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 Sophora davidii (Fabaceae) and its phylogenetic implications.

ABSTRACT: 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.

SUBMITTER: Sun H

PROVIDER: S-EPMC8942534 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Sun Huigai H Han Xiaowei X Ma Donglai D Li Yang Y Kang Tian T Sun Ruipeng R Zheng Yuguang Y Song Junna J

Mitochondrial DNA. Part B, Resources 20220317 3

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 sin ...[more]

PMID: 35342795

Similar Datasets

The complete chloroplast genome of Swertia davidii (gentianaceae) and its phylogenetic analysis.

Project description:To elucidate the genetic information and evolutionary relationships of Swertia, we initiated the sequencing of the complete chloroplast genome of Swertia davidii Franch. 1888, complemented by comparative analyses with closely related species. The chloroplast genome of S. davidii was 153,516 bp in length and exhibited a typical quadripartite structure. It contained two regions with Inverted Repeat lengths of 25,767 bp, located between one Large Single-Copy region (83,617 bp) and one Short Single-Copy region (18,365 bp). The chloroplast genome of S. davidii encoded 132 genes, including 87 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. The overall GC content was 38.15%. Maximum likelihood phylogenetic analysis of Swertia based on 26 available plastomes showed a close relationship between S. davidii and S. kouitchensi. This study will contribute to the genetic preservation of the species and the phylogenetic study of Swertia.

| S-EPMC11328818 | biostudies-literature

The complete chloroplast genome sequence and phylogenetic analysis of Nanhaia speciosa (Fabaceae).

Project description:Nanhaia speciosa (Fabaceae) is a woody perennial vine used as an important traditionally Chinese medicine. In this study, the complete chloroplast genome of Nanhaia speciosa was sequenced and assembled. The chloroplast genome of N. speciosa was 132,551bp in length including only one copy of the inverted repeat (IR). It encoded a total of 110 genes, containing 76 protein-coding genes, 30 tRNA and 4 rRNA. The overall GC content was 34.1%. Phylogenetic analysis using a matrix of 69 protein-coding genes illustrated that N. speciosa is most closely related to Wisteriopsis reticulata of tribe Wisterieae.

| S-EPMC8797743 | biostudies-literature

Complete Chloroplast Genome of Corethrodendron fruticosum (Papilionoideae: Fabaceae): Comparative and Phylogenetic Analysis.

Project description:Corethrodendron fruticosum is an endemic forage grasses in China with high ecological value. In this study, the complete chloroplast genome of C. fruticosum was sequenced using Illumina paired-end sequencing. The C. fruticosum chloroplast genome was 123,100 bp and comprised 105 genes, including 74 protein-coding genes, 4 rRNA-coding genes, and 27 tRNA-coding genes. The genome had a GC content of 34.53%, with 50 repetitive sequences and 63 simple repeat repetitive sequences that did not contain reverse repeats. The simple repeats included 45 single-nucleotide repeats, which accounted for the highest proportion and primarily comprised A/T repeats. A comparative analysis of C. fruticosum, C. multijugum, and four Hedysarum species revealed that the six genomes were highly conserved, with differentials primarily located in the conserved non-coding regions. Moreover, the accD and clpP genes in the coding regions exhibited high nucleotide variability. Accordingly, these genes may serve as molecular markers for the classification and phylogenetic analysis of Corethrodendron species. Phylogenetic analysis further revealed that C. fruticosum and C. multijugum appeared in different clades than the four Hedysarum species. The newly sequenced chloroplast genome provides further insights into the phylogenetic position of C. fruticosum, which is useful for the classification and identification of Corethrodendron.

| S-EPMC10298450 | biostudies-literature

The first complete chloroplast genome of Haymondia wallichii (Fabaceae) and its phylogenetic analysis.

Project description:Haymondia wallichii DC. was a scandent shrub. In this study, we sequenced the complete chloroplast (cp) genome of H. wallichii to investigate its phylogenetic relationship in Fabaceae. The total length of the cp genome was 153,668 bp, consisted of a large single copy (LSC) region of 84,310 bp, a small single copy (SSC) region of 17,918 bp, and a pair of inverted repeat regions (IRs) of 25,720 bp. The genome contained 132 genes, namely 37 tRNA genes, 87 protein-coding genes, and 8 rRNA genes. The overall GC content was 35.4%. The phylogenetic analysis indicated H. wallichii was closely related to Pueraria montana var. thomsonii and Pueraria montana var. lobata.

| S-EPMC8189082 | biostudies-literature

The complete chloroplast genome of Hydrangea davidii (Hydrangeaceae).

Project description:Hydrangea davidii, a perennial shrub of Hydrangeaceae, is an ornamental plant endemic to China. Here, we report the complete chloroplast genome of H. davidii. The complete chloroplast genome is totally 158,054 bp in length with a typical quadripartite structure. It consists a pair of inverted regions (IRs) of 26,140 bp, which were separated by a large single copy (LSC) region of 87,008 bp and a small single copy (SSC) region of 18,766 bp, respectively. The chloroplast genome encoded 131 genes, including 85 protein-coding genes, 8 rRNA genes and 38 tRNA genes. The GC content in the whole cp genome, LSC region, SSC region, and IR region are 37.8%, 36.0%, 31.7%, and 43.1%, respectively. In total, 49 SSRs were identified in the complete chloroplast genome. Phylogenetic analysis showed that H. davidii is closely related to Hydrangea platyarguta with a support rate of 100%.

| S-EPMC7594765 | biostudies-literature

Characterization of the complete chloroplast genome of shrubby sophora (Sophora flavescens Ait.).

Project description:Sophora flavescens, with high medicinal value, is a traditional Chinese medical plant wildly distributed in China. In this study, the complete chloroplast (cp) genome of Sophora flavescens was determined through Illumina sequencing method. The complete chloroplast genome of S. flavescens was 154,378 bp in length and contained a pair of IR regions (28,876 bp) separated by a small single copy region (18,110 bp) and a large single copy region (84,516 bp). The cp genome of S. flavescens encoded 130 genes including 84 protein-coding genes, 37 tRNA genes and eight ribosomal RNA genes. The overall GC content of S. flavescens cp genome is 36.6%. By phylogenetic analysis using ML method, S. flavescens showed the closest relationship with Sophora alopecuroides.

| S-EPMC7800985 | 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

The complete chloroplast genome of Corethrodendron multijugum (Fabaceae: Corethrodendron) and phylogenetic analysis.

Project description:Corethrodendron multijugum (Maxim.) (Fabaceae: Corethrodendron), also known as Hedysarum multijugum, is an important medicinal plant and is widely used in traditional Chinese medicine. To better understand the diversity and phylogeny of C. multijugum and other Fabaceae species, we sequenced and annotated the complete chloroplast genome of C. multijugum using the Illumina HiSeq 2500 platform. This complete genome was 122,994 bp long, and encodes a total of 110 genes, including 76 protein-coding genes (PCGs), 30 transfer RNA genes (tRNAs), and four ribosomal RNA unit genes (rRNAs). The C. multijugum plastid with a G + C content of 34.5% presents a negative AT -skew (-0.002) and a positive GC -skew (0.032). Phylogenetic analysis revealed that C. multijugum is more closely related to Hedysarum petrovii. This study provides genetic resource information for the further study of Corethrodendron.

| S-EPMC10236963 | biostudies-literature

The complete chloroplast genome of Epimedium davidii Franch. (Berberidaceae).

Project description:Epimedium davidii, which belongs to Berberidaceae, is mainly distributed in the southwest of China. In this study, the complete chloroplast genome of E. davidii was sequenced and assembled. The circular genome is 159,715 bp in length, which comprises a large single-copy region (LSC, 85,862 bp), a small single-copy region (SSC, 17,081 bp), and a pair of inverted repeat regions (IRa and IRb, 28,386 bp). The chloroplast genome of E. davidii contains 112 unique genes, of which 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis indicated that E. davidii was closely related to Epimedium acuminatum.

| S-EPMC7748688 | biostudies-literature

The complete chloroplast genome of Thermopsis lanceolata: genome structure and its phylogenetic relationships within the family Fabaceae.

Project description:Thermopsis lanceolata R. Br. belongs to the genus Thermopsis, Fabaceae. The alkaloids of T. lanceolata have anti-cancer, anti-heart rate disorders and other pharmacological effects. To explore the chloroplast genome of T. lanceolata and its phylogenetic relationship, a complete chloroplast genome of T. lanceolata was sequenced and annotated, and a phylogenetic tree was constructed. The complete chloroplast genome of T. lanceolata is a circular molecule of 151,526 bp, consisting of a large single copy (LSC) region of 83,780 bp, a small single copy (SSC) region of 15,566 bp, and a pair of inverted repeats (IRa and IRb) of 26,090 bp. The chloroplast genome of T. lanceolata contained 130 genes, including 85 protein-coding genes, 37 transfer RNA genes, and 8 ribosomal RNA genes. Phylogenetic analysis revealed a close relationship between T. lanceolata and T. turkestanica.

| S-EPMC9754016 | biostudies-literature