC) of 85,131 bp and a small single-copy region (SSC) of 13,275 bp, which were separated by a pair of 25,712 bp inverted repeat regions (IRs). The genome contained 130 genes, with 111 unique genes, including 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 37.09% with the values of the LSC, SSC, and IR regions are 34.40%, 29.63%, and 43.45%, respectively. Further, phylogenetic analysis suggested that the plastome of C. tortisepalum male mutant ‘Guanshihe’ is close to sequenced C. sinense, C. kanran, C. tortisepalum, and C. ensifolium plastomes.

The complete chloroplast genome sequence of Dendrocalamus sinicus

Dendrocalamus sinicus is the world’s largest bamboo species. In this study, the complete chloroplast genome (cpDNA) sequence of D. sinicus was determined from Illumina HiSeq pair-end sequencing data. The cpDNA is 139,441 bp in length, contains a large single-copy region (LSC) of 82,777 bp and a small single-copy region (SSC) of 12,803 bp, which were separated by a pair of inverted repeat (IR) regions of 21,296 bp. The genome contains 136 genes, including 89 protein-coding genes, 8 ribosomal RNA genes, and 40 transfer RNA genes. The overall GC content of the whole genome is 38.9%, and the corresponding values of the LSC, SSC, and IR regions are 37%, 33.2%, and 44.2%, respectively. Further, phylogenomic analysis showed that D. sinicus clustered together with D. latiflorus.

The complete chloroplast genome sequence of Mytilaria laosensis

The first complete chloroplast genome (cpDNA) sequence of Mytilaria laosensis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 159,941 bp in length, contains a large single-copy region (LSC) of 89,016 bp and a small single-copy region (SSC) of 18,127 bp, which were separated by a pair of inverted repeats (IR) regions of 26,399 bp. The genome contains 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 37.9%, and the corresponding values of the LSC, SSC, and IR regions are 35.9, 32.8, and 43.1%, respectively. Further phylogenomic analysis showed that M. laosensis and Chunia bucklandioides clustered in a clade in family Hamamelidaceae.

The complete chloroplast genome sequence of Spathodea campanulata

The first complete chloroplast genome (cpDNA) sequence of Spathodea campanulata was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 158,001 bp in length, contains a large single-copy region (LSC) of 84,923 bp and a small single-copy region (SSC) of 12,566 bp, which were separated by a pair of inverted repeat (IR) regions of 30,256 bp. The genome contains 131 genes, including 86 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 37.8% and the corresponding values of the LSC, SSC, and IR regions are 35.9, 32.6, and 41.7%, respectively. Further, phylogenomic analysis showed that S. campanulata clustered in a unique clade in family Bignoniaceae.

The complete chloroplast genome of Cerasus dictyoneura, an ornamental plant of China

The complete cp genome of Cerasus dictyoneura was 158,084 bp in length, consisting of a LSC of 86,275 bp and a SSC of 19,039 bp, which were separated by a pair of 26,385 bp IRs. The genome contained 131 genes, including 86 proteincoding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content is 36.7%, while the corresponding values of the LSC, SSC, and IR regions are 34.6, 29.5, and 42.6%, respectively. Furthermore, phylogenetic analysis based on 16 complete cp genome sequences indicated that C. dictyoneura is within Eurosids I.

The complete chloroplast genome sequence of Phlegmariurus carinatus

The first complete chloroplast genome (cpDNA) sequence of Phlegmariurus carinatus was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 150,349 bp in length, contains a large single-copy region (LSC) of 100,582 bp and a small single-copy region (SSC) of 19,455 bp, which were separated by a pair of inverted repeat (IR) regions of 15,156 bp. The genome contains 120 genes, including 79 protein-coding genes, 8 ribosomal RNA genes, and 33 transfer RNA genes. The overall GC content of the whole genome is 34.0%, and the corresponding values of the LSC, SSC, and IR regions are 31.6%, 30.4%, and 44.2%, respectively. Further phylogenomic analysis showed that P. carinatus and Huperzia serrata clustered in a clade in family Lycopodiaceae.

The complete chloroplast genome sequence of Gillenia trifoliata (Rosaceae)

Gillenia trifoliata (L.) Moench is an ornamental and medicinal species endemic to North America. In this study, a complete circular chloroplast genome of G. trifoliata was assembled and annotated. The chloroplast genome of G. trifoliata is 159,496 bp in size and consists of two IR (26,394 bp) regions separated by LSC (87,647 bp) and SSC (19,061 bp) regions. The GC content of the chloroplast genome is 36.5%. The chloroplast genome comprised of 112 different genes, including 78 protein-coding genes. The phylogenetic analysis revealed that G. trifoliata lies within subfamily Amygdaloideae and forms the progenitor lineage of the pome-bearing Maleae.

The first complete chloroplast genome sequence from Polemonium chinense (Polemoniaceae)

In this study, the complete chloroplast genome of Polemonium chinense was determined by next-generation sequencing technology. The plastome is 155,578 bp in length, with a large single-copy region (LSC) of 85,864 bp and a small single-copy region (SSC) of 18,246 bp, separated by a pair of inverted repeat regions (IRs) of 25,734 bp. It contains 135 genes, including 89 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 1 pseudogene. The overall GC content is 37.1%, while the corresponding values in the LSC, SSC and IR region are 35.1, 30.3, and 42.9%, respectively. The phylogenetic tree shows that Polemoniaceae is sister to Fouquieriaceae.

The complete chloroplast genome of Dipterocarpus turbinatus Gaertn. F

Dipterocarpus turbinatus Gaertn. F., naturally distributes in Southern China, which is an elite natural tree with high economic and medicinal value. In study, all chloroplast (cp) genome of Dipterocarpus turbinatus Gaertn. F. was assembled and characterized based on Illumina pair-end sequencing data. The complete chloroplast genome length was 152,279 bp. It contained a large (LSC, 83,862 bp) and a small (SSC, 20,215 bp) single copy region, separated by a pair of inverted repeats of 24,101 bp (IRs). The overall GC content of genome was 37.3%, the corresponding values of LSC, SSC, and IR regions were 35.3, 31.6, and 43.2%, respectively. There were 128 genes in the genome including 84 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Among all genes, 14 genes contain a single intron and 1 gene has two introns. The result showed that Dipterocarpus turbinatus Gaertn. F. was closely related to Vatica mangachapoi.