Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete plastid genome sequence of Chloranthus fortunei (A. Gray) Solms-Laub. in Chloranthaceae.

ABSTRACT: Chloranthus fortunei (A. Gray) Solms-Laub. is a perennial herb in a basal angiosperm family Chloranthaceae. Here, we reported the complete plastid genome of C. fortunei using Illumina short-read data. The total genome size was 157,063 bp in length, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The gene content and order were consistent with previously reported Chloranthus plastid genomes. The overall GC content of the C. fortunei plastid genome was 39.0%. In the phylogenetic result, genus Chloranthus was monophyletic and divided into two subclades: C. japonicus+C. angustifolius+C. fortunei, and C. henryi+C. spicatus+C. erectus. Our phylogenetic result was consistent with previous phylogenetic studies, and was supported by a previously proposed infrageneric classification of the genus Chloranthus.

SUBMITTER: Kang JS

PROVIDER: S-EPMC9621198 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

The complete plastid genome sequence of Chloranthus fortunei (A. Gray) Solms-Laub. in Chloranthaceae.

Kang Jong-Soo JS Kim Bo-Yun BY Yoo Ki-Oug KO

Mitochondrial DNA. Part B, Resources 20221025 10

Chloranthus fortunei (A. Gray) Solms-Laub. is a perennial herb in a basal angiosperm family Chloranthaceae. Here, we reported the complete plastid genome of C. fortunei using Illumina short-read data. The total genome size was 157,063 bp in length, containing 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The gene content and order were consistent with previously reported Chloranthus plastid genomes. The overall GC content of the C. fortunei plastid geno ...[more]

PMID: 36325282

Similar Datasets

Complete chloroplast genome of Chloranthus henryi (chloranthaceae).

Project description:The complete chloroplast genome of Chloranthus henryi, an important traditional Chinese herbal medicine, was sequenced and characterized in this study. The genome size is 157,990 bp in length with 37.3% GC content. Two inverted repeats of 26,151 bp are separated by a large single-copy region (87,148 bp), and a small single-copy region (18,569 bp). A total of 131 genes were identified, including 86 protein-coding genes, 37 tRNA genes and 8 rRNA genes. Eight plastome accessions from Chloranthales, Austrobaileyales, Nymphaeales, and Amborellales were selected to assess the phylogenetic placement of genus.

| S-EPMC7687406 | biostudies-literature

The complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890 (Chloranthaceae).

Project description:In this study, we sequenced and assembled the complete chloroplast genome of Chloranthus nervosus Collett ex Hemsl. 1890. The total length of the complete chloroplast sequence was found to be 158,002 bp. It consisted of a large single-copy (LSC) region of 87,127 bp, a small single-copy (SSC) region of 18,541 bp, and a pair of inverted repeat (IR) regions, each with a length of 26,167 bp. The overall GC content of the complete chloroplast genome was 38.9%, with the LSC region, SSC region, and IR regions exhibiting GC contents of 37.4%, 34.1%, and 43.1%, respectively. The annotation of the chloroplast genome revealed a total of 131 genes, comprising 86 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis revealed that the seven sampled species of Chloranthus were divided into two clades. Within the clade characterized by long filamentous anther connectives, C. nervosus showed the closest relation to C. japonicus. These findings validated the previous preliminary results on the phylogenetic relationships of the seven species of Chloranthus with strong support.

| S-EPMC10653614 | biostudies-literature

The complete chloroplast genome sequence of the plant Euonymus fortunei (Celastraceae).

Project description:Chloroplast (cp) genome sequences become a useful popular tool for population and phylogeny in recent reports. Here, the complete cp genome of the Euonymus fortunei has been reconstructed from the whole-genome Illumina sequencing data. The circular genome is 157,639 bp in size, and comprises a pair of inverted repeat (IR) regions of 26,668 bp each, a large single copy (LSC) region of 85,956 bp and a small single copy (SSC) region of 18,347 bp. The total GC content is 37.2%, while the corresponding values of the LSC, SSC, and IR region are 35.1%, 31.7%, and 42.7%, respectively. The cp genome contains 126 genes, including 89 protein-coding genes, eight ribosomal RNA genes, and 29 transfer RNA genes and one pseudogene. The maximum-likelihood phylogenetic analysis showed a strong sister relationship with Euonymus japonicus in Celastraceae. Our findings provide a foundation for further investigation of cp genome evolution in E. fortunei and other higher plants.

| S-EPMC7800781 | biostudies-literature

Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida.

Project description:In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.

| S-EPMC4591262 | biostudies-literature

The complete plastid genome sequence of Begonia guangxiensis.

Project description:Begonia guangxiensis was assessed as endangered according to Red List of Chinese Plants. In this study, we described the complete plastid genome of B. guangxiensis. The plastid genome sequence of B. guangxiensis is 157,648 bp in size, having a large single-copy region (LSC) of 86,514 bp, a small single-copy region (SSC) of 18,076 bp, and two inverted repeat (IR) regions of 26,529 bp. The complete plastid genome of B. guangxiensis encoding 112 unique genes including 79 protein-coding genes, 29 tRNA genes, and four rRNA genes. The overall GC content of the plastid genome is 35.9%. Phylogenetic analysis confirmed that B. guangxiensis is closely related to B. varipeltata.

| S-EPMC7707394 | biostudies-literature

The complete chloroplast genome sequence of Alniphyllum fortunei (Styracaceae) from Fujian, China.

Project description:Alniphyllum fortunei is a subtropical tree species, a large deciduous tree with a tall and straight trunk, which is an excellent fast-growing and broad-leaved tree species with a wide range of uses we resequenced complete chloroplast (cp) genome of A. fortunei from Fujian, China. The whole genome was 154,166 bp in length, consisting of a pair of inverted repeats (IR 26,658 bp), a large single-copy region (LSC 82,438 bp), and a small single-copy region (SSC 18,367 bp). The complete genome contained 139 genes, including 89 protein-coding genes, 40 tRNA, and 8 rRNA genes. The phylogenetic analyses based on the complete chloroplast genome sequence provided solid evidence that A. fortunei has a close relationship with A. pterospermum and Bruinsmia polysperma.

| S-EPMC7889130 | biostudies-literature

Anti-inflammatory Lindenane Sesquiterpene Dimers from the Roots of Chloranthus fortunei.

Project description:In this study, eight lindenane-type sesquiterpene dimers, including five previously undescribed sesquiterpene dimers (1-5), were isolated from the roots of Chloranthus fortunei, and their structures were elucidated using 1D/2D NMR, HRESIMS, and ECD calculations. Compound 1 presents the second example of a type of novel 8,9-seco lindenane-type sesquiterpene dimer, considered a product of 8/9-diketone oxidation. Compounds 2 and 3 represent the third and fourth examples, respectively, of this kind of C-11 methine dimer. Furthermore, compound 4 was considered as an artifact generated from the radical reaction of a known compound chlojaponilide F (6), which was explained by the density functional theory quantum calculation. All isolates were evaluated for their protective activity against the LPS-induced pulmonary epithelial cell line with compound 7 exhibiting the most potent bioactivity. Further in vitro biological evaluation demonstrated that 7 reduced the production of reactive oxygen species and interleukin-1β, further regulated by the expression of the NLRP3. These results show that compound 7 exhibits therapeutic potential for lung inflammatory diseases.

| S-EPMC11325489 | biostudies-literature

The Complete Chloroplast Genome Sequence of Eupatorium fortunei: Genome Organization and Comparison with Related Species.

Project description:Eupatorium fortunei Turcz, a perennial herb of the Asteraceae family, is one of the horticultural and medicinal plants used for curing various diseases and is widely distributed in China and other Asian countries. It possesses antibacterial, antimetastatic, antiangiogenic, and antioxidant properties along with anticancer potential. However, the intrageneric classification and phylogenetic relationships within Eupatorium have long been controversial due to the lack of high-resolution molecular markers, and the complete chloroplast (cp) genome sequencing has not been reported with new evolutionary insights. In the present study, E. fortunei was used as an experimental material, and its genome was sequenced using high-throughput sequencing technology. We assembled the complete cp genome, and a systematic analysis was conducted for E. fortunei, acquiring the correspondence of its NCBI accession number (OK545755). The results showed that the cp genome of E. fortunei is a typical tetrad structure with a total length of 152,401 bp, and the genome encodes 133 genes. Analysis of the complete cp genomes of 20 Eupatorieae shows that the number of simple sequence repeats (SSRs) ranged from 19 to 36 while the number of long sequence repeats was 50 in all cases. Eleven highly divergent regions were identified and are potentially useful for the DNA barcoding of Eupatorieae. Phylogenetic analysis among 22 species based on protein-coding genes strongly supported that E. fortunei is more closely related to Praxelis clematidea and belongs to the same branch. The genome assembly and analysis of the cp genome of E. fortunei will facilitate the identification, taxonomy, and utilization of E. fortunei as well as provide more accurate evidence for the taxonomic identification and localization of Asteraceae plants.

| S-EPMC9859021 | biostudies-literature

The complete chloroplast genome sequence of Cyrtomium fortunei (Dryopteridaceae), an important medical fern.

Project description:The complete chloroplast genome of an important medical fern Cyrtomium fortunei has been sequenced. Its genome is 151,699 bp in length with a pair of inverted repeats (IRs, 23,875 bp), separated by a small single copy region (SSC, 21,625 bp) and a large single copy region (LSC, 82,324 bp). It contains 132 genes, covering 88 protein coding genes, 35 tRNA genes, eight rRNA genes, and one pseudogene. Maximum likelihood analysis indicates that the phylogenetic tree is monophyletic with three clades. Cyrtomium fortunei is closely related to C. devexiscapulae, which further forms a sister clade to C. falcatum.

| S-EPMC7799596 | biostudies-literature

The complete plastid genome sequence of Ilex micrococca Maxim.

Project description:Ilex micrococca Maxim. is a widely distributed species of Aquifoliaceae in Eastern Asia. In this study, the complete chloroplast (cp) genome sequence of I. micrococca was assembled and characterized by high-throughput sequencing data. The entire cp genome was 157,782 bp in length, containing a large single-copy region (LSC) of 87,200 bp, and a small single-copy region (SSC) of 18,434 bp, which were separated by a pair of 26,074 bp inverted repeat (IR) regions. The cp genome contained 134 genes, including 89 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. Eighteen genes occur in double copies. The overall GC content is 37.6%. The phylogenetic tree reconstructed by 13 chloroplast genomes reveals that I. micrococca is most related with Ilex wilsonii. The complete cp genome provides valuable information for further phylogenetic and cp genetic engineering studies of this important Ilex species I. micrococca.

| S-EPMC7755317 | biostudies-literature