Bp Inverted Repeat Research Articles

Characterization of the complete chloroplast genome sequence of Blastus cochinchinensis (Melastomataceae)

Blastus Lour. belongs to tribe Sonerileae (Melastomataceae), comprising about 18 species worldwide. Herein, we presented, assembled, and annotated the first complete chloroplast genome of Blastus (B. cochinchinensis). The complete chloroplast genome (cp) size of B. cochinchinensis was 156,005 bp in length, containing a pair of 26,812 bp inverted repeat (IR) regions, which were separated by a large single-copy region (LSC) 85,926 bp and a small single-copy (SSC) region 16,455 bp. The overall GC content of the genome was 37.0%. The whole genome contained 129 unique genes, including 81 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that B. cochinchinens was sister to Barthea barthei. The present study provided B. cochinchinensis genomic information that may be found useful in conservation and molecular phylogenetic studies on Blastus.

The complete chloroplast genome of Curcuma longa L. (Zingiberaceae)

Curcuma longa L. is a widely distributed medicinal plant in Southeast Asia, especially in China. In this study, we reported and characterized the complete chloroplast genome sequence of C. longa. The chloroplast genome was determined to be 162,255 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 86,975 bp and 15,776 bp, respectively, which were separated by a pair of 29,752 bp inverted repeat (IR) regions. The genome is predicted to contain 133 genes, including 87 protein-coding genes, 38 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 36.2%. A phylogenetic tree reconstructed by 23 chloroplast genomes reveals that C. longa is mostly related to Curcuma roscoeana, with bootstrap support values of 100%.

The complete chloroplast genome of Changium smyrnioides Wolff

Changium smyrnioides Wolff, which could only be found in Eastern China, is a monotypic species of the genus Changium Wolff. In this study, the complete chloroplast genome sequence of C. smyrnioides was assembled and characterized by the 42.33 M high-throughput sequencing data. The chloroplast genome was 155,221 bp in length, consisting of large single-copy (LSC) and small single-copy (SSC) regions of 84,793 bp and 17,828 bp, respectively, which were separated by a pair of 26,300 bp inverted repeat (IR) regions. The genome is predicted to contain 131 genes, including 8 rRNA genes, 37 tRNA genes, and 86 protein-coding genes. The overall GC content of the genome is 37.7%. A phylogenetic tree reconstructed by 37 chloroplast genomes reveals that Chuanminshen violaceum is mostly related species to C. smyrnioides. The work reported here is the first complete chloroplast genome of C. smyrnioides which may provide useful information to the evolution of Changium genus.

Characterization of the complete chloroplast genome of Dalbergia cultrata (Leguminosae)

Dalbergia cultrata is a Near Threatened species with high ecological and economic values. In this study, its chloroplast genome was assembled using Illumina pair-end sequencing dataset. The chloroplast genome has a quadripartite structure with 156,385 bp in length and contains a pair of 16,392 bp inverted repeat (IR) regions, which were separated by large single copy (LSC: 86,040 bp) region and small single copy (SSC: 37,561 bp) region. A total of 121 genes were annotated, including 77 protein-coding genes (PCGs), 36 tRNAs, and 8 rRNAs. The overall GC content was 36.1%. The phylogenetic analysis revealed that D. cultrata has close relationship to D. hainanensis and D. odorifera. This complete chloroplast genome can be readily used for population genetic studies of D. cultrata.

The complete chloroplast genome sequence of Melliodendron wangianum (Styracaceae)

Melliodendron wangianum Hu (Styracaceae) is a rare endemic tree of Styracaceae in China. In this work, we set forth the complete chloroplast (cp) genome sequence of M. wangianum using next-generation sequencing. The entire cp genome was determined to be 157,196 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 90,210 bp and 18,4561 bp, respectively, which were separated by a pair of 24,265 bp inverted repeat (IR) regions. The genome contained 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the genome is 37.19%. Phylogenetic analysis confirmed the traditional family-level Taxonomy of Melliodendron, indicating that M. wangianum is closely related to a sister species to M. xylocarpum in Styracaceae.

Characterization of the complete chloroplast genome of Asparagus filicinus (Asparagaceae: Asparagoideae: Asparagus), a traditional Tibetan medicinal plant

Asparagus filicinus is a traditional medicinal plant with the treatment of pneumonia and cancer, which has been classified as threatened due to habitat destruction and over-harvesting. In this study, its complete chloroplast genome was assembled from the whole genome Illumina sequencing data. The circular genome was 156,674 bp long, containing a large single copy (LSC) region of 85,003 bp and a small single copy (SSC) region of 18,663 bp, which were separated by a pair of 26,504 bp inverted repeat (IR) regions. It encoded a total of 126 genes, including 72 protein-coding genes, 46 tRNA genes and eight rRNA genes. The most of gene species occurred as a single copy, while 17 gene species occurred in double copies. The overall A + T content was 62.4%, while the corresponding values of the LSC, SSC and IR regions were 64.5, 68.4 and 57.1%, respectively. Phylogenetic analysis indicated that A. filicinus was relatively close to two species belonging to the subgenus Asparagus.

The complete chloroplast genome of Actinidia macrosperma

Actinidia macrosperma (A. macrosperma) is a medicinal plant in China, which has been well known for its activities against leprosy and cancers. In this study, we assembled and characterized the complete chloroplast (cp) genome sequence of A. macrosperma in an effort to provide genomic resources for promoting its conservation. The cp genome is 156,231 bp in length, containing a pair of 23,720 bp inverted repeat (IR) regions, which is separated by a large single copy region (LSC) of 88,214 bp and a small single copy region (SSC) of 20,577 bp. A total of 132 genes were annotated in this cp genome, including 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis highly supported that A. macrosperma was evolutionarily close to another Actinidia species Actinidia deliciosa.

The complete plastome of bloodroot (Sanguinaria canadensis, Papaveraceae), a spring ephemeral from eastern North America

The complete plastome of Sanguinaria canadensis was sequenced, which is 160,117 bp in length, consisting of 87699 bp large single-copy (LSC), a 19,136 bp small single copy (SSC), and a pair of 26,638 bp inverted repeat (IR) regions. The S. canadensis plastome encodes 137 annotated genes including 37 tRNA genes, 8 rRNA genes, and 89 protein coding genes. Phylogenetic analysis strongly supported that it is a member of Chelidonieae.

Assembly and phylogenetic analysis of the complete chloroplast genome sequence of Actinidia setosa

The complete chloroplast (cp) genome sequence of Actinidia setosa (A. setosa) was sequenced and assembled into a circular genome of 156,728 bp length using Illumina paired-end data. The cp genome composed of a pair of 24,090 bp inverted repeat (IR) regions separated by a large single copy region (LSC) of 88,256 bp and a small single copy region (SSC) of 20,292 bp. Additionally, a total of 131 genes, including 85 protein-coding genes, 38 tRNA genes and 8 rRNA genes, were identified in the A. setosa cp genome. Phylogenetic analysis showed that A. setosa was evolutionarily close to other two kiwifruits A. deliciosa and A. chinensis.

The complete chloroplast genome sequence of Styrax odoratissimus (Styracaceae)

Styrax odoratissimus Champ. ex Benth., also known as the extraordinary aromatic plant of Styracaceae, has been seriously threatened due to human activities. In this study, the complete chloroplast (cp) genome sequence of S. odoratissimus was determined by applying next-generation sequencing. The entire cp genome was determined to be 157,921 bp in length. It contained large single-copy (LSC) and small single-copy (SSC) regions of 87,524 bp and 18,301 bp, respectively, which were separated by a pair of 26,048 bp inverted repeat (IR) regions. The genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of S. odoratissimus genome is 36.96% and the corresponding values in LSC, SSC, and IR regions are 34.80, 30.27, and 42.92%, respectively. A phylogenetic tree reconstructed by 31 chloroplast genomes reveals that S. odoratissimus is most related to Styrax grandiflorus Griffith.

Characterization of the complete chloroplast genome of Paederia scandens (Rubiaceae): a Chinese folk medicinal plant

Paederia scandens has been used as a traditional medicine in Asian countries to treat jaundice, dysentery, and the pain of rheumatism. The complete chloroplast (cp) genome sequence of P. scandens was reported and characterized in this study. The cp genome is 153,626 bp in length, composed of a pair of 26,513 bp inverted repeat (IR) regions separated by a large single-copy (LSC) region of 83,712 bp and a small single-copy (SSC) region of 16,888 bp. There were 131 predicted genes (86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes) in the genome, and the overall GC content of the genome is 37.7%. Phylogenetic analysis based on the cp genome data showed that P. scandens was sister to the clade formed by Galium mollugo and G. aparine.

The complete chloroplast genome sequence of Melliodendron xylocarpum (Styracaceae)

Melliodendron xylocarpum Handel-Mazzetti is a rare tree, distinct member of the family Styracaceae. In this study, we determined the complete chloroplast (cp) genome sequence of M. xylocarpum in an effort to provide genomic resources useful for promoting its conservation. The entire cp genome was determined to be 157,165 bp in length. It contains the typical structure and gene content of angiosperm plastome, The plastome contains a large single-copy (LSC) and a small single-copy (SSC) regions of 90,193 and 18,486 bp, respectively, which were separated by a pair of 24,243 bp inverted repeat (IR) regions. The genome contained 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The GC content of M. xylocarpum genome is 37.21%. The complete plastome sequence of M. xylocarpum will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Styracaceae. Phylogenetic analysis revealed that M. xylocarpum is closely related to Changiostyrax dolichocarpus H.S.Lo & D.Fang, but forms an independent evolutionary branch.

The complete chloroplast genome of brown flatsedge, Cyperus fuscus (Cyperaceae)

Cyperus fuscus known as brown flatsedge plays an important role in sand fixation and water purification. The first complete chloroplast genome sequences of pioneering plant C. fuscus were reported in this study. The complete chloroplast genome was 167,660 bp in length, containing a large single copy region (LSC) of 79,790 bp and a small single copy region (SSC) of 12,192 bp, which were separated by a pair of 37,839 bp inverted repeat regions (IRs). The chloroplast genome contains 135 genes, including 92 protein-coding genes, eight ribosomal RNA genes, and 35 transfer RNA genes. The overall GC content is 36.3%, while the corresponding values of the LSC, SSC, and IR region are 35.1%, 28.3%, and 38.5%, respectively. Further, the maximum-likelihood phylogenetic analysis showed a strong sister relationship with Cyperus difformis in Cyperaceae. Our findings provide a foundation for further study of chloroplast genome evolution and genetics information in C. fuscus.

The complete chloroplast genome of Gentaina urnula (Gentianaceae)

Gentiana urnula, is an alpine medicinal endemic to the Qinghai-Tibetan Plateau. In this study, the complete chloroplast DNA sequence of G. urnula was assembled，and its genome is 149,064 bp in length, including a large single-copy region (LSC) of 81,158 bp and a small single-copy region (SSC) of 17,034 bp, which was separated by a pair of 25,436 bp inverted repeat regions (IRs). A total of 130 genes are detected, including 86 protein-coding genes, 37 tRNA genes, and 7 rRNA genes. The complete chloroplast genomes of G. urnula will help to study the genetic diversity and phylogenetic analysis of Gentianales.

The complete chloroplast genome of Zabelia dielsii (Graebn.) Rehd. (Caprifoliaceae), an important horticultural plant in China

The genus Zabelia R. Br. has been an important horticultural plant in the family Caprifoliaceae. However, due to the lack of efficient molecular markers and conservation efforts in recent decades, accompanied with deforestation, the germplasm resources are under severe threat, yet the systematic position of Zabelia is not clearly understood. In the present study, we analyzed the complete chloroplast (cp) genome of Zabelia dielsii (Graebn.) Rehd., which represents the first reported case of Zabelia. It was 155,584 bp in length, comprising a pair of 23,434 bp inverted repeat regions (IRs) separated by a large single-copy (LSC) region (89,521 bp) and a small single-copy (SSC) region (19,062 bp). Phylogenetic analysis supported the monophyly of Caprifoliaceae and suggested that Z. dielsii was closely related to Kolkwitzia amabilis and Dipelta floribunda. This complete chloroplast genome will contribute to further studies on population genetics, phylogeny, and conservation biology in Zabelia.

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 of Quercus fabri (Fagaceae) from China

The complete chloroplast (cp) genome sequence of Quercus fabri Hance has been characterized in this study. The length of cp genome was 161,227 bp, containing a large single-copy region (LSC) of 90,539 bp and a small single-copy region (SSC) of 19,048 bp, which were separated by a pair of 25,820 bp inverted repeat regions (IRs). The genome contained 134 genes, including 86 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The overall GC content is 36.82%. Further, phylogenetic analysis suggested that Q. fabri is clustered to section Quercus.

The complete chloroplast genome of Houttuynia cordata Thunb. (Family: Saururaceae)

The chloroplast genome sequence of Houttuynia cordata has been characterized from Illumina pair-end sequencing. The complete chloroplast genome was 161,090 bp in length, containing a large single-copy (LSC) region of 88,180 bp and a small single-copy (SSC) region of 19,204 bp, which were separated by a pair of 26,853 bp inverted repeat regions. Furthermore, phylogenetic analysis revealed that H. cordata is a sister of Piper cenocladum.

The complete chloroplast genome of Aconitum coreanum (H. Lév.) Rapaics (Ranunculaceae)

Aconitum coreanum (H. Lév.) Rapaics listed in the Korean Red List is a medicinal herb. We presented complete chloroplast genome, which is 157,024 bp long and has four subregions: 87,637 bp of large single-copy and 16,901 bp of small single-copy regions, which are separated by two 26,243 bp inverted repeat regions including 132 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast is 38.0%. Phylogenetic trees show that A. coreanum occupied a basal position at subgenus Aconitum clade and two A. coreanum isolated from midwestern and eastern regions of Korea are clustered together.

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.