Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of the complete plastome of Aster pekinensis (Asteraceae), a perennial herb.

ABSTRACT: Aster pekinensis is a perennial herb that distributes widely in China, Korea, and Eeastern Russia. The complete plastome of A. pekinensis is reported here. It is a circular molecular of 152,815 bp in length and consists of a large single-copy region (LSC: 84,530 bp), a small single-copy region (SSC: 18,219 bp), and two inverted repeats (IR: 25,033 bp) regions. GC content is 37.3%. This plastome encodes 113 unique genes, including 79 protein-coding genes, 30 tRNAs, and 4 rRNAs. Phylogenomic analysis of 17 plastomes within Aster and closely related genera revealed that A. pekinensis was sister to the clade comprising A. flaccidus and A. altaicus.

SUBMITTER: Zhang X

PROVIDER: S-EPMC7995869 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Characterization of the complete plastome sequence of perennial sowthistle, Sonchus arvensis (Asteraceae).

Project description:The first complete chloroplast genome sequence of Sonchus arvensis, a herbaceous perennial, and its phylogenetic position relative to a member of the annual weedy and woody perennial species of Sonchus were reported in this study. Here, we assembled the complete plastome sequence of 151,967 base pairs (bp) in length, comprising 84,251 bp of a large single copy (LSC) and 18,184 bp (SSC) of small single copy confined between 24,766 bp of inverted repeats (IR). The genome contained 130 genes, including 87 protein-coding genes, six ribosomal RNA, and 37 transfer RNA genes. The overall GC content was 37.6% (LSC, 35.8%; SSC, 31.5%; IRs, 43.0%). Phylogenetic analysis confirmed that perennial S. arvensis is sister to the clade containing the weedy species of Sonchus.

| S-EPMC7783150 | biostudies-literature

The complete chloroplast genome of Aster sampsonii (Hance) Hemsl, a perennial herb.

Project description:Aster sampsonii (Hance) Hemsl is endemic to China. The complete chloroplast genome of Aster sampsonii was studied here. The genome was 152,686 base pair (bp) in length, containing a large single-copy (LSC) region of 84,345 bp, a small single-copy region (SSC) of 18,249 bp and a pair of inverted repeats (IRs) of 25,046 bp. It contains 132 unique genes, including 86 protein-coding genes, 36 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The GC content of the complete chloroplast genome sequence was 37.3%. Phylogenetic analyses using complete chloroplast genomes showed that Aster sampsonii is most closely related to Aster hypoleucus (NC_046503.1).

| S-EPMC8354157 | biostudies-literature

Characterization of the complete plastome of Spiraea trilobata (Rosaceae), a perennial shrub.

Project description:The complete plastome of Spiraea trilobata, a shrub, is determined. The plastome is 155,981 bp in length and comprises a large single-copy region (84,417 bp), a small single-copy region (18,878 bp), and a pair of inverted repeats regions (26,343 bp). A total of 113 unique genes are annotated for the plastome of S. trilobata, containing 79 protein coding genes (PCGs), 30 tRNAs, and four rRNAs. The GC content of this plastome is 36.8%. Phylogenomic analysis based on 17 plastomes reveals that S. trilobata is sister to Spiraea blumei. Compared with S. blumei, S. trilobata lacks both trnM-CAU and ycf1. In addition, the GC content of both species is the same.

| S-EPMC8788365 | biostudies-literature

Development and characterization of SSR markers for Aster savatieri (Asteraceae).

Project description:Simple sequence repeat (SSR) markers were developed for Aster savatieri (Asteraceae) and the serpentine variety A. savatieri var. pygmaeus to re-evaluate their taxonomic status. Using RNA-Seq data, 22 expressed sequence tag (EST)-SSR markers were developed. Polymorphisms were assessed in A. savatieri and in A. savatieri var. pygmaeus. The average number of alleles ranged from four to 15, and expected heterozygosity ranged from 0.417 to 0.870. Transferability was examined in six representative species of Japanese Aster and in Solidago virgaurea subsp. asiatica var. asiatica, a member of the tribe Astereae (Asteraceae); most of the loci were transferable to these examined species. These markers will be useful for genetic studies of variation in A. savatieri and other Aster species that occur in Japan.

| S-EPMC4915918 | biostudies-literature

Characterization of the complete plastome of Atriplex centralasiatica (Chenopodiaceae), an annual halophytic herb.

Project description:Atriplex centralasiatica, an annual halophytic herb, is one of the most important Chinese herbal medicines, forages and indicator plants for saline-alkali soil. In this study, we report the complete plastome of A. centralasiatica. The plastome was 152,237?bp in length and comprises a large single-copy region (83,721?bp), a small single-copy region (18,096?bp), and a pair of inverted repeats (25,210?bp). It encodes 113 unique genes, including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs. The overall GC content of this plastome was 37.3%. Phylogenomic analysis based on 21 plastomes revealed that A. centralasiatica was closely related to the genus Chenopodium.

| S-EPMC7687555 | biostudies-literature

Characterization of the complete plastid genome of the perennial herb Astragalus complanatus Bunge (Fabales: Fabaceae).

Project description:Astragalus complanatus Bunge is a perennial herb with high medicinal value, and is endemic to China. The plastid genome of A. complanatus was determined to be 124,213 bp in length with an A + T-biased nucleotide composition (65.7% A + T). The plastid genome harbors a total of 111 genes, including 75 protein-coding, 32 tRNA, and 4 rRNA genes. The presence of one or two introns was detected in 11 protein-coding genes and 6 tRNA genes. Phylogenetic analysis revealed that A. complanatus failed to cluster together with the seven congeners, implying that its phylogenetic placement may need further investigation.

| S-EPMC8604494 | biostudies-literature

Characterization of the complete plastome of Thalictrum aquilegiifolium var. sibiricum (Ranunculaceae), an annual herb.

Project description:Thalictrum aquilegiifolium var. sibiricum, is an annual herb that grows on slopes or in mountain gullies in areas of damp forest. In this study, we report for the first time the complete plastome sequence of T. aquilegiifolium var. sibiricum. The plastome sequence is 156,244 bp in length and comprises a large single-copy region (85,447 bp), a small single-copy region (17,599 bp), and a pair of inverted repeat regions (26,480 bp). The genome encodes 112 unique genes, including 78 protein-coding genes, 30 tRNAs, and four rRNAs, and has total GC content of 38.4%. Phylogenomic analysis based on the plastome sequences of 20 species in the family Ranunculaceae indicated that T. aquilegiifolium var. sibiricum is clustered with Thalictrum minus.

| S-EPMC9318298 | biostudies-literature

Characterization of the complete chloroplast genome sequence of Chinese endemic species of Aster batangensis (Asteraceae: Astereae) and its phylogenetic implications.

Project description:This study was the first report complete chloroplast genome of Aster batangensis (Astereae: Asteraceae), the perennial herb endemic to China. The plastid genome of Aster batangensis include 132 unique genes, with 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Among these genes, 21 duplicate genes, including10 protein-coding genes, 7 tRNA genes, and 4 rRNA genes were detected. The complete genome size of Aster batangensis has a typical quadripartite circular structure with 152,605 bp in total length, consisting a large single copy (LSC) of 84,351 bp and a small single copy (SSC) of 18,212 bp, separated by a pair of invested repeats (IR) of 25,021 bp. The average GC content of whole plastome sequence is 37.3%, and the LSC, SSC and IR regions is 35.3%, 31.3%, and 43.0%, respectively. The phylogenetic analysis by the maximum likelihood method showed that A. batangensis was closely related to the other members of Astereae (e.g. Aztecaster matudae, Conyza bonariensis, Lagenophora cuchumatanica, Baccharis tricuneata, Baccharis genistelloides).

| S-EPMC8526030 | biostudies-literature

Complete plastome sequence of Torenia concolor Lindley (Linderniaceae): an ornamental herb.

Project description:In this study we firstly reported the complete chloroplast genome of Torenia concolor, a species of Linderniaceae. The complete chloroplast genome of T. concolor is 153,853 bp in length with a typical quadripartite structure, consisting of a large single-copy region (LSC, 85,446 bp), a single-copy region (SSC, 18,837 bp), and a pair of inverted repeats (IRs, 24,785 bp). There are 114 genes annotated, including 80 unique protein-coding genes, 4 unique ribosomal RNA genes, and 30 transfer RNA genes. To investigate the evolution status of T. concolor, as well as Linderniaceae, we constructed a phylogenetic tree with T. concolor and other 16 species based on their complete chloroplast genomes. According to the phylogenetic topologies, T. concolor was closely related to Pedicularis hallaisanensis.

| S-EPMC7687577 | biostudies-literature

The complete chloroplast genome of Aster hypoleucus (Asteraceae: Astereae): an endemic species from China.

Project description:This study was the first report about complete chloroplast genome of Aster hypoleucus (Asteraceae, Astereae), an endemic species in Xizang (China). The circular whole cp genome of A. hypoleucus was 152,300?bp in length, contained a large single-copy (LSC) region of 84,031?bp and a small single-copy (SSC) region of 18,269?bp. These two regions were separated by a pair of inverted repeat regions (IRa and IRb), each of them 25,000?bp in length. A total of 134 functional genes were encoded, consisted of 89 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome sequence was 37.3%, and the GC contents of the LSC, SSC, and IR regions were 35.2%, 31.2%, and 43.0%, respectively.

| S-EPMC7706685 | 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