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 Gynura japonica and its phylogenetic implications.

ABSTRACT: Gynura japonica (Asteraceae) is a folk herbal medicine with multi-pharmacological functions involving analgesic, hemostatic and antiangiogenic activities. The study was conducted to assemble the complete chloroplast (cp) genome of G. japonica through a genome-skimming approach. The assembled cp genome was 151,023 bp in size, with 62.8% AT content, consisting of a large single copy (LSC) of 83,185 bp, two copies of inverted repeat (IRa and IRb) of 24,847 bp, and a small single copy (SSC) of 18,144 bp. The cp genome of G. japonica contained 133 genes, including eight ribosomal RNA genes (rRNAs), 37 transfer RNA genes (tRNAs), 86 protein-coding genes (PCGs), and two pseudogenes (ψycf1 and ψrps19). Our phylogenomic analysis based on whole plastid genomes strongly supports G. japonica is a sister to the clade including Crassocephalum crepidioides and Jacobaea vulgaris.

SUBMITTER: Li M

PROVIDER: S-EPMC9341369 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete chloroplast genome of Gynura japonica and its phylogenetic implications.

Li Mimi M Xian Xin X Ren Bingru B Wang Hongjiang H Li Weilin W Chen Jian J

Mitochondrial DNA. Part B, Resources 20220729 7

Gynura japonica (Asteraceae) is a folk herbal medicine with multi-pharmacological functions involving analgesic, hemostatic and antiangiogenic activities. The study was conducted to assemble the complete chloroplast (cp) genome of G. japonica through a genome-skimming approach. The assembled cp genome was 151,023 bp in size, with 62.8% AT content, consisting of a large single copy (LSC) of 83,185 bp, two copies of inverted repeat (IRa and IRb) of 24,847 bp, and a small single copy ...[more]

PMID: 35923637

Similar Datasets

Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis.

Project description:Camellia is an economically, ecologically and phylogenetically valuable genus in the family Theaceae. The frequent interspecific hybridization and polyploidization makes this genus phylogenetically and taxonomically under controversial and require detailed investigation. Chloroplast (cp) genome sequences have been used for cpDNA marker development and genetic diversity evaluation. Our research newly sequenced the chloroplast genome of Camellia japonica using Illumina HiSeq X Ten platform, and retrieved five other chloroplast genomes of Camellia previously published for comparative analyses, thereby shedding lights on a deeper understanding of the applicability of chloroplast information. The chloroplast genome sizes ranged in length from 156,607 to 157,166 bp, and their gene structure resembled those of other higher plants. There were four categories of SSRs detected in six Camellia cpDNA sequences, with the lengths ranging from 10 to 17bp. The Camellia species exhibited different evolutionary routes that lhbA and orf188, followed by orf42 and psbZ, were readily lost during evolution. Obvious codon preferences were also shown in almost all protein-coding cpDNA and amino acid sequences. Selection pressure analysis revealed the influence of different environmental pressures on different Camellia chloroplast genomes during long-term evolution. All Camellia species, except C. crapnelliana, presented the identical rate of amplification in the IR region. The datasets obtained from the chloroplast genomes are highly supportive in inferring the phylogenetic relationships of the Camellia taxa, indicating that chloroplast genome can be used for classifying interspecific relationships in this genus.

| S-EPMC6508735 | biostudies-literature

Complete Chloroplast Genome of Medicinal Plant Lonicera japonica: Genome Rearrangement, Intron Gain and Loss, and Implications for Phylogenetic Studies.

Project description:The complete chloroplast (cp) genome of Lonicera japonica, a common ornamental and medicinal plant in North America and East Asia, was sequenced and analyzed. The length of the L. japonica cp genome is 155,078 bp, contains a pair of inverted repeat regions (IRa and IRb), of 23,774 bp each, as well as large (LSC, 88,858 bp) and small (SSC, 18,672 bp) single-copy regions. A total of 129 genes were identified in the cp genome, 16 of which were duplicated within the IR regions. Relative to other plant cp genomes, the L. japonica cp genome had a unique rearrangement between trnI-CAU and trnN-GUU. In L. japonica cpDNA, rps19, rpl2, and rpl23 move to the LSC region, from the IR region. The ycf1 pesudogene in the IR region is lost, and only one copy locates in the SSC region. Comparative cp DNA sequence analyses of L. japonica with other cp genomes reveal that the gene order, and the gene and intron contents, are slightly different. The introns in ycf2 and rps18 genes are found for the first time. Four genes (clpP, petB, petD, and rpl16) lost introns. However, its genome structure, GC content, and codon usage were similar to those of typical angiosperm cp genomes. All preferred synonymous codons were found to use codons ending with A/T. The AT-rich sequences were less abundant in the coding regions than in the non-coding ones. A phylogenetic analysis based on 71 protein-coding genes supported the idea that L. japonica is a sister of the Araliaceae species. This study identified unique characteristics of the L. japonica cp genome that contribute to our understanding of the cpDNA evolution. It offers valuable information for the phylogenetic and specific barcoding of this medicinal plant.

| S-EPMC6155926 | biostudies-literature

Characteristics and phylogenetic analysis of the complete chloroplast genome of Paeonia japonica (Paeoniaceae).

Project description:Paeonia japonica, distributed throughout Asia, is a traditional medicinal herb in Korea, with many potential beneficial effects including pain-relieving, anti-inflammatory, and anti-cancer activities. Despite its high pharmacological value, the genetic information on Paeonia japonica remains limited. In this study, the chloroplast genome of P. japonica was sequenced using next-generation sequencing (NGS) technology and genome and phylogeny were analyzed using multiple tools. The chloroplast genome of P. japonica was 152,731 bp in length with an inverted repeat region of 26,656 bp, including a large single-copy region of 84,389 bp and a small single copy region of 17,030 bp. The P. japonica chloroplast genome included 113 genes comprising 80 protein-coding genes, 27 tRNA, and 5 rRNA genes. Phylogenetic analysis indicated that P. japonica and P. obovata share a close evolutionary relationship.

| S-EPMC7954510 | biostudies-literature

The complete chloroplast genome of Atractylodes japonica Koidz. ex Kitam. and its phylogenetic inference.

Project description:Atractylodes japonica Koidz. ex Kitam. is a perennial herbal plant, and its dried rhizomes have been widely used as traditional medicine in China and Japan. In this study, we assembled and annotated the complete chloroplast (cp) genome sequence of A. japonica using the high-throughput sequencing approach. The cp genome of A. japonica is 153,208 bp in length with the overall GC content of 37.7%, including two inverted repeat (IR) regions of 25,147 bp, which was separated by a large single-copy (LSC) region of 84,255 bp and a small single-copy (SSC) region of 18,659 bp. 113 unique genes were annotated in the genome, including 80 protein-coding genes, 29 represented tRNA genes, and four denoted rRNA genes. A maximum-likelihood phylogenetic analysis with 38 complete cp sequences showed that Atractylodes formed a monophyletic clade, and A. japonica and A. koreana formed a subclade in Atractylodes. This study provides the chloroplast genome structure features and phylogenetic relationship of A. japonica.

| S-EPMC8344787 | biostudies-literature

The first complete chloroplast genome of Hylomecon japonica and its phylogenetic position within Papaveraceae.

Project description:Hylomecon japonica, a widespread species in East Asia, is a valuable horticultural and medicinal plant. Here, we obtained the first complete sequence of the H. japonica chloroplast genome. The complete cp genome was 160,011 bp long, with a large single-copy region (LSC, 88,165 bp) and a small single copy region (SSC, 18,378 bp) separated by a pair of inverted repeats (IRs, 26,734 bp). The cp genome contained 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis indicated that H. japonica is close related with Coreanomecon hylomeconoides.

| S-EPMC7687558 | biostudies-literature

Complete chloroplast genome of Isoetes japonica (Isoetaceae).

Project description:Isoetes japonica A. Braun is a heterosporous quillwort living in low-altitude areas in Japan. In the present study, the complete chloroplast genome of I. japonica was assembled and annotated. This chloroplast genome is a circular structure of 145,517 bp in length, comprising a pair of inverted repeat (IR) regions of 13,204 bp each, a large single copy (LSC) region of 91,868 bp, and a small single copy (SSC) region of 27,241 bp. The chloroplast genome contains 135 genes, including 78 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that I. japonica is sister to I. sinensis and I. yunguiensis. These results provide additional resources for the future studies on Isoetes species.

| S-EPMC9668274 | biostudies-literature

Complete chloroplast genome of Lonicera ligustrina Wall. (Caprifoliaceae) and its phylogenetic implications.

Project description:Lonicera ligustrina is a folk medicinal herb in China and India with highly potential medicinal value. Here, we reported the complete chloroplast (cp) genome of L. ligustrina (GenBank accession number: ON968694). The cp genome was 155,330 bp long, with a large single-copy region (LSC) of 88,855 bp and a small single-copy region (SSC) of 18,647 bp separated by a pair of inverted repeats (IRs) of 23,914 bp. We also reconstructed the phylogeny of Lonicera using maximum likelihood (ML) method, including our data and previously reported cp genomes of related taxa. The current study indicated that L. ligustrina is sister with the Nintooa clade of subgen. Lonicera.

| S-EPMC10461517 | biostudies-literature

Complete chloroplast genome of endangered species Dipterocarpus retusus Blume (Dipterocarpaceae) and its phylogenetic implications.

Project description:Dipterocarpus retusus Blume is an endangered species on the IUCN Red List. In this study, we reported the complete chloroplast (cp) genome of D. retusus (GenBank accession number: OP271853). The cp genome was 154,303 bp long, with a large single-copy (LSC) region of 85,586 bp and a small single-copy (SSC) region of 20,273 bp separated by a pair of inverted repeats (IRs) of 24,222 bp. It encodes 128 genes, including 84 protein-coding genes, 36 tRNA genes, and eight ribosomal RNA genes. We also reconstructed the cp genome phylogeny of Dipterocarpus, which indicated D. retusus was closely related with the sympatric species D. gracilis. This study may contribute valuable information to the phylogenetic relationships within the genus Dipterocarpus.

| S-EPMC11370694 | biostudies-literature

The complete chloroplast genome sequence of Dendrobium densiflorum and its phylogenetic implications.

Project description:Dendrobium is one of the largest genera in Orchidaceae with approximately 1500 species. Many of them have been used as Traditional Chinese Medicine (TCM) for hundreds of years. Here, the first complete chloroplast genome sequence of D. densiflorum was reported and characterized. The complete cpDNA of D. densiflorum is a circular molecule of 153,122 bp, which contains 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Our phylogenetic analysis indicated that the newly sequenced cpDNA of D. densiflorum could be used for the phylogenetic study of Dendrobium species.

| S-EPMC7782869 | biostudies-literature

The complete chloroplast genome of Sophora davidii (Fabaceae) and its phylogenetic implications.

Project description:Sophora davidii (Franch.) Pavol. is a deciduous or evergreen shrubs belonging to the genus Sophora, Fabaceae. The roots of S. davidii have been traditionally used as a medicinal herb in China to clear internal heat, relieve sore throat, and reduce swelling. Here we sequenced the whole genome of the chloroplast of S. davidii. The complete length of the chloroplast genome in S. davidii is 153,584 bp, containing a large single-copy region of 83,930 bp, a small single-copy region of 15,008 bp, and a pair of inverted repeats regions of 25,823 bp. The total guanine-cytosine (GC) percentage of the chloroplast genome was 36.7%. A total of 131 genes were annotated from the chloroplast genome of S. davidii, including 85 protein-coding genes, 8 rRNA genes and 38 tRNA genes. The phylogenetic analysis showed that S. davidii is closely related to the other three species of genus Sophora.

| S-EPMC8942534 | biostudies-literature