Browse
Submit Data
Databases
API
Help

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The complete chloroplast genome sequence of Bambusa lapidea (Bambusodae).

ABSTRACT: Bambusa lapidea is primarily distributed in Guangdong, Guangxi, Sichuan, Yunnan, and Hong Kong in China, occurring on plains, lower hills, and wetlands on both sides of rivers and adjacent to villages. Therefore, we sequenced and reported the complete chloroplast genome of B. lapidea for the first time. The complete chloroplast genome sequence of B. lapidea was generated by de novo assembly using whole-genome next generation sequencing. The genome was 139,525 bp in total length, including a large next-copy (LSC) region of 83,034 bp, a small single-copy (SSC) region of 12,893 bp, a pair of invert repeats (IR) regions of 21,799 bp. The plastid genome contained 127 genes including 83 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 14 chloroplast genomes indicates that B. lapidea is closely related to B. arnhemica sinospinosa and B. teres in Bambusodae.

SUBMITTER: Chen L

PROVIDER: S-EPMC8218836 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete chloroplast genome sequence of Bambusa pervariabilis (Bambusodae).

Project description:Bambusa pervariabilis is mostly produced in south China; usually cultivated on the banks of the rivers and near villages. We determined the complete chloroplast (cp) genome sequence of B. pervariabilis using Illumina sequencing data. The complete cp sequence is 139,393 bp, include large single-copy (LSC) region of 82,969 bp, small single-copy (SSC) region of 12,874 bp, a pair of invert repeats (IR) regions of 21,775 bp. Plastid genome contain 132 genes, 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 28 cp genomes indicates that B. pervariabilis is closely related to Bambusa multiplex in Bambusodae.

| S-EPMC7748570 | biostudies-literature

Complete chloroplast genome sequence of Bambusa subtruncata (Bambusodae).

Project description:Bambusa subtruncata is found in Xinyi county, Maoming city, Guangdong province, China. In the current study, we sequenced the complete chloroplast genome of B. subtruncata and reported for the first time. The genome was 139,444 bp in total length, including a large single-copy (LSC) region of 82,956 bp, a small single-copy (SSC) region of 12,897 bp, and a pair of invert repeats (IR) regions of 21,798 bp. Plastid genome comprised of 127 genes in total; 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on 25 chloroplast genomes indicates that B. subtruncata is closely related to Bambusa emeiensis in Bambusodae.

| S-EPMC7783132 | biostudies-literature

The complete chloroplast genome sequence of Bambusa albolineata (bambusodae).

Project description:Bambusa albolineata (local name: Hua Zhu) is found in Zhejiang, Jiangxi, Fujian, Taiwan, and Guangdong provinces of China, and is often cultivated on low hills, flatlands, and along streams and rivers. Due to its long internodes and flexible material, it is used as timber wood in China. In the current research, the complete chloroplast (CP) genome of B. albolineata was sequenced and reported for the first time. The complete CP genome sequence was 139,326 bp, including a large single-copy (LSC) region of 82,862 bp, a small single-copy (SSC) region of 12,870 bp, and a pair of invert repeats (IR) regions of 21,798 bp. Besides, the plastid genome consisted of 129 genes; having 82 protein-coding genes, 39 tRNA genes, and eight rRNA genes. The overall GC content of the genome was 44.2%. The phylogenetic analysis based on the complete chloroplast genome indicates that B. albolineata is strongly related to B. flexuosa and B. boniopsis.

| S-EPMC8386721 | biostudies-literature

The complete chloroplast genome sequence of Bambusa contracta L.C.Chia & H.L.Fung (Bambusodae).

Project description:Bambusa contracta L. C. Chia & H. L. Fung is widely distributed in the foothills of Guangxi province, China, and used as a raw material for the production of various bamboo weaving products. In the present work, the complete chloroplast genome sequence of B. contracta was characterized by Illumina pair-end sequencing. The chloroplast genome of B. contracta was 139,470 bp in total length, containing a large single-copy (LSC) region of 83,187 bp, a small single-copy (SSC) region of 12,897 bp, and two inverted repeats (IR) regions of 21,693 bp. The genome consisted of a total of 127 genes, with 83 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Based on 14 chloroplast genomes, the phylogenetic analysis revealed that B. contracta is closely related to B. emeiensis in Bambusodae.

| S-EPMC8245092 | biostudies-literature

The complete chloroplast genome sequence of Bambusa beecheyana var.pubescens (Bambusodae).

Project description:Bambusa beecheyana var. pubescens is mainly distributed in South China to Southwest China, growing on hillsides or river banks. In the current study, we sequenced the complete chloroplast genome of B.beecheyana var. pubescens and reported for the first time. The genome is 139,402 bp in total length, include a large single-copy (LSC) region of 82,936 bp, small single-copy (SSC) region of 12,868 bp, a pair of invert repeats (IR) regions of 21,799 bp. Plastid genome contains 132 genes, 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 25 chloroplast genomes indicates that B. beecheyana var. pubescens is closely related to Bambusa oldhamii, Bambusa ventricosa and Bambusa ventricosa multiplex in Bambusodae.

| S-EPMC7783032 | biostudies-literature

Complete chloroplast genome sequence of Gigantochloa verticillata (Bambusodae).

Project description:Gigantochloa verticillata is produced in Mengla and Jinghong, Yunnan Province, China, and cultivated in Hong Kong. Vietnam, Thailand, India, Indonesia, and Malaysia are distributed and cultivated. We determined the complete chloroplast genome sequence for G. verticillata using Illumina sequencing data. The complete chloroplast sequence is 139,489 bp, including large single-copy (LSC) region of 83,062 bp, small single-copy (SSC) region of 12,877 bp, and a pair of invert repeats (IR) regions of 21,775 bp. Plastid genome contain 132 genes, 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 23 chloroplast genomes indicates that G. verticillata is closely related to Dendrocalamus latiflorus in Bambusodae.

| S-EPMC7748771 | biostudies-literature

Complete chloroplast genome sequence of Bambusa rigida (Bambuseae).

Project description:Bambusa rigida is a tropical woody bamboo widely distributed in Sichuan and southeastern of China with important economic and ecological values. We performed a complete chloroplast (cp) genome of B. rigida using Illumina NovaSeq PE150 platform. The length of complete cp sequence is 139,500 bp in size with a pair of inverted repeat (IR) regions of 43,587 bp, which separates a large single-copy (LSC) region of 83,036 bp and a small single-copy (SSC) region of 12,875 bp. Plastid genome contains 132 genes, including 84 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 30 cp genomes indicates that B. rigida is closely related to Bambusa ventricosa in Bambuseae.

| S-EPMC7781895 | biostudies-literature

The complete chloroplast genome sequence of Bambusa stenoaurita (Bambusoideae).

Project description:Bambusa stenoaurita is an excellent sympodial bamboo species, which is cultivated for its shoots in some parts of China. Here, we sequenced and reported the complete chloroplast genome of B. stenoaurita for the first time. The complete chloroplast genome sequence of B. stenoaurita was generated by de novo assembly using whole-genome next-generation sequencing. The genome was 139,451 bp in total length, including a large single-copy region of 82,958 bp, a small single-copy region of 12,897 bp, a pair of invert repeats regions of 21,798 bp. The plastid genome contained 134 genes including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 23 chloroplast genomes demonstrates that B. stenoaurita is closely related to B. emeiensis in Bambusoideae.

| S-EPMC8284116 | biostudies-literature

The complete chloroplast genome sequence of Bambusa vulgaris cv. Wamin.

Project description:Bambusa vulgaris cv. Wamin is an attractive ornamental bamboo species of southern China. It has large swollen internodes and weeping culms, and it has considerable economic importance. In the present study, we sequenced the complete chloroplast genome of B. vulgaris cv. Wamin and reported it for the first time. The genome was 139,528 bp in total length, including a large single-copy (LSC) region of 83,038 bp, a small single-copy (SSC) region of 12,893 bp, and a pair of invert repeats (IR) regions of 21,799 bp. Plastid genome contained 138 genes, 82 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the genome was 38.9%. The phylogenetic analysis based on the complete chloroplast genome reveals that B. vulgaris cv. Wamin is closely related to Bambusa teres. This research strengthens the genetic information of both the B. vulgaris cv. Wamin and the phylogenetic analyses of Gramineae.

| S-EPMC8158187 | biostudies-literature

Complete nucleotide sequence of Dendrocalamus latiflorus and Bambusa oldhamii chloroplast genomes.

Project description:Although bamboo is one of the most important woody crops in Asia, information on its genome is still very limited. To investigate the relationship among Poaceae members and to understand the mechanism of albino mutant generation in vitro, the complete chloroplast genome of two economically important bamboo species, Dendrocalamus latiflorus Munro and Bambusa oldhamii Munro, was determined employing a strategy that involved polymerase chain reaction (PCR) amplification using 443 novel primers designed to amplify the chloroplast genome of these two species. The lengths of the B. oldhamii and D. latiflorus chloroplast genomes are 139,350 and 139,365 bp, respectively. The organization structure and the gene order of these two bamboos are identical to other members of Poaceae. Highly conserved chloroplast genomes of Poaceae facilitated sequencing by the PCR method. Phylogenetic analysis using both chloroplast genomes confirmed the results obtained from studies on chromosome number and reproductive organ morphology. There are 23 gaps, insertions/deletions > 100 bp, in the chloroplast genomes of 10 genera of Poaceae compared in this study. The phylogenetic distribution of these gaps corresponds to their taxonomic placement. The sequences of these two chloroplast genomes provide useful information for studying bamboo evolution, ecology and biotechnology.

| S-EPMC2762994 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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