Browse
Submit Data
Databases
API
Help

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization and phylogenetic analysis of the complete chloroplast genome of Amaranthus viridis (Amaranthaceae).

ABSTRACT: Amaranthus viridis is an important medicinal herb. In this study, the complete chloroplast genome (plastome) of A. viridis was repotred. It was a circular molecular of 150,452 bp in length and consists of a large single-copy region (LSC, 83,832 bp), a small single-copy region (SSC, 17,914 bp), and two inverted repeats (IRs, 24,353 bp for each) regions. The overall GC content was 36.6%. This plastome encodes 113 unique genes, including 79 protein-coding genes, 30 tRNAs, and four rRNAs. The phylogenetic tree of 18 Amaranthaceae chloroplast genomes supported that A. viridis was closely related to A. hybridus.

SUBMITTER: Ding DB

PROVIDER: S-EPMC8354152 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the first complete chloroplast genome of Amaranthus hybridus (Caryophyllales: Amaranthaceae) with phylogenetic implications.

Project description:In the present study, the complete chloroplast genome of Amaranthus hybridus was sequenced and assembled. The complete chloroplast genome of Amaranthus hybridus is 150,709 in size, with the GC content of 36.56%. The chloroplast genome of Amaranthus hybridus contained 86 protein-coding genes (PCGs), eight ribosomal RNA (rRNA) genes, and 37 transfer RNA (tRNA) genes. Phylogenetic analysis based on combined chloroplast gene dataset indicated that the Amaranthus hybridus exhibited a close relationship with A. hypochondriacus and A. caudatus.

| S-EPMC8555552 | biostudies-literature

The complete chloroplast genome sequences for four Amaranthus species (Amaranthaceae).

Project description:The amaranth genus contains many important grain and weedy species. We further our understanding of the genus through the development of a complete reference chloroplast genome. A high-quality Amaranthus hypochondriacus (Amaranthaceae) chloroplast genome assembly was developed using long-read technology. This reference genome was used to reconstruct the chloroplast genomes for two closely related grain species (A. cruentus and A. caudatus) and their putative progenitor (A. hybridus). The reference genome was 150,518 bp and possesses a circular structure of two inverted repeats (24,352 bp) separated by small (17,941 bp) and large (83,873 bp) single-copy regions; it encodes 111 genes, 72 for proteins. Relative to the reference chloroplast genome, an average of 210 single-nucleotide polymorphisms (SNPs) and 122 insertion/deletion polymorphisms (indels) were identified across the analyzed genomes. This reference chloroplast genome, along with the reported simple sequence repeats, SNPs, and indels, is an invaluable genetic resource for studying the phylogeny and genetic diversity within the amaranth genus.

| S-EPMC5033369 | biostudies-literature

Characterization and phylogenetic analysis of the complete plastome of Amaranthus retroflexus L. (Amaranthaceae), an annual weeds.

Project description:The complete plastome of Amaranthus retroflexus L., a field weed, was identified in this study. The genome size was 150,710 bp and consists of a large single-copy (LSC: 83,892 bp) region, a small single-copy (SSC: 18,100 bp) region, and two inverted repeats (IRs: 24,359 bp) regions. GC content was 36.6%. A total of 113 genes were identified, including 79 protein-coding genes, four rRNA genes, and 30 tRNA genes. Twenty chloroplast genomes from Amaranthaceae were selected to reconstruct phylogenetic tree and the result supported that A. retroflexus was sister to A. hypochondriacus and A. caudatus.

| S-EPMC8425639 | biostudies-literature

The complete chloroplast genome sequence of spleen amaranth (Amaranthus dubius Mart. ex Thell., Amaranthaceae).

Project description:Amaranthus dubius is a leafy vegetable widely cultivated in Asia and Africa. The complete chloroplast genome of Amaranthus dubius was sequenced and assembled in this study. The complete chloroplast genome is 150,520 bp. A total of 130 genes were identified, including 85 protein-coding genes, eight rRNA genes, and 37 tRNA genes. The overall GC content of this genome was 36.6%. The phylogenetic tree based on 10 chloroplast genomes in Amaranthaceae supports that A. dubius is sister to A. hypochondriacus and A. caudatus.

| S-EPMC8547846 | biostudies-literature

Characterization of the complete chloroplast genome of an annual herb, Chenopodium album (Amaranthaceae).

Project description:Chenopodium album is an annual herb from Amaranthaceae with worldwide distribution. It is a leafy vegetable as well as an important subsidiary grain crop with high nutritional value and medicinal value. In this study, we reported the complete chloroplast genome of C. album. The total chloroplast genome was 152,167 bp in length, containing a large single-copy region (LSC, 83,676 bp), a small single-copy region (SSC, 18,105 bp), and a pair of inverted repeat regions (IRs, 25,193 bp). The complete chloroplast genome contains 110 genes, including 78 protein-coding genes, 28 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes with an overall GC content of 37.3%. Phylogenetic analysis showed that C. album was sister to C. acuminatum within Chenopodioideae. The complete chloroplast genome of C. album will provide useful resources for the development and utilization of this species and the phylogenetic study of Amaranthaceae.

| S-EPMC8253191 | biostudies-literature

Characterization of the complete chloroplast genome of an annual halophyte, Chenopodium glaucum (Amaranthaceae).

Project description:The complete chloroplast genome (plastome) of Chenopodium glaucum, an annual halophytic herb, was determined. The plastome was 152,191 bp in size, containing a large single-copy region (83,675 bp), a small single-copy region (18,130 bp), and two inverted repeats regions (25,193 bp). The overall GC content of this plastome was 37.2%. In total, 113 unique genes were annotated including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs. Phylogenomic analysis showed that C. glaucum was sister to C. album.

| S-EPMC7707789 | biostudies-literature

The complete chloroplast genome characterization and phylogenetic analysis of Canarium album.

Project description:Canarium album is one of the precious and characteristic fruit trees of China. In this study, we first presented the complete chloroplast genome of C. album by using BGISEQ-500 sequencing. Its complete chloroplast genome is 163,140 bp in size, containing a pair of inverted repeat regions of 30,729 bp, a large single copy region of 87,748 bp and a small single copy region of 13,934 bp. The chloroplast genome contains 117 unique genes, including 83 protein coding genes, 30 tRNA and 4 rRNA genes. Phylogenetic analysis based on complete chloroplast genomes indicated that C. album was closest to Boswellia sacra.

| S-EPMC7706554 | biostudies-literature

Complete chloroplast genome of medicinal plant Aconitum carmichaelii: genome characterization and phylogenetic analysis.

Project description:The complete chloroplast genome sequence of an important medicinal plant of the family Ranunculaceae, Aconitum carmichaelii Debx., was characterized in this study. The assembled chloroplast genome was 154,776?bp in length, which included a large single-copy (LSC), a small single-copy (SSC), and two inverted repeat (IR) regions of 86,330bp, 15,986?bp, and 26,193?bp, respectively. The GC content of the genome was 38.1%. Phylogenetic analysis with the whole nucleotide sequences of reported Aconitum chloroplast genomes indicated a close relationship of A. carmichaelii with A. kusnezoffii.

| S-EPMC7800505 | biostudies-literature

The complete chloroplast genome of Chenopodium acuminatum Willd. (Amaranthaceae).

Project description:The complete chloroplast genome (plastome) of the Chenopodium acuminatum was assembled and annotated in this study. The complete plastome was composed of circular DNA molecules with a total length of 152,200 bp, comprising a large single-copy region (83,683 bp), a small single-copy region (18,131 bp), and two inverted repeat regions (25,193 bp). GC content of this complete plastome was 37.2%. In total, 113 unique genes were annotated, including 79 protein-coding genes (PCGs), 30 transfer RNAs, and 4 ribosomal RNAs. Phylogenomic analysis showed that C. acuminatum was closely related to C. album.

| S-EPMC7832583 | biostudies-literature

Comparative analysis of the complete chloroplast genome sequences in psammophytic Haloxylon species (Amaranthaceae).

Project description:The Haloxylon genus belongs to the Amaranthaceae (formerly Chenopodiaceae) family. The small trees or shrubs in this genus are referred to as the King of psammophytic plants, and perform important functions in environmental protection, including wind control and sand fixation in deserts. To better understand these beneficial plants, we sequenced the chloroplast (cp) genomes of Haloxylon ammodendron (HA) and Haloxylon persicum (HP) and conducted comparative genomic analyses on these and two other representative Amaranthaceae species. Similar to other higher plants, we found that the Haloxylon cp genome is a quadripartite, double-stranded, circular DNA molecule of 151,570 bp in HA and 151,586 bp in HP. It contains a pair of inverted repeats (24,171 bp in HA and 24,177 bp in HP) that separate the genome into a large single copy region of 84,214 bp in HA and 84,217 bp in HP, and a small single copy region of 19,014 bp in HA and 19,015 bp in HP. Each Haloxylon cp genome contains 112 genes, including 78 coding, 30 tRNA, and four ribosomal RNA genes. We detected 59 different simple sequence repeat loci, including 44 mono-nucleotide, three di-nucleotide, one tri-nucleotide, and 11 tetra-nucleotide repeats. Comparative analysis revealed only 67 mutations between the two species, including 44 substitutions, 23 insertions/deletions, and two micro-inversions. The two inversions, with lengths of 14 and 3 bp, occur in the petA-psbJ intergenic region and rpl16 intron, respectively, and are predicted to form hairpin structures with repeat sequences of 27 and 19 bp, respectively, at the two ends. The ratio of transitions to transversions was 0.76. These results are valuable for future studies on Haloxylon genetic diversity and will enhance our understanding of the phylogenetic evolution of Amaranthaceae.

| S-EPMC5111891 | 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