Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

SUBMITTER: Chang KC

PROVIDER: S-EPMC8797728 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The complete chloroplast genome and phylogenetic position of Thamnocalamus unispiculatus (Poaceae: Bambusoideae: Arundinarieae).

Project description:Thamnocalamus unispiculatus T.P.Yi & J.Y.Shi 2007 is an important bamboo species with significant ecological and economic value. This study presents the complete chloroplast genome sequence of T. unispiculatus. The sequence was 139,726 bp in length and exhibited a typical quadripartite structure, containing four regions: large single copy regions (LSC, 83,283 bp), small single copy regions (SSC, 12,851 bp) and a pair of inverted repeats (IRs, 21,726 bp). A total of 130 genes were annotated, including 86 protein-coding genes, 36 transfer RNA genes, and eight ribosomal RNA genes. Phylogenetic analysis indicated that T. unispiculatus and T. spathiflorus are sister species, supporting the conclusion that Thamnocalamus is a monophyletic group. The chloroplast genome of T. unispiculatus promotes the protection and exploration of biodiversity, phylogenetic relationships, and genetic research in Bambusoideae.

| S-EPMC9248960 | biostudies-literature

Genome skimming reveals the complete chloroplast genome of Ampelocalamus naibunensis (Poaceae: Bambusoideae: Arundinarieae) with phylogenomic implication.

Project description:Ampelocalamus naibunensis is one drooping bamboo with an important ornamental value endemic to Taiwan Island. To date, the genetic and genomic information of this species is little known. Here we characterized the complete chloroplast genome of A. naibunensis using genome skimming approach. The complete chloroplast genome is 139,860?bp, with a large single copy region (LSC) of 83,380?bp and a small single copy region (SSC) of 13,014?bp separated by a pair of inverted repeats (IRs) of 21,822?bp. The genome encodes a total of 129 genes, of which 111 are unique, containing 76 protein-coding genes, 4 ribosomal RNAs and 31 transfer RNAs. Sixteen distinct genes contain one or two introns, and the GC content of the cp genome is 38.9%. Phylogenomic analysis strongly supports the placement of A. naibunensis in the Chimonocalamus lineage (III), distantly related to A. calcareus (XI) within temperate woody bamboos.

| S-EPMC7799681 | biostudies-literature

The complete chloroplast genome of Chimonobambusa hejiangensis (Poaceae: Arundinarieae) and phylogenetic analysis.

Project description:Chimonobambusa hejiangensis is a kind of bamboo that has excellent edible and economic value, which is endemic to southwest China. The study used next-generation sequencing to obtain the complete chloroplast (cp) genome sequence of C. hejiangensis. The cp genome of C. hejiangensis has a total length of 138,908 bp, and consisted of an 82,495-bp large single-copy region, an 12,743-bp small single-copy region, and two 21,835-bp IR regions. In total, 112 unique genes were found in the cp genome, including 77 protein coding, 31 tRNA, and 4 rRNA genes. Phylogenetic analysis indicated that C.hejiangensis and C. tumidissinoda are sister species within the Arundinarieae genus, where Chimonocalamus and Ampelocalamus are more closely related to them.

| S-EPMC8018436 | 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 Schizostachyum dumetorum var. xinwuense (Bambusoideae: Poaceae).

Project description:Schizostachyum dumetorum var. xinwuense (T.H.Wen & J.Y.Chin) N.H.Xia is an arborescent bamboo that is native to Jiangxi, China. The bamboo culm wall of this species is extremely thin, which has high economic value and ecological benefits. Here, we assembled the complete chloroplast genome of S. dumetorum var. xinwuense using Illumina pair-end sequencing data in this work. The total genome size of S. dumetorum var. xinwuense was 139,230 bp in length, containing a large single-copy (LSC) region of 82,876 bp, a small single-copy (SSC) region of 12,877 bp, and a pair of inverted repeat (IR) regions of 21,777 bp. The overall GC content of the genome was 38.87%, and the corresponding GC values of the LSC, SSC, and IR regions were 36.98%, 32.83%, and 44.17%, respectively. The genome contained a total of 112 genes, including 75 protein-coding, 30 tRNA, and seven rRNA. Phylogenetic analysis of S. dumetorum var. xinwuense positioned it in a strongly supported clade with Arundinaria appalachiana. These data show the phylogenetic location of Schizostachyum dumetorum var. xinwuense within the family of the Bambusoideae and contribute to the biodiversity and systematics of the Bambusoideae.

| S-EPMC7995811 | biostudies-literature

A complete chloroplast genome of bamboo cultivar Phyllostachys edulis f. bicolor (Poaceae: Bambusoideae).

Project description:Phyllostachys edulis f. bicolor, a beautiful ornamental bamboo species, is a new variant of P. edulis, with yellow stems and green grooves between nodes. In this study, we assembled and annotated the complete chloroplast (cp) genome of this variety for the first time. The complete cp genome size of P. edulis f. bicolor was 139,678 bp in length and a total of 130 unique genes were annotated, including 85 protein-coding genes, 37 tRNA encoding genes, and eight rRNA encoding genes. Phylogenetic analysis results provided evidence that P. edulis f. bicolor was closely related to P. edulis 'heterocycla'. This study contributes to better understanding of intraspecific type evolution of P. edulis.

| S-EPMC10132244 | biostudies-literature

The identity of Sasaoblongula C.H.Hu (Poaceae, Bambusoideae, Arundinarieae): evidence from morphology and molecular data.

Project description:Sasaoblongula was described in 1987 based on a cultivated plant at the bamboo garden of Sun Yat-sen University. This species has two or three branches at the upper nodes, which differ from the rest of Sasa species that have a single branch per node. During the field trip to Baishi Town, Yunfu City, Guangdong Province in July 2021, one bamboo species with oblong foliage leaves was collected and matches the isotype. Then, our question was to test the identity of S.oblongula concerning other Sasa species based on morphology and molecular data. To do that, we sequenced the whole chloroplast genome of S.oblongula and did a phylogenetic analysis. Our morphological results indicate that the new collection is S.oblongula. The phylogenetic tree showed that S.oblongula is close to Pseudosasa, instead of Sasa species. Therefore, we transferred it to the genus Pseudosasa, and a revised description of P.oblongula is provided here.

| S-EPMC10189642 | biostudies-literature

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

Project description: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.

| S-EPMC7995827 | biostudies-literature

A new genus of temperate woody bamboos (Poaceae, Bambusoideae, Arundinarieae) from a limestone montane area of China.

Project description:Ampelocalamuscalcareus is a climbing and slender bamboo, known from south Guizhou, China. This species grows in broadleaved forests of limestone montane areas. Recent molecular phylogenetic analyses demonstrated that A.calcareus was sister to all other lineages of the tribe Arundinarieae rather than a member of Ampelocalamus. The morphological features and habitats of A.calcareus and related genera including Ampelocalamus, Drepanostachyum and Himalayacalamus were compared and discussed. The characteristics of the branch complements, nodes and foliage leaves distinguish A.calcareus from morphologically similar taxa. On the basis of molecular and morphological evidence, we propose to establish a new genus, Hsuehochloa, to accommodate A.calcareus and to honour the late Chinese bamboo taxonomist Chi-Ju Hsueh (Ji-Ru Xue). In addition, we describe the inflorescence of Hsuehochloa for the first time.

| S-EPMC6195630 | biostudies-literature

The complete chloroplast genome of Bambusa ventricosa (Bambusoideae: Bambuseae).

Project description:Bambusa ventricosa is one important ornamental bamboo. In this study, we generated the complete chloroplast (cp) genome of B. ventricosa via genome-skimming method. The complete cp genome is 139,460 base-pairs (bp) in size, with a pair of inverted repeats of 21,794?bp which separate a large single copy region of 82,996?bp and a small single copy region of 12,876?bp. The genome contains a total of 131 genes, including 84 protein-coding genes, 8 ribosomal RNAs and 39 transfer RNAs. The GC content of the cp genome is 38.9%. Moreover, phylogenomic inference robustly placed B. ventricosa in the paleotropical woody bamboos lineage.

| S-EPMC7799739 | 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