Browse
Submit Data
Databases
API
Help

Dataset Information

44 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Zanthoxylum acanthopodium DC. (Rutaceae) and its phylogenetic analysis.

ABSTRACT: We sequenced the complete chloroplast genome of Zanthoxylum acanthopodium via high-throughput sequencing technology, and analyzed its structural characteristics and phylogenetic relationships. The chloroplast exhibits a genome length of 158,473 bp, including a pair of inverted repeat regions (IRa and IRb) of 27,369 bp, a small single-copy (SSC) region of 17,629 bp and a large single-copy (LSC) region of 85,570 bp. The annotation analysis identified 112 genes, containing 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The phylogenetic analysis showed that Z. acanthopodium was closely related to Z. piperitum and Z. tragodes.

SUBMITTER: Li HL

PROVIDER: S-EPMC7594859 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Zanthoxylum acanthopodium DC. (Rutaceae) and its phylogenetic analysis.

Li Hai-Ling HL Zhou Nong N Guo Dong-Qin DQ

Mitochondrial DNA. Part B, Resources 20201027 3

We sequenced the complete chloroplast genome of Zanthoxylum acanthopodium via high-throughput sequencing technology, and analyzed its structural characteristics and phylogenetic relationships. The chloroplast exhibits a genome length of 158,473 bp, including a pair of inverted repeat regions (IRa and IRb) of 27,369 bp, a small single-copy (SSC) region of 17,629 bp and a large single-copy (LSC) region of 85,570 bp. The annotation analysis identified 112 genes, containing 78 protein-coding ...[more]

PMID: 33367039

Similar Datasets

The complete chloroplast genome of Zanthoxylum piasezkii Maxim. (Rutaceae) and its phylogenetic analysis.

Project description:Zanthoxylum piasezkii Maxim. is a widely distributed species of edible medicinal plant in China. It has been used for traditional spicy condiment and medicinal ingredients for quite a long time. In this study, the complete chloroplast genome sequence of Z. piasezkii was first reported and characterized from sequencing data. The complete chloroplast genome was determined to be 158,728 bp in length, consisting of a large single-copy (LSC) region (85,918 bp) and a small single copy (SSC) region (17,612 bp), which were separated by a pair of 27,599 bp inverted repeat (IR) regions. The chloroplast genome is predicted to contain 132 genes, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of cpDNA is 38.4%. The phylogenetic analysis of 12 complete chloroplast genomes reveals that Z. piasezkii is mostly related to the congeneric Z. bungeanum.

| S-EPMC7872585 | biostudies-literature

The complete chloroplast genome sequence of Zanthoxylum undulatifolium Hemsl. (Rutaceae).

Project description:Zanthoxylum undulatifolium is an excellent economic tree species with important medical value. This study reports the first complete chloroplast genome sequence of Z. undulatifolium. Its whole chloroplast genome is 158,400 bp in length, including a large single-copy (LSC) region of 85,898 bp, a small single-copy (SSC) region of 17,610 bp, and two inverted repeat (IR) regions of 27,446 bp. The chloroplast genome contains a total of 132 genes, comprising 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome is 38.46%, with the corresponding values in the LSC, SSC, and IR regions are 36.87%, 33.51%, and 42.55%, respectively. Phylogenetic analysis revealed the sister relationship between Z. undulatifolium and Z. bungeanum.

| S-EPMC8856060 | biostudies-literature

Characterization of the complete chloroplast genome of Zanthoxylum esquirolii Levl. (Rutaceae).

Project description:Zanthoxylum esquirolii Léveillé 1914 is mainly distributed in southwest China, and its wild germplasm resources are scarce and in urgent need of conservation. In this study, we report the first complete chloroplast genome sequence of Z. esquirolii using next-generation sequencing. The circular genome is 158,390 bp in length, containing two inverted repeat (IR) regions of 27,622 bp separated by a large single copy (LSC) region of 85,580 bp and a small single copy (SSC) region of 17,566 bp. The chloroplast genome contains a total of 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome was 38.46%, with corresponding values in the LSC, SSC, and IR regions of 36.84%, 33.55%, and 42.51%, respectively. The phylogenetic tree revealed that Z. esquirolii Levl. formed a clade with Z. piperitum DC., Z. bungeanum Maxim., Z. simulans Hance and Z. sp. NH-2018, and had a strongly supported sister relationship with Z. bungeanum.

| S-EPMC9518235 | biostudies-literature

Complete chloroplast genome sequence of Zanthoxylum nitidum (Rutaceae), an important medicinal shrub.

Project description:Zanthoxylum nitidum (Rutaceae) is a scandent prickly shrub and widely distributed in South China. It's well known for its valuable medicinal values due to contains some important secondary metabolites. Here, we first report and characterize its complete chloroplast genome based on Illumina paired-end sequencing data. The complete plastid genome was 157,253 bp, which contained inverted repeats (IR) of 27,618 bp separated by a large single-copy (LSC) and a small single copy (SSC) of 84,382 bp and 17,635 bp, respectively. The cpDNA contains 132 genes, comprising 87 protein-coding genes, 37 tRNA genes, 8 rRNA genes. The overall GC content of the plastome is 38.5%. The phylogenetic analysis of 20 selected chloroplast genomes demonstrated that Z. nitidum is closely related to the congeneric Z. bungeanum.

| S-EPMC7707648 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Citrus clementina (Rutaceae).

Project description:Citrus, which is widely cultivated in tropical and subtropical climates, is one of the most important crops in the world. Here, we assembled and annotated the complete chloroplast genome of Citrus clementina (C. clementina) using Illumina sequencing data. This chloroplast genome exhibited a typical quadripartite structure of 154,042 bp in length, and the overall GC content was 38.42%. A total of 134 genes (90 protein-coding genes, 36 tRNAs, and eight rRNAs) were predicted in this chloroplast genome. Phylogenetic analysis strongly supported that C. clementina was evolutionarily close to Citrus sunki.

| S-EPMC8439215 | biostudies-literature

The complete chloroplast genome of Zanthoxylum stenophyllum Hemsl. (Rutaceae), a traditional Chinese medicinal plant.

Project description:Zanthoxylum stenophyllum Hemsl., a type species for the genus Zanthoxylum (Rutaceae), is a traditional medicinal plant. We studied the complete chloroplast genome of this species using BGISEQ-500 platform. The chloroplast genome was 158,314 bp in size with a GC content of 38.45%. The genome contained two short inverted repeat (IRa and IRb) regions of 27,052 bp, a large single-copy region (LSC, 86,029 bp) and a small single-copy region (SSC, 18,181 bp). The annotated complete chloroplast genome contains 133 distinct genes, including 88 protein-coding genes, 37 transfer RNAs (tRNAs), and 8 ribosomal RNAs (rRNAs). Phylogenetic analysis indicated that Z. stenophyllum is clustered with Z. schiniflium and Z. pinnatum in the same branch with 100% bootstrap support. This complete chloroplast genome provides valuable genomic information for the molecular phylogeny and sustainable utilization of Zanthoxylum.

| S-EPMC9487917 | biostudies-literature

Assembly and phylogenetic analysis of the complete chloroplast genome of Citrus aurantium (Rutaceae).

Project description:Citrus aurantium (C. aurantium), belonging to the family Rutaceae, is usually utilized as a flavoring and acidifying agent for food. This study assembled and characterized the complete chloroplast (cp) genome of C. aurantium. The cp genome was 160,140 bp in length, containing a pair of inverted repeats (IRs, 26,996 bp each), which is separated by a large single-copy (LSC, 87,763 bp) region and a small single copy (SSC, 18,385 bp) region. The cp genome has overall GC content of 38.48% and 135 genes, composing of 90 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Phylogenetic analysis based on 25 cp genomes highly supported that C. aurantium was evolutionarily close to Cirtus sinensis (C. sinensis).

| S-EPMC7510620 | biostudies-literature

The complete chloroplast genome sequence of Zanthoxylum ailanthoides Sieb. et. Zucc (Rutaceae): an important medicinal plant.

Project description:Zanthoxylum ailanthoides is a deciduous tree, with important medicinal and economic values. The complete chloroplast genome sequence of Z. ailanthoides was assembled and the phylogenetic relationship to other species was inferred in this study. The chloroplast genome is 157,209 bp in length, including two inverted repeats of 26,408 bp, a large single-copy of 86,099 bp and a small single copy of 18,294 bp. Moreover, the chloroplast genome contains 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome is 38.4%. The phylogenetic analysis indicated that Z. ailanthoides was grouped with a clade containing the species of Z. multijugum, Z. calcicola, Z. oxyphyllum, Z. stenophyllum, and the genus was closely related to Phellodendron. This study contributes to a better understanding of the phylogenetic relationships among Zanthoxylum species.

| S-EPMC11018064 | biostudies-literature

Characterization and phylogenetic analysis of the complete chloroplast genome of Emilia sonchifolia (L.) DC.

Project description:Emilia sonchifolia is a herb with antioxidant, anti-inflammatory, antitumor, and wound healing properties. The complete chloroplast genome (cp genome) of the genus Emilia was sequenced for the first time. The cp genome of E. sonchifolia is 151,474 bp in length. It contained a large single-copy (LSC) region (84,004 bp), and small single-copy (SSC) region (17,980 bp), and two inverted repeats (IRs, 24,745 bp). Phylogenetic analysis of 24 species was conducted. E. sonchifolia was found to be closely related to Pericallis hybrida and Dendrosenecio spp. The sequenced cp genome would be useful to understand the phylogeny and genomic studies of the genus Emilia.

| S-EPMC9815244 | biostudies-literature

Complete chloroplast genome of Senna spectabilis (DC.) H.S. Irwin & Barneby (Fabaceae) and phylogenetic analysis.

Project description:Senna spectabilis (DC.) H.S. Irwin & Barneby is a popular ornamental tree as well as a traditional medical plant in Cameroon. In this study, we sequenced and annotated the complete chloroplast genome of S. spectabilis and reconstructed the phylogenetic relationship of the tribe Cassieae. The length of the chloroplast genome was determined to be 162,754 bp, containing a pair of inverted repeats of 25,413 bp which separated by a small single-copy (SSC) region of 20,161 bp and a large single-copy (LSC) region of 91,767 bp. The cp genome encodes 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The percentage of total GC content of this genome was 35.7%. The phylogenetic analysis indicates that S. spectabilis with the sampled Senna species formed a well-supported monophyletic clade.

| S-EPMC7782949 | biostudies-literature