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The complete chloroplast genome sequence of Bupleurum chinense DC. (Apiaceae).

ABSTRACT: Bupleurum chinense DC. is a traditional medicinal herb species widely distributed in most provinces of China. In this study, we constructed and annotated a complete circular chloroplast (cp) genome of B. chinense. The cp genome of B. chinense is 155,545?bp in length, including two inverted repeat (IR) regions of 26,305?bp, separated by a large single-copy (LSC) region of 85,430?bp and a small single-copy (SSC) region of 17,505?bp. The GC content of whole cp genome is 37.68%. The genome contains 113 different genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A maximum-likelihood phylogenomic analysis showed that Bupleurum formed a monophyletic group, and was sister to other groups of Apiaceae.

SUBMITTER: Zhang F

PROVIDER: S-EPMC7707502 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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The complete chloroplast genome sequence of Bupleurum chinense DC. (Apiaceae).

Zhang Fei F Zhao Zhenyu Z Yuan Qingjun Q Chen Suiqing S Huang Luqi L

Mitochondrial DNA. Part B, Resources 20191018 2

Bupleurum chinense DC. is a traditional medicinal herb species widely distributed in most provinces of China. In this study, we constructed and annotated a complete circular chloroplast (cp) genome of B. chinense. The cp genome of B. chinense is 155,545 bp in length, including two inverted repeat (IR) regions of 26,305 bp, separated by a large single-copy (LSC) region of 85,430 bp and a small single-copy (SSC) region of 17,505 bp. The GC content of whole cp genome is 37.68%. ...[more]

PMID: 33366133

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Assembly and comparative analysis of the complete mitochondrial genome of Bupleurum chinense DC.

Project description:BackgroundBupleurum chinense(B. chinense) is a plant that is widely distributed globally and has strong pharmacological effects. Though the chloroplast(cp) genome of B. chinense has been studied, no reports regarding the mitochondrial(mt) genome of B. chinense have been published yet.ResultsThe mt genome of B.chinense was assembled and functionally annotated. The circular mt genome of B. chinense was 435,023 bp in length, and 78 genes, including 39 protein-coding genes, 35 tRNA genes, and 4 rRNA genes, were annotated. Repeat sequences were analyzed and sites at which RNA editing would occur were predicted. Gene migration was observed to occur between the mt and cp genomes of B. chinense via the detection of homologous gene fragments. In addition, the sizes of plant mt genomes and their GC content were analyzed and compared. The sizes of mt genomes of plants varied greatly, but their GC content was conserved to a greater extent during evolution. Ka/Ks analysis was based on code substitutions, and the results showed that most of the coding genes were negatively selected. This indicates that mt genes were conserved during evolution.ConclusionIn this study, we assembled and annotated the mt genome of the medicinal plant B. chinense. Our findings provide extensive information regarding the mt genome of B. chinense, and help lay the foundation for future studies on the genetic variations, phylogeny, and breeding of B. chinense via an analysis of the mt genome.

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The complete chloroplast genome sequence of Libanotis buchtormensis (Apiaceae).

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The complete chloroplast genome sequence of Ostericum koreanum (Apiaceae).

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The complete chloroplast genome sequence of Polygonum chinense L.

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Characterization of the complete chloroplast genome of Bupleurum hamiltonii N. P. Balakr. (Apiaceae) and its phylogenetic implications.

Project description:Bupleurum hamiltonii has a thin, wood, grayish-yellow root and is reputed to possess medicinal value. This study employs the de novo method using high-throughput sequencing data to assemble the complete chloroplast genome for this species. The total B. hamiltonii genome is 155,320 bp in length, containing a large single-copy region of 85,280 bp, a small single-copy region of 17,468 bp, a pair of inverted repeat regions of 26,286 bp, and has a GC content of 37.8%. The genome encodes 113 unique genes, of which there are 79 protein-coding, 30 tRNA, and four rRNA genes. In addition, 18 genes contained introns, petB, petD, and rpl16 are coded for by two exons, and rps12 is identified as a trans-splicing gene. Phylogenetic analysis results strongly suggest that B. hamiltonii is closely related to B. marginatum. This study provides valuable genetic information to facilitate reliable identification.

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The complete chloroplast genome sequence of Capsicum chinense Jacq. (Solanaceae).

Project description:Capsicum chinense is one of the domesticated pepper species and well known for its distinctive pungency. The complete chloroplast genome sequence of C. chinense was generated by de novo assembly using next generation sequencing data. The chloroplast genome is 156 807 bp long, containing large single-copy region of 87 290 bp and small single-copy region of 17 911 bp separated by a pair of inverted repeats of 25 803 bp. A total of 113 genes were predicted including 79 protein-coding genes, 30 tRNA genes and four rRNA genes. Phylogenomic analysis revealed that C. chinense chloroplast genome was most closely related to Capsicum annuum var. glabriusculum (American bird pepper), a wild progenitor of C. annuum.

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

Project description: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.

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The complete mitochondrial genome sequences of Bupleurum falcatum (Apiales: Apiaceae).

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Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis.

Project description:Bupleurum chinense DC is a plant widely used in Chinese traditional medicine. Saikosaponins are the major bioactive constituents of B. chinense DC. Saikosaponins biosynthesis in Bupleurum has been more intensively studied than any other metabolic processes or bioactive constituents. However, whole-genome sequencing and chromosome-level assembly for Bupleurum genus have not been reported yet. Here, we report a high-quality chromosome-level genome of B. chinense DC. through the integration of PacBio long-read sequencing, Illumina short-read sequencing, and Hi-C sequencing. The genome was phased into haplotype 0 (621.27 Mb with a contig N50 of 16.86 Mb and a scaffold N50 of 92.25 Mb) and haplotype 1 (600.48 Mb with a contig N50 of 23.90 Mb and a scaffold N50 of 102.68 Mb). A total of 45,909 and 35,805 protein-coding genes were predicted in haplotypes 0 and 1, respectively. The enrichment analyses suggested that the gene families that expanded during the evolution of B. chinense DC are involved in the biosynthesis of isoquinoline alkaloid, tyrosine, and anthocyanin. Furthermore, we analyzed the genes involved in saikosaponin biosynthesis and determined the candidate P450 and UGT genes in the third stage of saikosaponins biosynthetic, which provided new insight into the saikosaponins biosynthetic. The genomic data provide a valuable resource for future investigations of the molecular mechanisms, biological functions, and evolutionary adaptations of B. chinense DC.

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