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 of a solid type of Phyllostachys nidularia (Bambusoideae: Poaceae), a species endemic to China.

ABSTRACT: Phyllostachys nidularia (Bambusoideae: Poaceae), widely distributed in the Yangtze River Basin and various provinces (regions) in southern China, is one of the most important small and medium-sized bamboo species used in both bamboo shoots and timber. In the present study, we assembled a complete chloroplast genome of the economically important bamboo form Phyllostachys nidularia f. farcta H.R.Zhao & A.T.Liu using whole genome sequencing data previously reported. The complete chloroplast (cp) genome is 139,706 bp in length. A total of 129 unique genes were annotated, including 82 protein-coding, 39 tRNA, and eight rRNA genes. Phylogenetic analysis results supported that P. nidularia f. farcta was closely related to Phyllostachys reticulata. This work would help us better understand the evolution of the Phyllostachys cp genome.

SUBMITTER: Jie Z

PROVIDER: S-EPMC7995827 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome of Phyllostachys glauca (Bambusoideae), a dominant bamboo species in limestone mountains endemic to China.

Project description:Phyllostachys glauca is a dominant species in limestone mountains endemic to China. Here, we characterized its complete chloroplast genome. It is a circular DNA molecule of 139,689 bp in length, including a pair of 21,798 bp inverted repeats (IRs), a 12,872 bp small single-copy (SSC) region and an 83221 bp large single-copy (LSC) region. The total GC content of P. glauca chloroplast genome was 38.9%, and it encodes a total of 137 functional genes, including 89 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. The phylogenetic analysis shows that P. glauca is highly clustered in the Phyllostachys clade (V), sister to the lineage of P. nigra var. henonis + P. sulphurea.

| S-EPMC7783095 | biostudies-literature

The complete chloroplast genome of Phyllostachys edulis f. curviculmis (Bambusoideae): a newly ornamental bamboo endemic to China.

Project description:Phyllostachys edulis (Bambusoideae) is a temperate woody bamboo with a long history of cultivation in China. Phyllostachys edulis f. curviculmis is the latest new forma that repored in 2018. Here, we performed the complete chloroplast genomes of P. edulis and P. edulis f. curviculmis using genome skimming. The length of two chloroplast genomes was 139,678 bp, and their GC contents were 38.9%. The sequences of each species contained 132 unique genes, including 39 tRNA, eight rRNA, and 85 protein-coding genes. Moreover, in subspecies-level, P. edulis 'Pachyloen' and P. edulis f. curviculmis are identical to P. edulis in the terms of chloroplast genome size, structure, and composition, further indicating their affinity.

| S-EPMC7971251 | biostudies-literature

The complete chloroplast genome sequence of Acidosasa gigantea (Bambusoideae: Arundinarieae): an ornamental bamboo species endemic to China.

Project description:We, at first, fully characterized the complete chloroplast genome of the woody bamboo Acidosasa gigantea using genome skimming and focused on comparative analyses among Acidosasa and Indosasa. This newly sequenced chloroplast genome (GenBank NO. MN917206) is a typical circular structure with 139,711 bp in length and comprises of an 83,295 bp large single-copy (LSC) region, a 12,824 bp small single-copy (SSC) region, and a pair of 21,796 bp inverted repeats (IRs). The GC content of A. gigantea is 38.9% and the sequences contained 132 unique genes were successfully annotated, including 39 tRNA genes, 8 rRNA genes, and 85 protein-coding genes. Phylogenetic analysis shows that A. gigantea is highly clustered in the Arundinaria clade (clade VI) of Arundinarieae, a sister of the clade of Acidosasa purpurea and was not clustered on the same branch as Indosasa sinica. Therefore, it is more accurate to classify A. gigantea into Acidosasa.

| S-EPMC7748808 | biostudies-literature

The complete chloroplast genome of Phyllostachys angusta McClure (Poaceae).

Project description:Phyllostachys angusta McClure is a precious wood-use bamboo resource, with almost straight stem. The complete chloroplast genome of the P. angusta McClure was assembled for the first time from Illumina pair-end sequencing data in this work. The total genome size of P. angusta McClure was 139,678 bp in length, containing a large single-copy (LSC) region of 83,212 bp, a small single-copy (SSC) region of 12,870 bp, and a pair of inverted repeat (IR) regions of 21,798 bp. The overall GC content of the genome was 38.89%, and the corresponding values of the LSC, SSC, and IR regions were 36.97, 33.17, and 44.22%, respectively. A total of 131 genes were annotated, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. Phylogenetic analysis results strongly supported that P. angusta McClure was closely related to P. reticulate.

| S-EPMC7832504 | biostudies-literature

The complete chloroplast genome of Phyllostachys edulis f. tubiformis (Bambusoideae): a highly appreciated type of ornamental bamboo in China.

Project description:Phyllostachys edulis (Carr.) H. de Lehaie f. tubiformis (S.Y.Wang) Ohrnberger (shengyin bamboo in Chinese) is a dwarf form of moso bamboo, which has important ornamental value. In this study, the complete chloroplast genome of P. edulis f. tubiformis was reported. The complete chloroplast genome of P. edulis f. tubiformis is a double-circular DNA of 139,678 bp in length with 38.89% G + C content, and contains 126 genes, including 84 protein-coding genes, eight ribosomal RNA (rRNA) genes, and 34 transfer RNA (tRNA) genes. Phylogenetic analysis results strongly supported that P. edulis f. tubiformis was clustered with the other infra-species of P. edulis, although its morphology is quite different from moso bamboo.

| S-EPMC8751489 | biostudies-literature

Gelidocalamus xunwuensis (Poaceae, Bambusoideae), a new species from southeastern Jiangxi, China.

Project description:Gelidocalamus xunwuensis W.G.Zhang & G.Y.Yang, a new species collected from Xunwu County of Jiangxi Province in China, is described and illustrated. The new species is similar to G. stellatus in the habit, but differs by internodes sparsely hairy with granuliferous warts, culm sheath stiffly hairy, culm sheath blade broadly lanceolate to narrowly triangular, each node with a ring of appressed trichomes below, foliage leaves broadly lanceolate to narrowly oblong, and new shoots occurring in late October.

| S-EPMC5624199 | biostudies-literature

The complete chloroplast genome of Pseudosasa usawae (Poaceae: Bambusoideae: Arundinarieae) in Taiwan.

Project description:Pseudosasa usawae is an endemic species in Taiwan, and grows at an altitude of 600-1200 m. In this study, we fully characterized the complete chloroplast genome of P. usawae. The complete chloroplast sequence was 139,660 bp, including large single-copy (LSC), small single-copy (SSC), and a pair of invert repeats (IR) region of 83,271, 12,803, and 21,793 bp. Besides, the plastid genome comprised a total of 129 genes, including protein-coding, tRNA, and rRNA genes as 83, 38, and 8 genes. Phylogenetic analysis reveals that P. usawae is closely associated with Phyllostachys genus clade, sister to the lineage of Phyllostachys.

| S-EPMC8797728 | biostudies-literature

The complete chloroplast genome sequence of Fargesia qinlingensis (Poaceae): an endemic to China.

Project description:The complete chloroplast genome of Fargesia qinlingensis (Poaceae) has been reconstructed from the whole-genome Illumina sequencing data. The complete chloroplast genome sequence of F. qinlingensis obtained in this study was 139,640?bp in length, with a large single copy (LSC) region of 83,220?bp, a small single copy (SSC) region of 12,826?bp, separated by two inverted repeat (IR) regions of 21,797?bp each. The GC content was 38.9%, and in the LSC, SSC, and IR regions were 37.0%, 33.2%, and 44.2%, respectively. A total of 130 genes were annotated, including 83 protein-coding genes (PCGs), 39 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The result of the phylogenetic analysis showed that F. qinlingensis was more closely related to the species of F. denudata.

| S-EPMC7800314 | biostudies-literature

The complete chloroplast genome of Phyllostachys heteroclada f. solida (Poaceae).

Project description:Phyllostachys heteroclada f. solida is a precious wood-use bamboo resource, with almost solid stem. The complete chloroplast genome of the Phyllostachys heteroclada f. solida was the first time to assemble from Illumina pair-end sequencing data in this work. The total genome size of Phyllostachys heteroclada f. solida was 156,559 bp in length, containing a large single-copy (LSC) region of 89,200 bp, a small single-copy (SSC) region of 14,876 bp, and a pair of inverted repeat (IR) regions of 23,798 bp. The overall GC content of the genome was 36.12%, and the corresponding values of the LSC, SSC, and IR regions were 36.98, 33.15, and 44.22%, respectively. A total of 136 genes were annotated, including 88 protein-coding genes, 40 tRNA genes, and 8 rRNA genes. Phylogenetic analysis results strongly supported that Phyllostachys heteroclada f. solida was closely related to Phyllostachys reticulate.

| S-EPMC7889091 | biostudies-literature

Two new species of Fargesia (Poaceae, Bambusoideae) from southwestern China.

Project description:Two new species of Fargesia, one from Xizang (Tibet) and one from Yunnan, China, are described and illustrated. Fargesia viridis D.Z. Li & X.Y. Ye is characterized by its densely white powder, nearly solid internodes, yellow setose sheath scar and culm sheaths, and 4-6 leaves of large size. Fargesia purpurea D.Z. Li & X.Y. Ye has thinner culms (0.5-1.4 cm in diameter), a ring of 4-5 mm tall brown setae below nodes, fewer branches, glabrous sheath scar and culm sheaths, differentiated from the related species.

| S-EPMC7746660 | 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