Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome of Homalocladium platycladum (Polygonaceae) and its phylogenetic analysis.

ABSTRACT: Homalocladium platycladum is a fascinating ornamental plant that has long been used in Chinese medicine. Here, we characterize the complete chloroplast genome sequence of this plant (GenBank: NC_062330). This circular genome has a total length of 163,202 bp containing a large single-copy region (87,820bp), a small single-copy region (13,538bp), and a pair of inverted repeat regions (30,922bp). A total of 130 predicted genes were identified, including 85 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis demonstrated that H. platycladum belongs to the Polygonaceae family and is highly analogous with Homalocladium and Muehlenbeckia families.

SUBMITTER: Chen Z

PROVIDER: S-EPMC9487949 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete chloroplast genome of Homalocladium platycladum (Polygonaceae) and its phylogenetic analysis.

Chen Zijie Z Fu Qingxiang Q Tai Changrui C Zhai Wei W Zhao Kai K

Mitochondrial DNA. Part B, Resources 20220915 9

Homalocladium platycladum is a fascinating ornamental plant that has long been used in Chinese medicine. Here, we characterize the complete chloroplast genome sequence of this plant (GenBank: NC_062330). This circular genome has a total length of 163,202 bp containing a large single-copy region (87,820bp), a small single-copy region (13,538bp), and a pair of inverted repeat regions (30,922bp). A total of 130 predicted genes were identified, including 85 protein-coding genes, 37 transfer R ...[more]

PMID: 36147370

Similar Datasets

Characterization of the complete chloroplast genome of Rumex nepalensis (Polygonaceae).

Project description:Rumex nepalensis (Polygonaceae) is a fairly common perennial herb of high altitudes. In this study, we determined the complete chloroplast genome (plastome) of R. nepalensis with genome-skimming method. The complete plastome of R. nepalensis was 159,110 bp in length with a quadripartite structure, including a large single-copy region of 84,810 bp, a small single-copy region of 13,044 bp, and a pair of inverted repeats regions of 30,628 bp. The overall guanine-cytosine (GC) content was 37.5%. A total of 112 unique genes was annotated in this plastome, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. In the ML tree, R. nepalensis was sister to R. crispus, and Rumex was sister to a clade comprising Rheum and Oxyria within Polygonaceae famliy.

| S-EPMC7782026 | biostudies-literature

Characterization of the complete chloroplast genome of Rumex dentatus L. (Polygonaceae).

Project description:Rumex dentatus L. is a flowering plant with promising therapeutic effects. Here, we reported the complete chloroplast genome sequence of R. dentatus. The length of the complete genome is 159,103 bp, with a pair of inverted repeat regions (IRb/IRa, 30,628 bp) separated by a large single-copy (LSC, 84,848 bp) region and a small single-copy (SSC, 12,999 bp) region. The overall GC content of the genome was 37.6%, and the corresponding values in the LSC, SSC, and IR regions were 35.8%, 32.6%, and 41.1%, respectively. There are 129 genes, including 84 protein coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic tree showed that R. dentatus was most relative to the species of R. nepalensis and R. crispus.

| S-EPMC8967193 | biostudies-literature

The complete chloroplast genome and phylogenetic analysis of Persicaria jucunda (Meisn.) Migo (Polygonaceae).

Project description:Persicaria jucunda is a plant distributed at meadow or wetland. Our study reports the complete chloroplast genome. The chloroplast genome of P. jucunda is a typical tetrameric structure with a total length of 159,843 bp, containing a large single-copy (LSC) region of 84,350 bp, a small single-copy (SSC) region of 13,151 bp, and two inverted repeat regions (IRs) of 31,171 bp. The total GC content was 38.2%, 36.5% for the LSC region, 33.2% for the SSC region, and 41.5% for the IR region. The P. jucunda chloroplast genome contains 128 genes, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 36 chloroplast genomes showed similarity to P. foliosa and P. kawagoeana among the species analyzed. The chloroplast genome provides a valuable genetic resource for phylogenetic studies.

| S-EPMC11780699 | biostudies-literature

Characterization of the complete chloroplast genome of medicinal plant Rheum officinale (Polygonaceae).

Project description:The complete chloroplast (cp) genome of Rheum officinale Baill. was determined based on the Illumina Sequencing data. The cp genome is 161,563 bp in length. The overall G + C content of the cp genome was 37.31%. The R. officinale cp genome contains 129 genes, including 84 protein-coding genes, eight rRNA genes (four rRNA species), and 37 tRNA genes (20 tRNA species). A neighbour-joining phylogenetic tree clarified that the cp genome of R. officinale was closely related to that of R. palmatum in Polygonaceae.

| S-EPMC7687616 | biostudies-literature

Characterization of the complete chloroplast genome of traditional Tibetan herb, Rheum Pumilum Maxim. (Polygonaceae).

Project description:The complete chloroplast genome sequence of traditional Tibetan herb, Rheum pumilum Maxim. was analyzed. The complete chloroplast genome of R. pumilum is 162,213 bp in size and has a 27.27% GC content. In the typical circular quadripartite structure, there was a pair of inverted repeat (IR) regions with 31,023 bp in length, which separated by a large single-copy (LSC) region (87,424 bp) and a small single-copy (SSC) region (12,743 bp). The chloroplast genome of R. pumilum contained 131 unigenes, which was composed of 86 protein-coding genes, 37 tRNA and 8 rRNA genes. Moreover, 238 SSRs were identified and 58.8% of them existed in LSC region. A maximum likelihood (ML) phylogenetic analysis based on chloroplast genomes indicated that R. pumilum was closely related to R. pulmatum, R. tangutica, and R. officinale. Our results would provide a valuable resource for resource utilization and the phylogenetic studies of Rheum in Polygonaceae.

| S-EPMC7721034 | biostudies-literature

Complete chloroplast genome characterization and phylogenetic analysis of Clematis mandshurica (Ranunculaceae).

Project description:The complete chloroplast genome sequence of Clematis mandshurica Ruprecht (1867), a specie of the Ranunculaceae family, and its phylogenetic relationships with other species have been reported in this study. The complete chloroplast genome of C. mandshurica is 159,563 bp in length, including a large single-copy (LSC) region of 79,360 bp, a small single-copy (SSC) region of 18,121 bp, and a pair of identical inverted repeat regions (IRs) of 31,041 bp. The genome encodes a total of 132 genes, including 90 protein-coding genes, 34 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis reveals that C. mandshurica was found to be closest to Clematis taeguensis. The complete chloroplast genome of C. mandshurica contributes to a better understanding of phylogenetic relationships among Clematis species.

| S-EPMC9103393 | biostudies-literature

The complete chloroplast genome characterization and phylogenetic analysis of Canarium album.

Project description:Canarium album is one of the precious and characteristic fruit trees of China. In this study, we first presented the complete chloroplast genome of C. album by using BGISEQ-500 sequencing. Its complete chloroplast genome is 163,140 bp in size, containing a pair of inverted repeat regions of 30,729 bp, a large single copy region of 87,748 bp and a small single copy region of 13,934 bp. The chloroplast genome contains 117 unique genes, including 83 protein coding genes, 30 tRNA and 4 rRNA genes. Phylogenetic analysis based on complete chloroplast genomes indicated that C. album was closest to Boswellia sacra.

| S-EPMC7706554 | biostudies-literature

Complete chloroplast genome of medicinal plant Aconitum carmichaelii: genome characterization and phylogenetic analysis.

Project description:The complete chloroplast genome sequence of an important medicinal plant of the family Ranunculaceae, Aconitum carmichaelii Debx., was characterized in this study. The assembled chloroplast genome was 154,776 bp in length, which included a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IR) regions of 86,330bp, 15,986 bp, and 26,193 bp, respectively. The GC content of the genome was 38.1%. Phylogenetic analysis with the whole nucleotide sequences of reported Aconitum chloroplast genomes indicated a close relationship of A. carmichaelii with A. kusnezoffii.

| S-EPMC7800505 | biostudies-literature

Characterization and phylogenetic analysis of the complete chloroplast genome of Juncus effusus L.

Project description:Juncus effusus L., a perennial herbaceous species of family Juncaceae, is distributed mainly in warm areas worldwide. We studied the complete chloroplast (cp) genome of J. effusus through next-generation sequencing technology. The whole cp genome contained 170,612 base pairs, with the GC ratio as 35.99%. The 70 genes annotated from the cp genome include 32 protein coding genes, eight rRNA genes and 30 tRNA genes. The genome's large single-copy region (LSC) was 80,640 bp, with the small single-copy region (SSC) 64,718 bp, and inverted repeat (IR) 12,627 bp. Furthermore, a phylogenetic tree was generated to evaluate evolutionary relationship between J. effusus and relevant species. This study will be beneficial for the further understanding and application of J. effusus.

| S-EPMC8118462 | biostudies-literature

Characterization and phylogenetic analysis of the complete chloroplast genome of Ophiorrhiza pumila (Rubiaceae).

Project description:Ophiorrhiza pumila (Rubiaceae) is an herbaceous plant that grows streamside in forest gullies or wetlands in the shade. Complete chloroplast genome of O. pumila was obtained and analyzed its phylogeny relationship within Rubiaceae plants. The results showed that the genome had a typical quadripartite structure of 154,385 bp, and contained a total of 112 unique genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. Phylogenetic analysis suggested that O. pumila is sister to a highly supported clade composed of 10 species including Morinda officinalis, Gynochthodes cochinchinensis, Saprosma merrillii, Hedyotis ovata, Foonchewia guangdongensis, Dunnia sinensis, Paederia scandens, Leptodermis scabrida, Rubia cordifolia, and Galium mollugo. The complete chloroplast genome provides valuable information for the phylogenetic analysis of O. pumila.

| S-EPMC8205021 | biostudies-literature