Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome of Ophiopogon bodinieri Levl. and its phylogenetic position.

ABSTRACT: Ophiopogon bodinieri Levl. is an important turfgrass and ornamental cover plants which is widely used in urban garden construction in southern China. In this study, we sequenced the complete chloroplast genome of O.bodinieri on the Illumina HiSeq Platform. The chloroplast genome is 157,078 bp in length, with a typical quadripartite structure and consisting of a pair of inverted repeat (IR) regions (26,477 bp) separated by a large single copy (LSC) region (85,374 bp) and a small single copy (SSC) region (18,750 bp). It was predicted to contain a total of 132 genes, with an overall GC content of 38.63%. Phylogenetic analysis suggested O.bodinieri is closely relatedto Goodyera velutina, Anoectochilus emeiensis and Ludisia discolor.

SUBMITTER: Guo X

PROVIDER: S-EPMC7995887 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete chloroplast genome of an endangered endemic tree, handeliodendron bodinieri (levl.) rehder (sapindaceae) from karst forests of southwest China.

Project description:Handeliodendron bodinieri (Sapindaceae) is an endangered monotypic species endemic to the karst forests in southwest China whose populations are now fragmented and the total number of individuals evidently decreased. In this research, we characterized the chloroplast (cp) genome of H. bodinieri using genome skimming. The whole cp genome was 155,291 bp long and comprised 137 genes, including 8 unique rRNAs, 40 tRNAs, and 89 protein-coding genes. The overall guanine-cytosine content of H. bodinieri cp genome was 37.8%. The phylogenetic analysis suggested that H. bodinieri is closely related to the genus Mangifera. This study will be useful for future studies on conservation genetics of this economically important endemic plant.

| S-EPMC7707296 | biostudies-literature

The complete chloroplast genome of Lonicera pampaninii Levl. and its phylogenetic analysis.

Project description:Lonicera pampaninii Levl, a Chinese herbal medicine widely used in the folk, has the effect of clearing away heat and detoxifying similar to other plants of the Lonicera. However, its genetic relationship with these plants is unclear. In this work, the cp genome of Lonicera pampaninii Levl. was assembled by the high-throughput Illumina pair-end sequencing data. The circular cp genome is 155,249 bp in size, including a large single-copy (LSC) region of 89,068 bp and a small single-copy (SSC) region of 18,635 bp, which were separated by two inverted repeat (IR) regions (23,773 bp each). A total of 120 genes were predicted, including eight ribosomal RNAs (rRNAs), 33 transfer RNAs (tRNAs), and 79 protein-coding genes (PCGs). Furthermore, phylogenetic analysis revealed a strong sister relationship between L. pampaninii and other two congeneric species (Lonicera confusa and Lonicera japonica). This study provides useful information for future genetic study of L. pampaninii.

| S-EPMC8462834 | biostudies-literature

Complete chloroplast genome sequence of Mucuna prurien and its phylogenetic position.

Project description:Mucuna pruriens is traditional medicinal plant originated in South Africa. We characterize the complete plastid genome of M. pruriens, which is a circular-mapping molecule 152,119 bp in length. The genome has a large single-copy region (LSC) of 78,258 bp and a small single-copy region (SSC) of 18,735 bp, respectively. Additionally, the overall GC content of the chloroplast genome was 35.37%. The genome contains 138 genes, including 96 protein-coding, 38 tRNA, and four rRNA genes. The gene content and structure are conserved compared to other species in the genus Glycine. The chloroplast genome and existing data were used to infer its phylogenetic position. The results showed that M. pruriens clustered together with Glycine max and G. soja. These findings provide potential genetic markers that can aid in understanding the genetic diversity of M. pruriens.

| S-EPMC8330721 | biostudies-literature

Characterization of the complete chloroplast genome of Zanthoxylum esquirolii Levl. (Rutaceae).

Project description:Zanthoxylum esquirolii Léveillé 1914 is mainly distributed in southwest China, and its wild germplasm resources are scarce and in urgent need of conservation. In this study, we report the first complete chloroplast genome sequence of Z. esquirolii using next-generation sequencing. The circular genome is 158,390 bp in length, containing two inverted repeat (IR) regions of 27,622 bp separated by a large single copy (LSC) region of 85,580 bp and a small single copy (SSC) region of 17,566 bp. The chloroplast genome contains a total of 132 genes, including 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome was 38.46%, with corresponding values in the LSC, SSC, and IR regions of 36.84%, 33.55%, and 42.51%, respectively. The phylogenetic tree revealed that Z. esquirolii Levl. formed a clade with Z. piperitum DC., Z. bungeanum Maxim., Z. simulans Hance and Z. sp. NH-2018, and had a strongly supported sister relationship with Z. bungeanum.

| S-EPMC9518235 | biostudies-literature

The complete chloroplast genome sequence of Laplacea alpestris and its phylogenetic position.

Project description:Laplacea alpestris is a member of the genus Laplacea, which distributes in Central and South America. Genetic information of L. alpestris would provide guidance for the phylogenetic position of this species. Here, we reported and characterized its complete chloroplast (cp) genome using Illumina pair-end sequencing data. The total chloroplast genome size of this species was 157,211 bp, including inverted repeats (IRs) of 26,103 bp, separated by a large single copy (LSC) and a small single copy (SSC) of 86,749 and 18,256 bp, respectively. A total of 132 genes, including 37 tRNA, 8 rRNA, and 87 protein-coding genes were identified. Phylogenetic analysis showed that L. alpestris formed a monophyletic clade with Laplacea fruticosa, and then grouped with Apterosperma oblata. The systematic position of Southeast Asian Laplacea species needs further studies.

| S-EPMC7717450 | biostudies-literature

Complete chloroplast genome of Plantago asiatica and its phylogenetic position in Plantaginaceae.

Project description:Plantago asiatica, an herbaceous perennial species of Plantaginaceae, has been used as a traditional herbal medicine plant in China. In this study, the complete chloroplast (cp) genome of P. asiatica was sequenced and assembled using genome skimming data. The cp genome was 165,045 bp in length including the large single-copy (LSC, 82,964 bp) and small single-copy (SSC, 4,633 bp) regions separated by two copies of inverted region (IR, 38,724 bp). The cp genome encoded 113 unique genes, consisting of 79 protein-coding genes, 30 tRNA genes, and four rRNA genes, additionally with 27 duplicated genes in the IR regions. Phylogenetic analysis indicated that the representative species from Plantago was monophyletic and they were divided into four subgenera. P. asiatica belongs to the subgenus Plantago and was sister to P. rigida with high bootstrap value support.

| S-EPMC9103697 | biostudies-literature

The complete chloroplast genome of Diplodiscus trichospermus and phylogenetic position of Brownlowioideae within Malvaceae.

Project description:BackgroundMalvaceae is an economically important plant family of 4,225 species in nine subfamilies. Phylogenetic relationships among the nine subfamilies have always been controversial, especially for Brownlowioideae, whose phylogenetic position remains largely unknown due to the lack of samples in previous analysis datasets. To greatly clarify the phylogenetic relationship of Malvaceae, we newly sequenced and assembled the plastome of Diplodiscus trichospermus taxonomically located in Brownlowioideae, and downloaded the allied genomes from public database to build a dataset covering all subfamily members of Malvaceae.ResultsThe annotation results showed that the plastome of Diplodiscus trichospermus has a typical quadripartite structure, comprising 112 unique genes, namely 78 protein-coding genes, 30 tRNA genes and 4 rRNA genes. The total length was 158,570 bp with 37.2% GC content. Based on the maximum likelihood method and Bayesian inference, a robust phylogenetic backbone of Malvaceae was reconstructed. The topology showed that Malvaceae was divided distinctly into two major branches which were previously recognized as Byttneriina and Malvadendrina. In the Malvadendrina clade, Malvoideae and Bombacoideae formed, as always, a close sister clade named as Malvatheca. Subfamily Helicteroideae occupied the most basal position and was followed by Sterculioideae which was sister to the alliance of Malvatheca, Brownlowioideae, Dombeyoideae, and Tilioideae. Brownlowioideae together with the clade comprising Dombeyoideae and Tilioideae formed a sister clade to Malvatheca. In addition, one specific conservation SSR and three specific palindrome sequences were observed in Brownlowioideae.ConclusionsIn this study, the phylogenetic framework of subfamilies in Malvaceae has been resolved clearly based on plastomes, which may contribute to a better understanding of the classification and plastome evolution for Malvaceae.

| S-EPMC10521492 | biostudies-literature

The complete chloroplast genome of Butomus umbellatus L. and its phylogenetic position.

Project description:Butomus umbellatus, which belongs to Butomaceae, is a plant species typical of littoral communities of river and stream shores. Here, we reported and characterized the complete chloroplast (cp) genome of B. umbellatus and analyzed its phylogenetic position based on the complete cp genome sequences of 10 species within the core Alimatales. The cp genome is 158,107 bp in length, which consists of a large single-copy region (LSC, 88,140 bp； GC content: 34.8%), a small single-copy region (SSC, 19,695 bp; GC content: 30.1%), and a pair of inverted repeat regions (IRs, 25,136 bp; GC content: 42.9%). It harbours 113 unique genes, including 79 protein-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes with an overall GC content of 36.8%. The phylogeny inference showed that Butomaceae and Hydrochariaceae formed a high supported clade, which was sister to Alismataceae. This result was similar to the floral development from petaloid Alismatales, and also similar to the phylogenetic studies of Alismales based on 83 plastid genes, but with much higher bootstrap support.

| S-EPMC7707564 | biostudies-literature

The complete chloroplast genome of Zelkova serrata and its phylogenetic position within Ulmaceae.

Project description:The complete chloroplast genome sequence of the Tertiary relict tree Zelkova serrata was reported in this study. The chloroplast genome is 158,875 bp in length with a typical angiosperm quantitative structure consisting of a large single copy (87,412 bp) and a small single copy (18,683 bp) separated by a pair of inverted repeat (26,390 bp). Genome annotation revealed a total of 129 genes comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenomic analysis based on the whole plastomes indicated that Z. serrata and Z. schneideriana formed a well-supported monophyletic clade sister to genus Ulmus in Ulmaceae.

| S-EPMC7510571 | biostudies-literature

The complete chloroplast genome of Rhododendron molle and its phylogenetic position within Ericaceae.

Project description:Rhododendron mole (Blume) G. Don is an attractive ornamental and valuable medicinal plant which widely distributed in the southern regions of China. In order to promote the studies on the genetic diversity of this species, we assembled the complete chloroplast (cp) genome of R. molle by using the genome skimming approach. The results showed that the cp genome of R. molle exhibited a quadripartite cycle with 197,877 bp, comprising of two inverted repeats (IRs) of 43,831 bp separated by a large single copy (LSC) region of 110,189 bp and a quite small single copy (SSC) region of 26 bp. It encodes 146 genes, including 92 protein-coding, 46 tRNA, and eight rRNA genes. The overall GC content of the cp genome was 36.0%. The phylogenetic analysis indicated that R. molle is closely related to R. delavayi. Thus, the cp genome sequence of R. molle provides a rich source of genetic information for studies on Rhododendron taxonomy, phylogeny, and evolution, as well as lays the foundation for further development and utilization of R. molle.

| S-EPMC8354172 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data