Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Codonopsis lanceolata (Campanulaceae).

ABSTRACT: The complete chloroplast genome sequence of Codonopsis lanceolata was determined by next generation sequencing. The total length of chloroplast genome of C. lanceolata was 169,447?bp long, including a large single-copy (LSC) region of 85,253?bp, a small single-copy (SSC) region of 8060?bp, and a pair of identical inverted repeat regions (IRs) of 38,067?bp. A total of 110 genes was annotated, resulting in 79 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. The phylogenetic analysis of C. lanceolata with related chloroplast genome sequences in this study provided the taxonomical relationship of C. lanceolata in the genus Campanula.

SUBMITTER: Lee J

PROVIDER: S-EPMC7799679 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Codonopsis lanceolata (Campanulaceae).

Lee Junki J Kim So-Yeon SY Lim Jong-Sung JS Sook Chun Hyang H Kwon Kisung K Koh Youngho Y Kang Tae Sun TS Kang Jung-Hwa JH Kim Eun-Jeong EJ Nah Gyoungju G

Mitochondrial DNA. Part B, Resources 20180910 2

The complete chloroplast genome sequence of Codonopsis lanceolata was determined by next generation sequencing. The total length of chloroplast genome of C. lanceolata was 169,447 bp long, including a large single-copy (LSC) region of 85,253 bp, a small single-copy (SSC) region of 8060 bp, and a pair of identical inverted repeat regions (IRs) of 38,067 bp. A total of 110 genes was annotated, resulting in 79 protein-coding genes, 27 tRNA genes, and 4 rRNA genes. The phylogenetic ana ...[more]

PMID: 33474421

Similar Datasets

The complete chloroplast genome of Codonopsis tsinglingensis (Campanulaceae), an endemic Chinese medicine species in Qinling mountains.

Project description:Codonopsis tsinglingensis, belonging to the Campanulaceae family, is a perennial medicinal herb highly valued in Chinese traditional medicine. The complete chloroplast genome of C. tsinglingensis was sequenced using the Illumina Hiseq 4000 platform. The size of the C. tsinglingensis chloroplast genome is 170,253 bp, with an average GC content of 38.3%. This circular molecule has a typical quadripartite structure containing a large single copy (LSC) region of 85,408 bp, a small single copy (SSC) region of 8179 bp, and two inverted (IRs) repeat regions of 38,333 bp. The genome contains 138 genes, including 92 protein-coding genes, 38 transfer RNA genes (tRNA), 8 ribosomal RNA genes (rRNA). Phylogenetic analysis based on complete chloroplast genome sequences of 14 species indicates that C. tsinglingensisis closely related to Codonopsis minima in the Campanulaceae family.

| S-EPMC7707307 | biostudies-literature

The chromosome-level genome assembly of lance asiabell (Codonopsis lanceolata), a medicinal and vegetable plant of the Campanulaceae family.

Project description:Codonopsis lanceolata (2n = 2x = 16) belongs to the Campanulaceae family and is a valuable medicinal and vegetable plant primarily found in East Asia. Several studies have demonstrated its excellent pharmacological effects, for example in bronchial treatment. However, genomic information of C. lanceolata is scarce, hindering studies on crop improvement of the species. Here, we report a high-quality chromosome-level genome assembly of C. lanceolata based on a hybrid method using Nanopore long-read, Illumina short-read, and Hi-C data. The assembled genome was completed as 1,273 Mb (84.5% of the estimated genome size), containing eight pseudo-chromosomes, ranging from 101.3 to 184.3 Mb. The genome comprised of 71.3% repeat sequences and 46,005 protein-coding genes, of which 85.7% genes were functionally annotated. Completeness of the assembled genome and genes was assessed to be 97.5% and 90.4%, respectively, by Benchmarking Universal Single-Copy Orthologs analysis. Phylogenetic and synteny analysis revealed that C. lanceolata was closely related to Platycodon grandiflorus in the Campanulaceae family. Gene family evolution revealed significant expansion of related genes involved in saponin biosynthesis in the C. lanceolata genome. This is the first reference genome reported for C. lanceolata. The genomic data produced in this study will provide essential information for further research to improve this medicinal plant and will broaden the understanding of the Campanulaceae family.

| S-EPMC9929348 | biostudies-literature

The complete chloroplast genome sequence of Campanula zangezura (Campanulaceae).

Project description:The complete chloroplast genome sequence of Campanula zangezura was determined by Illumina pair-end sequencing. The complete cp genome was 166,331 bp in length, containing a large single-copy (LSC) region of 100,034 bp and a small single-copy (SSC) region of 7781 bp, which were separated by a pair of 29,258 bp inverted repeats (IRs). A total of 113 unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Among these genes, 17 genes contained one or two introns. The ML tree based on 74 protein-coding genes showed that C. zangezura formed a sister to the Campanula punctata and Campanula takesimana clade.

| S-EPMC7748725 | biostudies-literature

Complete chloroplast genome sequence of Campanula punctata Lam. (Campanulaceae).

Project description:The complete chloroplast genome of Campanula punctata Lam. was determined in this study. The total genome size was 169 341 bp in length, containing a pair of inverted repeats (IRs) of 29 637 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 102 323 bp and 7744 bp, respectively. The overall GC contents of the plastid genome were 38.8%. One hundred thirteen unique genes were annotated, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. In these genes, 15 genes contained one intron and 2 genes had two introns. A phylogenetic tree showed that Campanula punctata was closely related to Campanula takesimana.

| S-EPMC7871831 | biostudies-literature

The complete chloroplast genome of Adenophora triphylla (Asterales: Campanulaceae).

Project description:Adenophora triphylla (A. triphylla) is an important oriental herb belonging to the Campanulaceae family. A. triphylla complete chloroplast genome is composed of 239,431 bp, which form a large single-copy region (LSC, 178,906 bp), a small single-copy region (SSC, 55,819 bp), and 2 inverted repeats (IRs, 2,353 bp). There are 108 genes annotated, including 74 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. Phylogeny indicates that A. triphylla was belong to Adenophora genus as a sister group and most closely related to Adenophora divaricate.

| S-EPMC7819130 | biostudies-literature

Complete chloroplast genome sequence of Adenophora racemosa (Campanulaceae): Comparative analysis with congeneric species.

Project description:Adenophora racemosa, belonging to the Campanulaceae, is an important species because it is endemic to Korea. The goal of this study was to assemble and annotate the chloroplast genome of A. racemosa and compare it with published chloroplast genomes of congeneric species. The chloroplast genome was reconstructed using de novo assembly of paired-end reads generated by the Illumina MiSeq platform. The chloroplast genome size of A. racemosa was 169,344 bp. In total, 112 unique genes (78 protein-coding genes, 30 tRNAs, and 4 rRNAs) were identified. A Maximum likelihood (ML) tree based on 76 protein-coding genes divided the five Adenophora species into two clades, showing that A. racemosa is more closely related to Adenophora stricta than to Adenophora divaricata. The gene order and contents of the LSC region of A. racemosa were identical to those of A. divaricata and A. stricta, but the structure of the SSC and IRs was unique due to IR contraction. Nucleotide diversity (Pi) >0.05 was found in eleven regions among the three Adenophora species not included in sect. Remotiflorae and in six regions between two species (A. racemosa and A. stricta).

| S-EPMC7971521 | biostudies-literature

The complete chloroplast genome of Codonopsis convolvulacea subsp. vinciflora.

Project description:Codonopsis convolvulacea subsp. vinciflora is a commonly used and endangered herb in Tibetan medicine. The chloroplast genome was determined to be 187,634 bp in length and contained a large single-copy and a small single-copy region of 102,174 bp and 8552 bp, respectively. The genome is predicted to contain 140 genes, including 90 protein-coding genes, 42 tRNA genes, and 8 rRNA genes. The overall GC content of the genome is 38.72%. A phylogenetic tree reconstructed by 11 chloroplast genomes reveals that Codonopsis convolvulacea subsp. vinciflora is mostly related to C. tsinglingensis with bootstrap support values of 100%.

| S-EPMC8253173 | biostudies-literature