Browse
Submit Data
Databases
API
Help

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Huang X

PROVIDER: S-EPMC8189082 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Huang Xianjun X Xia Conglong C Zhao Yuan Y Xu Li L

Mitochondrial DNA. Part B, Resources 20210607 7

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 r ...[more]

PMID: 34151003

Similar Datasets

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

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 first complete chloroplast genome sequence of Vicia ramuliflora (Fabaceae).

Project description:Vicia ramuliflora belongs to the Fabaceae. It is a perennial herb, with high economic value. The cpDNA of V. ramuliflora was 124,682 bp long with IR loss. It contains 109 genes, including 76 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The overall GC content is 35.1%. The phylogenetic tree indicates that Vicia species formed a monophyletic lineage with high bootstrap value. This study has provided new genome information for the phylogenetic analysis of Fabaceae.

| S-EPMC7748550 | 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

The complete chloroplast genome of Allium wallichii Kunth (Amaryllidaceae).

Project description:Allium wallichii Kunth is a herb species with potentially extensive applications because of its edible, ornamental, and pharmaceutical values. The structural characteristics and phylogenetic relationships of its chloroplast genome were determined here for the first time. The complete cp genome was found to be 152,496 bp long, with a GC content of 37.04%. It consists of four distinct regions: a large single copy (LSC) region of 82,510 bp, a small single copy (SSC) region of 17,460 bp, and two inverted repeat (IR) regions of 26,263 bp each. The genome encodes 129 genes, including 86 protein-coding genes, 37 tRNA genes, and six rRNA genes. Our phylogenetic analysis revealed that A. wallichii was closely related to Allium wallichii var. platyphyllum, which are included in the section Bromatorrhiza, subgenus Amerallium Traub of the genus Allium. Our report provides valuable information on the genetic diversity of Allium species.

| S-EPMC10557535 | biostudies-literature

The first complete chloroplast genome sequence of Pentaphragma spicatum Merr. (Pentaphragmataceae) and phylogenetic analysis.

Project description:Pentaphragma spicatum Merr. is an endemic wild edible plant of China belonging to the Pentaphragmataceae family. It is widely consumed by Shangsi County resident in Guangxi Fangchenggang. Initially, Pentaphragma was classified as a genus within the Campanulaceae family, but, later it was treated as part of the Pentaphragmataceae family. However, the chloroplast genome of Pentaphragmataceae has not yet been reported. In this study, we sequenced the first complete chloroplast (cp) genome of P. spicatum from Guangxi, China. The whole genome was 154,229 bp in length, consisting of a pair of inverted repeats (IR each 25,572 bp), a large single-copy region (LSC 84,884 bp), and a small single-copy region (SSC 18,201 bp). The complete genome contained 129 genes, including 87 protein-coding genes, 34 tRNA, and 8 rRNA genes. The overall GC content of the whole genome was 37.71%. Based on a maximum-likelihood phylogenetic analysis, it has been determined that P. spicatum is not phylogenetically related to Campanulaceae and supports the decision to classify it as a separate family, Pentaphragmataceae. The complete chloroplast genome of P. spicatum will help enhance and integrate the existing genome data of Asterales. This will provide insights into the phylogenetic relationship within Campanulaceae.

| S-EPMC10776070 | biostudies-literature

The first complete chloroplast genome sequence of Lanxangia tsaoko and phylogenetic analysis.

Project description:Lanxangia tsaoko is a famous Chinese traditional medicine with long history. In this study, the complete chloroplast (cp) genome of L. tsaoko was characterized and assembled using a high-throughput sequencing method. The complete cp genome is 164,008 bp in length, including a large single copy (LSC) region of 89,134 bp and a small single copy (SSC) region of 15,372 bp separated by two inverted repeat (IR) regions of 29,751 bp. A total of 137 genes were identified, including 88 protein-coding genes (PCG), 38 transfer RNA genes, 8 ribosomal RNA genes, and 3 pseudogenes. The phylogenetic analysis revealed that L. tsaoko is located in Zingiberaceace, closely related to Amomum and Alpinia with a 100% bootstrap support.

| S-EPMC7687529 | 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