Browse
Submit Data
Databases
API
Help

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Park HS

PROVIDER: S-EPMC7871856 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Park Hyun-Seung HS Lee Jundae J Lee Sang-Choon SC Yang Tae-Jin TJ Yoon Jae Bok JB

Mitochondrial DNA. Part B, Resources 20160328 1

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- ...[more]

PMID: 33644333

Similar Datasets

Characterization of the complete chloroplast genome of a Peruvian landrace of Capsicum chinense Jacq. (Solanaceae), arnaucho chili pepper.

Project description:In this study, we sequenced the first complete chloroplast (cp) genome of a Peruvian chili pepper landrace, "arnacucho" (Capsicum chinense). This cp genome has a 156,931 bp in length with typical quadripartite structure, containing a large single copy (LSC) region (87,325 bp) and a 17,912 bp small single-copy (SSC) region, separated by two inverted repeat (IR) regions (25,847 bp); and the percentage of GC content was 37.71%. Arnaucho chili pepper chloroplast genome possesses 133 genes that consists of 86 protein-coding genes, 37 tRNA, eight rRNA, and two pseudogenes. Phylogenetic analysis revealed that this Peruvian chili pepper landrace is closely related to the undomesticated species C. galapagoense; all belong to the Capsiceae tribe.

| S-EPMC8741228 | biostudies-literature

The complete chloroplast genome of Capsicum frutescens (Solanaceae).

Project description:PREMISE OF THE STUDY:We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. METHODS AND RESULTS:Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. CONCLUSIONS:The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.

| S-EPMC4873274 | biostudies-literature

Complete chloroplast genome sequence of Passiflora serrulata Jacq. (Passifloraceae).

Project description:This study was the first report for the complete chloroplast genome of Passiflora serrulata Jacq. (Passifloraceae). The cp genome was 149,683 bp in length contained two inverted repeats (IRs) of 25,470 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 86,252 bp and 13,491 bp, respectively. A total of 110 functional genes were encoded, comprised 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. The GC content was 37.0%. The maximum likelihood phylogenetic tree indicated that P. serrulata was recovered as the member of subg. Passiflora and most closely related to the clade formed by P. serratodigitata and P. ligularis.

| S-EPMC7832543 | biostudies-literature

The complete chloroplast genome sequence of Polygonum chinense L.

Project description:Polygonum chinense is a traditional natural plant pharmaceutical with antimicrobial, antioxidant, and antidiarrheal effects and mainly distributed in China and Southeast Asian countries. The complete chloroplast sequence of P. chinense has been determined in this study. The cpDNA was 158,981 bp in length, containing a pair of inverted repeats of 30,872 bp each separated by a large and small single-copy region of 84,347 and 12,890 bp, respectively. The genome contained 86 protein-coding genes, eight rRNA genes, and 37 tRNA genes. The overall GC content of the chloroplast genome was 38%. Phylogenetic tree demonstrated that P. chinense closely related to Rheum palmatum and Rheum wittrockii.

| S-EPMC7782515 | biostudies-literature

Complete chloroplast genome sequence of Nicotiana tabacum TN90 (Solanaceae).

Project description:This study reported the complete nucleotide sequence of the Nicotiana tabacum TN90 chloroplast (cp) genome. The cpDNA was 155 992 bp in length and contained 133 individual genes (79 protein encoding genes, 30 tRNA genes and four rRNA genes). Maximum-likelihood (ML) phylogenetic tree for 17 species with Arabidopsis thaliana, Oryza sativa, and Anomochloa marantoidea as an outgroup resulted in a single tree with - lnL =542 222.71, where the Nicotiana tabacum TN90 plastid was clustered with three previous reported Nicotiana species: N. tomentosiformis, N. undulata and N. tabacum. The TN90 variety of tobacco cp genome sequence reported in this study will accelerate tobacco improvement in the future.

| S-EPMC7800119 | biostudies-literature

The complete chloroplast genome sequence of Nicotiana debneyi (Solanaceae).

Project description:In present study, we report the complete chloroplast genome of Nicotiana debneyi, a species endemic to eastern coast of Australia. The total genome size of N.debneyi is 156,073 bp in length, containing a large single-copy region of 86,672 bp, a small single-copy region of 18,581 bp, and two inverted repeat regions of 25,410 bp. The all GC content of N.debneyi chloroplast genome is 38.4%. It encodes a total of 129 unique genes, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes, of which seven tRNA, four rRNA and seven protein-coding genes are duplicated in the IR. Sixteen genes contain a single intron, and only two genes have two introns. Phylogenetic analysis results strongly supported that N.debneyi was closely related to Nicotiana sylvestris and Nicotiana tabacum.

| S-EPMC7995905 | biostudies-literature

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

Project description: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.

| S-EPMC7707502 | biostudies-literature

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.

| S-EPMC7707252 | biostudies-literature

Complete chloroplast genome sequence of Coyote tobacco (Nicotiana attenuata, Solanaceae).

Project description:In this study, we announce the complete chloroplast genome sequence of Nicotiana attenuata. The genome sequence of 155,941?bp consists of two inverted repeat (IRa and IRb) regions of 25,438?bp each, a large single-copy (LSC) region of 86,513?bp and a small single-copy (SSC) region of 18,524?bp. The overall GC content is 37.9% and the GC contents of LSC, IRs, and SSC are 36%, 43.2%, and 32.1%, respectively. The plastome with 129 annotated unique genes includes 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Using the whole chloroplast genome sequences alignment of 16 Solanaceae species a phylogenetic hypothesis is presented validating the position of N. attenuata within Nicotianeae.

| S-EPMC7800028 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Anisodus acutangulus (Solanaceae).

Project description:Anisodus acutangulus is a Solanaceae perennial plant, which is endemic to China and classified as an endangered species. In this study, we have sequenced the complete chloroplast genome of A. acutangulus, which is 156,079 bp in length, containing a large single-copy (LSC) region of 86,526 bp, a small single-copy (SSC) region of 17,741 bp and comprises a pair of inverted repeat regions (IRs) of 25,906 bp. Totally 134 genes were annotated, including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Its overall GC content is 37.6%. Phylogenetic analysis using total chloroplast genome DNA sequence of 21 species revealed that A. acutangulus was closely related to Hyoscyamus niger with 100% bootstrap value.

| S-EPMC7748740 | biostudies-literature