Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of the national tree of Peru, quina (Cinchona officinalis L., Rubiaceae).

ABSTRACT: Here, we report the first complete chloroplast (cp) genome of Cinchona officinalis. This cp genome has a 156,984 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (83,929 bp) and an 18,051 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (27,502 bp). The total GC content was 37.75%. Quina tree chloroplast genome possesses 135 genes that consisted of 89 protein-coding genes, 37 tRNA, eight rRNA, and one pseudogene. Phylogenetic analysis showed that C. officinalis is sister to C. pubescens and sister to them is Isertia laevis; all belong to the Cinchonoideae sub-family.

SUBMITTER: Arbizu CI

PROVIDER: S-EPMC8425725 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of the national tree of Peru, quina (Cinchona officinalis L., Rubiaceae).

Arbizu Carlos I CI Ferro-Mauricio Rubén D RD Chávez-Galarza Julio C JC Guerrero-Abad Juan Carlos JC Vásquez Héctor V HV Maicelo Jorge L JL

Mitochondrial DNA. Part B, Resources 20210906 9

Here, we report the first complete chloroplast (cp) genome of Cinchona officinalis. This cp genome has a 156,984 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (83,929 bp) and an 18,051 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (27,502 bp). The total GC content was 37.75%. Quina tree chloroplast genome possesses 135 genes that consisted of 89 protein-coding genes, 37 tRNA, eight rRNA, and one pseudogene ...[more]

PMID: 34514158

Similar Datasets

The complete chloroplast genome of coffee tree, Coffea arabica L. 'Typica' (Rubiaceae).

Project description:We presented complete chloroplast genome of Coffea arabica L. 'Typica' which is 155,187 bp long and has four subregions: 85,159 bp of large single copy (LSC) and 18,135 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.4% and those in the LSC, SSC, and IR regions are 35.4%, 31.3%, and 43.0%, respectively. Interestingly, almost most of sequence variations identified against five coffee chloroplast genomes are insertions and deletions.

| S-EPMC7687381 | biostudies-literature

The complete chloroplast genome of coffee tree, Coffea arabica L. 'Blue Mountain' (Rubiaceae).

Project description:We presented complete chloroplast genome of Coffea arabica BM1 which is 155,189 bp long and has four subregions: 85,159 bp of large single copy (LSC), and 18,135 bp of small single copy (SSC) regions are separated by 25,946 bp of inverted repeat (IR) regions including 131 genes (86 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content of the chloroplast genome is 37.4% and those in the LSC, SSC, and IR regions are 35.4, 31.3, and 43.0%, respectively. Low level of cultivar specific sequence variations was found among seven coffee chloroplast genomes.

| S-EPMC7687557 | biostudies-literature

The complete chloroplast genome of Coffea liberica (Gentianales: Rubiaceae).

Project description:Coffee is one of the most popular beverages around the world. As one of the best-known coffee species, Liberian coffee (Coffea liberica Bull ex Hiern 1876) has a high resistance to leaf rust, a devasting disease caused by Hemileia vastatrix. However, there are few reports on the systematic position and phylogenetic relationship of C. liberica at the chloroplast (cp) genome level. Thus, we successfully assembled its cp genome. The full length is 154,799 bp with a GC content of 37.48%. We have further annotated the cp genome and predicted 85 protein-coding genes together with 8 rRNAs and 37 tRNAs. Furthermore, a large single copy region (LSC), a small single copy region (SSC), an inverted repeat region a (IRa) and an inverted repeat region b (IRb) are identified with lengths of 84,868 bp, 18,121 bp, 25,905 bp and 25,905 bp, respectively. The phylogenetic tree indicates that C. liberica is closely related to C. canephora, which is consistent with a previous result obtained from genotyping-by-sequencing.

| S-EPMC9364704 | biostudies-literature

The complete chloroplast genome of Damnacanthus indicus C.F.Gaertn. (Rubiaceae).

Project description:Damnacanthus indicus C.F.Gaertn. is an understorey shrub widely distributed in East Asia. In this study, the complete chloroplast genome of D. indicus was assembled and annotated. The chloroplast genome is 153,997 bp in total length, consisting of a large single-copy region (LSC 85,159 bp), a small single-copy region (SSC 17,584 bp) and two inverted repeat regions (25,627 bp for IRA and IRB,respectively). It contains 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis indicated that D. indicus is sister to Mitchella repens, suggesting a close relationship of the two genera.

| S-EPMC8009129 | biostudies-literature

The complete chloroplast genome of Galega officinalis L.

Project description:Galega officinalis L. is a perennial herb of the Fabaceae family. The flowers of G. officinalis L. are colorful and suitable for ornamental purposes. It can be used as a food complement for animals and humans, and it could promote lactation in animals and humans. In this study, we obtained the complete chloroplast genome of G. officinalis L. and found it is 125,086 bp in length. The GC content of this genome is 34.18%. Among the 112 unique genes in the chloroplast genome of G. officinalis L., 30 tRNA, 4 rRNA and 78 protein-coding genes were successfully annotated. We constructed the maximum likelihood (ML) tree with 26 species, and concluded that G. officinalis is phylogenetically closely related to the genus of Cicer, Glycine and Desmodium.

| S-EPMC7928000 | biostudies-literature

Characterization of the complete chloroplast genome of Trailliaedoxa gracilis (Rubiaceae).

Project description:Trailliaedoxa gracilis (Rubiaceae) is a Chinese endemic monotypic genus distributed in southwestern China. This study reported the complete chloroplast genome of T. gracilis assembled from Illumina sequencing reads. The chloroplast genome size is 152,407 bp, containing a single large copy (LSC) region of 82,957 bp, a short single copy (SSC) region of 17,936 bp, and a pair of inverted repeats (IRs) of 25,757 bp. A total of 127 genes were found, including 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes. A phylogenetic analysis using the maximum likelihood algorithm revealed that T. gracilis belonged to the subfamily Ixoroideae and had the closest relationship with Scyphiphora hydrophyllacea.

| S-EPMC9817128 | biostudies-literature

The complete chloroplast genome of Psychotria asiatica, Linnaeus 1759 (Rubiaceae).

Project description:Psychotria asiatica is a typical traditional medicinal plant. Herein, we acquired and characterized the complete chloroplast (cp) genome sequence of P. asiatica to provide genomic resources for conservation genetics and phylogenetic studies of P. asiatica. The cp genome of P. asiatica is 154,652 bp in length and consists of a large single-copy (LSC) region with 85,106 bp, a small single-copy (SSC) region with 17,960 bp, and two inverted repeat regions (IRs) with 25,793 bp. The cp genome of P. asiatica comprises 127 genes, including 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The phylogenetic result confirmed that P. asiatica was closely related to Psychotria kirkii within the Rubiaceae.

| S-EPMC9176369 | biostudies-literature

Cinchona officinalis

Project description:Cinchona officinalis genome sequencing

| PRJNA728344 | ENA

The complete chloroplast genome sequence of traditional Chinese medicine Uncaria macrophylla (Rubiaceae).

Project description:Uncaria macrophylla (Rubiaceae) is a medicinal vine plant of the Rubiaceae family that was distributed in East Asia and Southeast Asia. The first complete chloroplast genome of Uncaria macrophylla was sequenced and assembled in this study. The genome is 155,138 bp in length and contained 129 encoded genes in total, including 79 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The phylogenomic analysis showed that U. macrophylla was closely related to Uncaria rhynchophylla according to the current sampling extent.

| S-EPMC9045754 | biostudies-literature

The complete chloroplast genome of the traditional Chinese herb, Uncaria rhynchophylla (Rubiaceae).

Project description:Uncaria rhynchophylla is a vine plant belonging to the family Rubiaceae and has been used as medicine for a long time in China. In this study, the complete chloroplast (cp) genome sequence of U. rhynchophylla was first reported and characterized. The cp genome was 154,605 bp in length and contains a pair of inverted repeats (IRs, 34,165 bp each) separated by a large (84,327 bp) and small (12,966 bp) single-copy regions. A total of 113 unique genes were predicted, including 79 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis suggested that U. rhynchophylla was closer to Neolamarckia cadamba.

| S-EPMC7748432 | biostudies-literature