Browse
Submit Data
Databases
API
Help

Dataset Information

53 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chloroplast genome and phylogenetic analyses of Poncirus trifoliata (Rutaceae).

ABSTRACT: Poncirus trifoliata is an important medicinal plant that is used to treat human diseases. In this study, the complete chloroplast (cp) genome of P. trifoliata was assembled based on the Illumina sequencing reads. The cp genome of P. trifoliata was 160,260 bp and contained two short inverted repeat regions (27,029 bp) which were separated by a small single copy region (18,760 bp) and a large single copy region (87,442 bp). The cp genome encodes 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes and 4 ribosomal RNA genes. The topology of the phylogenetic tree showed that P. trifoliata is closely clustered with genus Citrus.

SUBMITTER: He SL

PROVIDER: S-EPMC7510678 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Chloroplast genome and phylogenetic analyses of Poncirus trifoliata (Rutaceae).

He Shui-Lian SL Tian Yang Y Yang Yang Y Shi Chong-Ying CY

Mitochondrial DNA. Part B, Resources 20200601 3

Poncirus trifoliata is an important medicinal plant that is used to treat human diseases. In this study, the complete chloroplast (cp) genome of P. trifoliata was assembled based on the Illumina sequencing reads. The cp genome of P. trifoliata was 160,260 bp and contained two short inverted repeat regions (27,029 bp) which were separated by a small single copy region (18,760 bp) and a large single copy region (87,442 bp). The cp genome encodes 113 unique genes, including 79 ...[more]

PMID: 33366973

Similar Datasets

Analysis of Poncirus polyandra (Rutaceae) chloroplast genome and its phylogenetic implications.

Project description:Poncirus polyandra is a threatened plant in China Now, the complete chloroplast (cp) genome of P. polyandra was assembled. The cp genome of P. polyandra was 160,212 bp in length, it consists of a pair of inverted repeats ((IRa and IRb) regions (27,016 bp) separated by the large single-copy (LSC, 87,407 bp) and small single-copy (SSC, 18,775 bp) regions. The cp genome encodes 105 unique genes, including 70 protein-coding genes, 30 transfer RNA genes, 4 ribosomal RNA genes, and 1 pseudogene. The phylogenetic tree of Rutaceae showed that P. polyandra was clustered together with genus Citrus and Poncirus.

| S-EPMC7687512 | 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 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

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 of Zanthoxylum acanthopodium DC. (Rutaceae) and its phylogenetic analysis.

Project description: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.

| S-EPMC7594859 | biostudies-literature

Comparative chloroplast genome and phylogenetic analyses of Chinese Polyspora.

Project description:Polyspora Sweet (Theaceae) are winter ornamental landscape plants native to southern and southeastern Asia, some of which have medicinal value. The chloroplast (cp) genome data of Polyspora are scarce, and the gene evolution and interspecific relationship are still unclear. In this study, we sequenced and annotated Polyspora chrysandra cp genome and combined it with previously published genomes for other Chinese Polyspora species. The results showed that cp genomes of six Chinese Polyspora varied in length between 156,452 bp (P. chrysandra) and 157,066 bp (P. speciosa), but all contained 132 genes, with GC content of 37.3%, and highly similar genes distribution and codon usage. A total of eleven intergenic spacer regions were found having the highest levels of divergence, and eight divergence hotspots were identified as molecular markers for Phylogeography and genetic diversity studies in Polyspora. Gene selection pressure suggested that five genes were subjected to positive selection. Phylogenetic relationships among Polyspora species based on the complete cp genomes were supported strongly, indicating that the cp genomes have the potential to be used as super barcodes for further analysis of the phylogeny of the entire genus. The cp genomes of Chinese Polyspora species will provide valuable information for species identification, molecular breeding and evolutionary analysis of genus Polyspora.

| S-EPMC9512918 | biostudies-literature

Characterization of the complete chloroplast genome of the medicinal plant Orixa japonica (Rutaceae) in Zhejiang Province and its phylogenetic analysis within family Rutaceae.

Project description:Orixa japonica Thunb. is an important medicinal plant belonging to the family Rutaceae. In this study, we determined the the complete chloroplast (cp) genome of O. japonica, which was 158,525 bp in length containing one large single copy region (85,965 bp), one small single copy region (18,552 bp), and a pair of inverted repeat regions (27,004 bp each). A total of 134 genes were annotated in the cp genome, including 88 protein coding genes, 37 tRNA genes, eight rRNA genes, and one pseudo gene ycf1. According to the phylogenetic analysis, O. japonica clustered together with Casimiroa edulis with high bootstrap value, indicating a close genetic relationship with subfamily Amyridoideae.

| S-EPMC8158279 | biostudies-literature

Chloroplast genome characteristic, comparative and phylogenetic analyses in Capsicum (Solanaceae).

Project description:BackgroundCapsicum (Solanaceae) is a globally important vegetable crop and is also used therapeutically in traditional medicine systems. However, little is known of the genetic variation within the commonly grown cultivars, the evolutionary relationships and differences in the chloroplast (cp.) genomes between Capsicum species remain unclear.ResultsThe cp. genomes of 32 Capsicum varieties in three species from 6 countries were investigated. The cp. genome of Capsicum was found to be ~ 156 kb in length and to contain 113 unique genes, of which 79 encoded proteins, 30 encoded transfer tRNAs, and 4 were for ribosomal RNAs. The 32 varieties that we chose for study represented 13 genotypes, containing a total of 608 indels, 83 SNPs, 47 SSRs and 281-306 repeat sequences. We then included several previously sequenced Capsicum cp. genomes, and found that the nine investigated species showed a number of differences in the characteristics of the four IR boundaries, and it was the non-coding regions that contained the most variable regions. We conducted a phylogenetic reconstruction using the cp. genomes of 43 representative species of Solanaceae, and the resulting phylogeny generally reflected the currently accepted classification, with the species of the pungent group having close relationship with one another.ConclusionsThis study provides a comprehensive analysis of Capsicum chloroplast genomes, revealing significant variations in IR boundaries and other genomic features. These findings enhance our understanding of Capsicum evolution and genetic diversity.

| S-EPMC11542203 | biostudies-literature

Phylogenetic relationships of Zieria (Rutaceae) inferred from chloroplast, nuclear, and morphological data.

Project description:Zieria Sm. (Rutaceae, Boronieae) is predominantly native to eastern Australia except for one species, which is endemic to New Caledonia. For this study, sequence data of two non-coding chloroplast regions (trnL-trnF, and rpl32-trnL), one nuclear region (ITS region) and various morphological characters, based on Armstrong's (2002) taxonomic revision of Zieria, from 32 of the 42 described species of Zieria were selected to study the phylogenetic relationships within this genus. Zieria was supported as a monophyletic group in both independent and combined analyses herein (vs. Armstrong). On the basis of Armstrong's (2002) non-molecular phylogenetic study, six major taxon groups were defined for Zieria. The Maximum-parsimony and the Bayesian analyses of the combined morphological and molecular datasets indicate a lack of support for any of these six major taxon groups. On the basis of the combined Bayesian analysis consisting of molecular and morphological characters, eight major taxon groups are described for Zieria: 1. Zieriacytisoides group, 2. Zieriagranulata group, 3. Zierialaevigata group, 4. Zieriasmithii group, 5. Zieriaaspalathoides group, 6. Zieriafurfuracea group, 7. Zieriamontana group, and 8. Zieriarobusta group. These informal groups, except for of the groups Zieriarobusta and Zieriacytisoides, correspond to the clades with posterior probability values of 100.

| S-EPMC4329389 | biostudies-literature

Phylogenetic relationships of Vepris (Rutaceae) inferred from chloroplast, nuclear, and morphological data.

Project description:The tribe Toddalieae Hook. F. (Rutaceae) has been controversial since its inception by Bentham and Hooker. The nine taxa examined, Acronychia J.R. & G.Foster, Diphasia Pierre, Diphasiopsis Mendonca, Fagaropsis Mildbr.ex. Siebenl., Oricia Pierre, Teclea Delile, Toddaliopsis Engl., Toddalia Juss. and Vepris Comm. ex. A. Juss, have been recognized under the tribe Toddalieae or Tribes Acronychia, Phellodendron and Toddalia. More recently Araliopsis Engl., Diphasia, Diphasiopsis, Oricia, Teclea, and Toddaliopsis have been incorporated into the genus Vepris, while Toddalia and Fagaropsis have continued to be recognized as closely related. For this study, sequence data of one non-coding chloroplast region (trnL-F) and one nuclear region (ITS) and various morphological characters, based on Mziray's taxonomic studies were examined to try to elucidate these relationships. This study found that the taxa Diphasia, Diphasiopsis, Oricia, Teclea, Toddaliopsis, Vepris, Toddalia eugeniifolia Engl. and Toddalia glomerata F. Hoffm. form a monophyletic group. Due to the amount of intrageneric and intraspecific variation, species delimitations were difficult to determine; however, these genera should be united into Vepris. The analyses also confirmed that Toddalia asiatica (L.) Lam., Zanthoxylon sp. and Fagaropsis angolensis (Engl.) H.M. Gardner are the closest relatives to this group.

| S-EPMC5342198 | biostudies-literature