Browse
Submit Data
Databases
API
Help

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome sequence of Gynostemma microspermum (Cucurbitaceae).

ABSTRACT: Gynostemma microspermum C. Y. Wu et S. K. Chen is an endemic creeping herbaceous species mainly distributed in dense forests on limestone in northwestern China. Here, the complete chloroplast genome sequence of G. microspermum was obtained by Illumina pair-end sequencing. The circular complete chloroplast genome of G. microspermum is 158,692 bp in length and contains a large single copy region (87,452 bp), a small single copy region (19,068 bp) and two short inverted repeat regions (26,086 bp). The genome sequence encodes 133 genes including 87 protein-coding genes, 37 transfer RNA genes, 8 ribosomal RNA genes and 1 pseudogene. The maximum likelihood (ML) phylogeny estimation shows that G. microspermum is sister to all other analyzed species of the genus Gynostemma with high bootstrap support.

SUBMITTER: Zhang X

PROVIDER: S-EPMC8667937 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Characterization of the complete chloroplast genome sequence of Gynostemma microspermum (Cucurbitaceae).

Zhang Xiao X Chen Xiaodan X Zhang Hao H Zhao Yuemei Y Ju Miaomiao M Zhao Guifang G

Mitochondrial DNA. Part B, Resources 20211210 1

Gynostemma microspermum C. Y. Wu et S. K. Chen is an endemic creeping herbaceous species mainly distributed in dense forests on limestone in northwestern China. Here, the complete chloroplast genome sequence of G. microspermum was obtained by Illumina pair-end sequencing. The circular complete chloroplast genome of G. microspermum is 158,692 bp in length and contains a large single copy region (87,452 bp), a small single copy region (19,068 bp) and two short inverted repeat ...[more]

PMID: 34912963

Similar Datasets

Complete chloroplast genome sequence of the medicinal plant Gynostemma pentaphyllum.

Project description:We report the complete chloroplast genome sequence of Gynostemma pentaphyllum, a well-known traditional Chinese medicine, which produces triterpenoid saponins similar to Panax ginseng. The assembled chloroplast genome (cpDNA) was 157,654 bp in length and structurally divided into four distinct regions, namely, large single copy region (86,794 bp), small single copy region (18,654 bp) and a pair of inverted repeat regions (26,103 bp). A total of 143 genes were annotated, including 87 protein-coding genes, 10 tRNA genes and 46 rRNA genes. Phylogenetic analysis revealed that the chloroplast genome sequence of G. pentaphyllum is most closely related to Cucumis melo.

| S-EPMC7800860 | biostudies-literature

The complete chloroplast genome sequence of the Siraitia Grosvenorii (Cucurbitaceae).

Project description:Siraitia grosvenorii is a famous Chinese plant used in traditional food and medicine with pharmacological effects. The complete chloroplast genome sequence of S. grosvenorii has been determined in this study. The total genome size is 158,834 bp in length and contains a pair of inverted repeats (IRs) of 26,288 bp, which were separated by large single-copy (LSC) and small single-copy (SSC) of 87,702 bp and 18,556 bp length, respectively. A total of 131 genes were predicted including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Phylogenetic analysis showed that S. grosvenorii belongs to the family Cucurbitaceae. The complete chloroplast genome of S. grosvenorii would play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies.

| S-EPMC7687387 | biostudies-literature

The complete chloroplast genome sequence of the Cucurbita pepo L. (Cucurbitaceae).

Project description:Cucurbita pepo is an important economic plant cultivated widely in the world. The complete chloroplast genome sequence of C. pepo is reported here. The genome is 157,343 bp in length and exhibits a typical quadripartite structure of the large (LSC, 87,970 bp) and small (SSC, 18,167 bp) single-copy regions, separated by a pair of inverted repeats (IRs, 25,603 bp). A total of 131 genes were predicted including 85 protein-coding genes, eight rRNA genes and 38 tRNA genes. Further, phylogenetic analysis showed that C. pepo were closely related to other species in the family Cucurbitaceae. The complete chloroplast genome of C. pepo would be taken as a useful molecular tool for species discrimination, taxonomy, and phylogenetic relationships in the family Cucurbitaceae.

| S-EPMC7799668 | biostudies-literature

The complete chloroplast genome sequence of the Citrullus colocynthis L. (Cucurbitaceae).

Project description:Citrullus colocynthis L. is one of the worldwide famous traditionally medicinal plants and widely applied in watermelon breeding for its multiple resistances. The complete nucleotide sequence of desert watermelon (Citrullus colocythis L.) chloroplast genome has been determined in this study. The genome was composed of 157,147 bp containing a pair of inverted repeats (IRs) of 26,149 bp, which was separated by a large single-copy region of 86,851 bp and a small single-copy region of 17,998 bp. A total of 123 genes were predicted including 86 protein-coding genes, eight rRNA genes and 29 tRNA genes. Phylogenetic analysis revealed that C. colocynthis were closely related to other two species in the genus Citrullus. The complete chloroplast genome of C. colocynthis would provide some significant information for Cucurbitaceae evolutionary and genomic studies.

| S-EPMC7800171 | biostudies-literature

The complete chloroplast genome sequence of the Cucurbita ficifolia Bouche (Cucurbitaceae).

Project description:Cucurbita ficifolia Bouché is an important germplasm resource used for rootstock and hypoglycemic food in Cucurbitaceae. The complete chloroplast genome sequence of C. ficifolia has been determined in this study. The total genome size is 157,533 bp in length and contains a pair of inverted repeats (IRs) of 25,639 bp, which were separated by large single copy (LSC) and small single copy (SSC) of 88,112 bp and 18,143 bp, respectively. A total of 130 genes were predicted including 86 protein-coding genes, eight rRNA genes and 36 tRNA genes. Further, Maximum-likelihood phylogenetic analysis revealed that C. ficifolia is a base clade of genus Cucurbita and closer to Cucurbita maxima. The chloroplast genome of C. ficifolia would promote the germplasm exploration, phylogenetic relationships, and molecular biology researches in Cucurbita.

| S-EPMC8491698 | biostudies-literature

The complete chloroplast genome sequence of Gynostemma yixingense and comparative analysis with congeneric species.

Project description:Gynostemma yixingense, an important medicinal member of the Cucurbitaceae family, is an endemic herbaceous species distributed in East China. It is morphologically similar to the plants in the same genus, which resulted in some confusion in identification and application. Meanwhile, there are still some controversies in taxonomy. Herein, the complete chloroplast genome sequence of G. yixingense was obtained by Illumina paired-end sequencing technology and compared to other chloroplast genome sequences of congeneric species. The complete chloroplast genome of G. yixingense is 157,910 bp in length with 36.94% GC content and contains a large single-copy (LSC) region of 86,791 bp, a small single-copy (SSC) region of 18,635 bp and a pair of inverted repeat (IR) regions of 26,242 bp. The whole genome contains 133 unique genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. In addition, 74 simple sequence repeats (SSRs) were identified, most of which were A/T rich. The phylogenetic analysis indicated that G. yixingense had the closest relationship to G. laxiflorum. The result of this study provided an important theoretical basis for chloroplast genome and phylogenetic analysis of G. yixingense.

| S-EPMC7521087 | biostudies-literature

Completion of Eight Gynostemma BL. (Cucurbitaceae) Chloroplast Genomes: Characterization, Comparative Analysis, and Phylogenetic Relationships.

Project description:Gynostemma BL., belonging to the family Cucurbitaceae, is a genus containing 17 creeping herbaceous species mainly distributed in East Asia. It can be divided into two subgenera based on different fruit morphology. Herein, we report eight complete chloroplast genome sequences of the genus Gynostemma, which were obtained by Illumina paired-end sequencing, assembly, and annotation. The length of the eight complete cp genomes ranged from 157,576 bp (G. pentaphyllum) to 158,273 bp (G. laxiflorum). Each encoded 133 genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes, and one pseudogene. The four types of repeated sequences had been discovered and indicated that the repeated structure for species in the Subgen. Triostellum was greater than that for species in the Subgen. Gynostemma. The percentage of variation of the eight cp genomes in different regions were calculated, which demonstrated that the coding and inverted repeats regions were highly conserved. Phylogenetic analysis based on Bayesian inference and maximum likelihood methods strongly supported the phylogenetic position of the genus Gynostemma as a member of family Cucurbitaceae. The phylogenetic relationships among the eight species were clearly resolved using the complete cp genome sequences in this study. It will also provide potential molecular markers and candidate DNA barcodes for future studies and enrich the valuable complete cp genome resources of Cucurbitaceae.

| S-EPMC5600969 | biostudies-literature

The complete chloroplast genome sequence of Melothria scabra (Cucurbitaceae).

Project description:Melothria scabra has gradually become an economically important plant worldwide. The complete chloroplast genome of M. scabra has a length of 156,744 bp, contains a large single-copy (LSC) region (86,387 bp), a small single-copy (SSC) region (18,055 bp), and two inverted repeats (IRs) with the same length of 26,151 bp. In total, 126 genes were detected, including 83 protein-encoding genes, 35 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. For phylogenetic analysis, M. scabra has a closer genetic relationship with Cucumis sativus and Citrullus lanatus. The complete chloroplast genome sequence of M. scabra would promote the germplasm exploration, phylogenetic relationships, and molecular biology researches in Melothria.

| S-EPMC11619021 | biostudies-literature

The complete chloroplast genome sequence of the Citrullus lanatus L. Subsp. Vulgaris (Cucurbitaceae).

Project description:Watermelon is one of the worldwide popular summer fruits and well-known for colourful, sweet, and juicy flesh. The complete nucleotide sequence of cultivated watermelon (Citrullus lanatus L. subsp. vulgaris) chloroplast genome has been determined in this study. The genome was composed of 156,906 bp containing a pair of inverted repeats (IRs) of 26,082 bp, which was separated by a large single-copy region of 70,063 bp and a small single-copy region of 17,895 bp. A total of 114 genes were predicted included 80 protein-coding genes, four rRNA genes, and 30 tRNA genes. Phylogenetic analysis revealed that C. lanatus and other three species belonging to the genus Cucumis were closely clustered into a clade, the family Cucurbitaceae.

| S-EPMC7800656 | biostudies-literature

The complete chloroplast genome sequence of Thladiantha nudiflora Hemsl. ex F.B.Forbes & Hemsl. 1887 (Cucurbitaceae).

Project description:Thladiantha nudiflora Hemsl. ex F.B.Forbes & Hemsl. 1887 (Cucurbitaceae) has been widely known as a traditional medicine plant. In this study, we sequenced, assembled, and annotated the complete chloroplast genome of T. nudiflora. The chloroplast genome of T. nudiflora is 156,824 base pair (bp) in length, containing a large single-copy region of 86,566 bp and a small single-copy region of 18,070 bp, separated by a pair of inverted repeats of 26,094 bp. The chloroplast genome contains 132 genes, including 87 protein-coding, 37 transfer RNA, and eight ribosomal RNA genes. Phylogenetic analysis of the chloroplast genome revealed that species of the genus Thladiantha were clustered together in the phylogenetic trees. This study will not only shed light on T. nudiflora's evolutionary position but also provide valuable chloroplast genomic information for future studies into the origins and diversification of the genus Thladiantha and the Cucurbitaceae family.

| S-EPMC10812858 | biostudies-literature