Browse
Submit Data
Databases
API
Help

Dataset Information

35 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequencing and phylogenetic analysis of the complete chloroplast genome of Arisaema heterophyllum Blume

ABSTRACT: Abstract Arisaema heterophyllum Blume is a perennial medicinal herb widely distributed in China, Korea and Japan. In this study, the complete chloroplast genome sequence of A. heterophyllum was assembled and characterized based on high-throughput sequencing data. The whole chloroplast genome is 170,610 bp in length and contains 95,485 bp large single-copy (LSC) and 22,605 bp small single-copy (SSC) regions separated by a pair of 26,260 bp inverted repeat (IR) regions. It contained a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes, with an overall GC content of 34.5%. A phylogenetic tree reconstructed by 30 chloroplast genomes reveals that A. heterophyllum is mostly related to the same genus A. ringens, A. franchetianum and A. erubescens. The complete chloroplast genome of A. heterophyllum was the firstly reported and deposited at GenBank under accession number MZ424448.

SUBMITTER: Yi S

PROVIDER: S-EPMC8547874 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

De novo sequencing and transcriptome assembly of Arisaema heterophyllum Blume and identification of genes involved in isoflavonoid biosynthesis.

Project description:Arisaema heterophyllum Blume (AhBl) is one of the valued medicinal plants. However, its genetic information is limited, which impedes further studies of this valuable resource. To investigate the genes involved in the isoflavonoid biosynthesis, we deeply performed transcriptome sequencing for AhBl. An average of 10.98 Gb clean reads were obtained based on root, tuber and leaf tissues, and 109,937 unigenes were yielded after de novo assembly. In total, 72,287 of those unigenes were annotated in at least one public database. The numbers of expressed unigenes in each tissue were 35,686, 43,363 and 47,783, respectively. The overall expression levels of transcripts in leaf were higher than those in root and tuber. Differentially expressed genes analysis indicated that a total of 12,448 shared unigenes were detected in all three tissues, 10,215 of which were higher expressed in tuber than that in root and leaf. Besides, 87 candidate unigenes that encode for enzymes involved in biosynthesis of isoflavonoid were identified and analyzed, and some key enzyme genes were experimentally validated by quantitative Real-Time PCR (qRT-PCR). This study provides a unique dataset for the systematic analysis of AhBl functional genes and expression characteristics, and facilitates the future study of the pharmacological mechanism of AhBl.

| S-EPMC6281570 | 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

Complete chloroplast genome of endangered species Dipterocarpus retusus Blume (Dipterocarpaceae) and its phylogenetic implications.

Project description:Dipterocarpus retusus Blume is an endangered species on the IUCN Red List. In this study, we reported the complete chloroplast (cp) genome of D. retusus (GenBank accession number: OP271853). The cp genome was 154,303 bp long, with a large single-copy (LSC) region of 85,586 bp and a small single-copy (SSC) region of 20,273 bp separated by a pair of inverted repeats (IRs) of 24,222 bp. It encodes 128 genes, including 84 protein-coding genes, 36 tRNA genes, and eight ribosomal RNA genes. We also reconstructed the cp genome phylogeny of Dipterocarpus, which indicated D. retusus was closely related with the sympatric species D. gracilis. This study may contribute valuable information to the phylogenetic relationships within the genus Dipterocarpus.

| S-EPMC11370694 | biostudies-literature

Arisaema heterophyllum

Project description:De novo sequencing and assembly of Arisaema heterophyllum Blume transcriptome

| PRJNA411914 | ENA

Arisaema heterophyllum

Project description:Arisaema heterophyllum Genome sequencing and assembly

| PRJNA838258 | ENA

Arisaema heterophyllum

Project description:Arisaema heterophyllum overview

| PRJNA838675 | ENA

Complete chloroplast genome of Achyranthes bidentata Blume.

Project description:Achyranthes bidentata Blume is an important herbal medicine. However, little genetic information about Achyranthes is available. To facilitate species identification, we sequenced its complete chloroplast genome using the Illumina MiSeq platform. The data show that the chloroplast genome of A. bidentata is 151,441 bp in size and comprises an 83,890 bp large single-copy region, a 17,261 bp small single-copy region, and two inverted repeat (IR) regions, IRa and IRb (each 25,145 bp). The genome contains 112 unique genes, including 79 protein-coding genes, 4 ribosomal RNAs genes, and 30 transfer RNAs genes. Phylogenetic analysis revealed that A. bidentata is most closely related to Alternanthera philoxeroides.

| S-EPMC7707250 | biostudies-literature

Characterization of the complete chloroplast genome of Dracocephalum heterophyllum (Lamiaceae).

Project description:Dracocephalum heterophyllum is a medicinal plant. The complete chloroplast genome sequence is 150,860 bp in length, which contains 133 complete genes, among them, 88 are protein-coding genes (88 PCGs), 8 are ribosomal RNA genes (8 rRNAs), and 37 are tRNA genes (37 tRNAs). The overall GC content of chloroplast DNA is 37.6%, the respective values of the LSC, SSC, and IR regions are 36.0%, 31.6%, and 43.0%. Phylogenetic tree shows that D. heterophyllum is a sister to D. moldavica and D. palmatum.

| S-EPMC8259819 | biostudies-literature

Complete Chloroplast Genome Sequencing and Phylogenetic Analysis of Two Dracocephalum Plants.

Project description:Dracocephalum tanguticum and Dracocephalum moldavica are important herbs from Lamiaceae and have great medicinal value. We used the Illumina sequencing technology to sequence the complete chloroplast genome of D. tanguticum and D. moldavica and then conducted de novo assembly. The two chloroplast genomes have a typical quadripartite structure, with the gene's lengths of 82,221?bp and 81,450?bp, large single-copy region's (LSC) lengths of 82,221?bp and 81,450?bp, and small single-copy region's (SSC) lengths of 17,363?bp and 17,066?bp, inverted repeat region's (IR) lengths of 51,370?bp and 51,352?bp, respectively. The GC content of the two chloroplast genomes was 37.80% and 37.83%, respectively. The chloroplast genomes of the two plants encode 133 and 132 genes, respectively, among which there are 88 and 87 protein-coding genes, respectively, as well as 37 tRNA genes and 8 rRNA genes. Among them, the rps2 gene is unique to D. tanguticum, which is not found in D. moldavica. Through SSR analysis, we also found 6 mutation hotspot regions, which can be used as molecular markers for taxonomic studies. Phylogenetic analysis showed that Dracocephalum was more closely related to Mentha.

| S-EPMC7787725 | biostudies-literature

The complete chloroplast genome of Achyranthes bidentata Blume.

Project description:Achyranthes bidentata is a popular Chinese medicine, that has its place in the treatment of spasm, osteodynia of the lumbar region and knees. The complete chloroplast (cp) genome of A. bidentata was determined. The complete cp genome is 151,543 bp in length and includes a large single-copy (LSC) region of 83,922 bp, a small single-copy (SSC) region of 17,251 bp, and a pair of inverted repeat regions (IRs) of 25,185 bp. It encodes 131 genes, including 86 protein-coding genes, eight rRNAs, and 37 tRNAs. Phylogenetic analysis indicates that four samples of A. bidentata formed a clade with a 100% bootstrap value.

| S-EPMC7971321 | 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