Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete chloroplast genome sequence of Pistia stratiotes (Araceae) and its phylogenetic implications.

ABSTRACT: Pistia stratiotes is an invasive aquatic weed in South China. In this study, the first complete chloroplast (cp) genome of P. stratiotes was reported and phylogenetic analysis was conducted with Araceae species based on the cp genome sequences. The genome is a circular molecule of 164,551 bp in length with 36.00% average GC content and includes a large single-copy region (90,705 bp), a small single-copy region (21,886 bp), and two inverted repeat regions (25,980 bp). It contains a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood tree indicated that P. stratiotes is related to the genus of Alocasia. The cp genome will provide useful molecular data for further phylogenetic and evolutionary analysis of P. stratiotes.

SUBMITTER: Quan G

PROVIDER: S-EPMC7510755 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete chloroplast genome sequence of Dalbergia species and its phylogenetic implications.

Project description:The pantropical plant genus Dalbergia comprises approximately 250 species, most of which have a high economic and ecological value. However, these species are among the most threatened due to illegal logging and the timber trade. To enforce protective legislation and ensure effective conservation of Dalbergia species, the identity of wood being traded must be accurately validated. For the rapid and accurate identification of Dalbergia species and assessment of phylogenetic relationships, it would be highly desirable to develop more effective DNA barcodes for these species. In this study, we sequenced and compared the chloroplast genomes of nine species of Dalbergia. We found that these chloroplast genomes were conserved with respect to genome size, structure, and gene content and showed low sequence divergence. We identified eight mutation hotspots, namely, six intergenic spacer regions (trnL-trnT, atpA-trnG, rps16-accD, petG-psaJ, ndhF-trnL, and ndhG-ndhI) and two coding regions (ycf1a and ycf1b), as candidate DNA barcodes for Dalbergia. Phylogenetic analyses based on whole chloroplast genome data provided the best resolution of Dalbergia, and phylogenetic analysis of the Fabaceae showed that Dalbergia was sister to Arachis. Based on comparison of chloroplast genomes, we identified a set of highly variable markers that can be developed as specific DNA barcodes.

| S-EPMC6938520 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Pennisetum glaucum and its phylogenetic implications.

Project description:Pennisetum glaucum is a high nutritive-value summer-annual forage crop, popular among livestock producers for grazing, silage, hay, and green chop. In this study, the complete chloroplast genome of the P. glaucum was assembled from the whole genome Illumine sequencing data. The size of the P. glaucum chloroplast genome is 138,119?bp, including a large single-copy region (81,034?bp), a small single-copy region (12,409?bp), and a pair of inverted repeats regions (22,338?bp). The overall GC content of the P. glaucum chloroplast genome was 38.6%. The chloroplast genome of P. glaucum encodes 110 different genes, including 76 protein-coding genes, 30 transfer RNAs (tRNA), and four ribosomal RNAs (rRNA). Phylogenetic analysis confirmed a close relationship of P. glaucum with species in the Panicoideae subfamily of the Poaceae family.

| S-EPMC7707298 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Tinospora sagittata and its phylogenetic implications.

Project description:Tinospora sagittata is a perennial vine of the family Menispermaceae and distributed in Hunan, Hubei, Guangxi, and Sichuan province of P. R. China. It has been used in Chinese traditional medicine for centuries. The chloroplast (cp) genome of T. sagittata, characterized using Illumina technology, is 163,662 bp in size. There are a total of 130 genes, coding for 85 proteins, 37 tRNAs, and 8 rRNAs. Phylogenetic relationship analysis based on 16 complete cp genome sequences exhibited that T. sagittata was phylogenetically closer to Menispermum dauricum and Stephania japonica.

| S-EPMC7748478 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Galinsoga parviflora and its phylogenetic implications.

Project description:Galinsoga parviflora is an invasive weed in southwest of Chinese agricultural systems and commonly used as medicine and food. In this study, the complete chloroplast genome of the G. parviflora was assembled from the whole genome Illumina sequencing data. The circular genome is 151,811 bp in size, which composed of one large single-copy (LSC) and one small single-copy (SSC) regions of 83,594 bp and 18,141 bp, respectively, and separated by a pair of inverted repeat (IR) regions of 25,038 bp each. It encodes a total of 113 gene species (80 protein-coding, 29 tRNA, and four rRNA species), in which 19 of them with double copies. The overall GC content is 37.7% while the GC content of the LSC, SSC, and IR regions are 35.8%, 31.3%, and 43.1%, separately. Phylogenetic analysis indicated that Galinsoga parviflora was closely related to Galinsoga quadriradiata.

| S-EPMC7687395 | biostudies-literature

The complete chloroplast genome sequence of Zelkova sinica and phylogenetic implications in Rosales

Project description:Abstract Zelkova sinica is a popular landscape plant in China because of its wide adaptation, strong disease resistance, large crown and beautiful fall color. Here, we assembled the complete chloroplast (cp) genome of Z. sinica based on genome skimming data. The cp genome is 158,924 bp in length including two copies of inverted region (IR, 26,427 bp) separated by the large single copy (LSC, 87,318 bp) and small single copy (SSC, 18,752 bp) regions. It encodes 111 unique genes, containing 77 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, with 18 duplicated genes in the IR regions. Phylogenetic analysis shows that Z. sinica is sister to Z. schneideriana in Ulmaceae family.

| S-EPMC8567943 | biostudies-literature

Characterization of the first complete chloroplast genome sequence of Celtis sinensis (Cannabaceae) and its phylogenetic implications.

Project description:Celtis sinensis Pers. is a popular garden landscape tree in riparian areas and a valuable resistant tree in many extreme environments. Here, we determined the first complete chloroplast genome of C. sinensis using high-throughput sequencing technology. Our results showed the chloroplast genome of C.sinensis was 159,092?bp long and displayed a typical quadripartite structure consisting of a pair of inverted repeats with a length of 26,895?bp and separating by two single-copy regions (LSC, 86,085?bp and SSC, 19,217?bp). Besides, the chloroplast genome of C. sinensis totally contained 131 genes, including 87 protein coding genes, 36 transfer RNAs and eight ribosomal RNAs. Additionally, a maximum likelihood phylogenetic analysis based on the 19 chloroplast genomes demonstrated the monophyly of Cannabaceae and C. sinensis formed a sister clade to Celtis biondii.

| S-EPMC7707679 | biostudies-literature

The complete chloroplast genome sequence of Acorus tatarinowii (Araceae) from Fujian, China.

Project description:Acorus tatarinowii is a useful traditional Chinese medicine (TCM) and is officially documented in the Chinese Pharmacopeia with the name 'Shi Chang Pu'. It belongs to the Araceae family and is used for the treatment of dementia, epilepsy, amnesia and insomnia. We resequenced complete chloroplast (cp) genome of A. tatarinowii from Fujian, China. The whole genome was 153,453 bp in length, consisting of a pair of inverted repeats (IR 25,795 bp), a large single-copy region (LSC 83,631 bp), and a small single-copy region (SSC 18,232 bp). The complete genome contained 132 genes, including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The overall GC content of the whole genome was 38.7%. A maximum-likelihood phylogenetic analysis showed that A. tatarinowii is sister to A. tatarinowii which was collected in Yunnan, China. The complete chloroplast genome of A. tatarinowii will help improve and integrate the existing genome data of monocots and provide insights into the phylogenetic relationship among basal angiosperms, monocots and dicots.

| S-EPMC7782871 | biostudies-literature

The complete chloroplast genome sequence of Dendrobium densiflorum and its phylogenetic implications.

Project description:Dendrobium is one of the largest genera in Orchidaceae with approximately 1500 species. Many of them have been used as Traditional Chinese Medicine (TCM) for hundreds of years. Here, the first complete chloroplast genome sequence of D. densiflorum was reported and characterized. The complete cpDNA of D. densiflorum is a circular molecule of 153,122 bp, which contains 76 protein-coding genes, 30 tRNA genes, and four rRNA genes. Our phylogenetic analysis indicated that the newly sequenced cpDNA of D. densiflorum could be used for the phylogenetic study of Dendrobium species.

| S-EPMC7782869 | biostudies-literature

The complete chloroplast genome of Arisaema bockii Engler and its phylogenetic analysis in the family Araceae

Project description:Abstract Arisaema bockii Engler is a perennial herbaceous medicinal plant, which is widely distributed in many provinces in China such as Anhui, Jiangsu, and Zhejiang. In this study, the complete chloroplast genome sequence of A. bockii was assembled and characterized based on high-throughput sequencing data. The total length of chloroplast genome was 175,537 bp, including large single-copy (LSC) and small single-copy (SSC) regions of 98,870 bp and 23,345 bp, respectively, which were separated by a pair of 27,161 bp inverted repeat (IR) regions. The genome contained 129 genes, including 84 protein-coding genes, 36 tRNA genes, 8 rRNA genes, and one pseudogene. The overall GC content of the genome was 33.6%. A phylogenetic tree reconstructed by 30 chloroplast genomes revealed that A. bockii was mostly related to the same genus species A. ringens, A. franchetianum and A. erubescens. The work reported the first complete chloroplast genome of A. bockii, which may provide some useful information to the evolution of the family Araceae.

| S-EPMC8547865 | biostudies-literature

The complete chloroplast genome of Typhonium giganteum (Araceae).

Project description:The complete chloroplast genome sequence of Typhonium giganteum, a species of the Araceae family, was characterized from the de novo assembly of HiSeq (Illumina Co.) paired-end sequencing data. The chloroplast genome of T. giganteum was 165,289 bp in length, with a large single-copy (LSC) region of 91,747 bp, a small single-copy (SSC) region of 22,550 bp, and a pair of identical inverted repeat regions (IRs) of 25,496 bp. The genome contained a total of 132 genes, including 86 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis of T. giganteum with 12 related species revealed the closest taxonomical relationship with Pinellia pedatisecta in the Araceae.

| S-EPMC7782031 | 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