Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome of Meconopsis integrifolia (Papaveraceae).

ABSTRACT: Meconopsis integrifolia (Maxim.) Franch is a traditional Tibetan medicinal material. In this study, we sequenced and assembled the complete chloroplast genome of M. integrifolia. The chloroplast genome is 152,714 bp in length, containing a pair of inverted repeated (IR) region of 25,627 bp that are separated by a large single copy (LSC) region of 83,706 bp, and a small single copy (SSC) region of 17,754 bp. Moreover, a total of 126 functional genes were annotated, including 86 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. In the maximum likelihood phylogenetic tree, M. integrifolia clustered closely with three Papaver species.

SUBMITTER: Li R

PROVIDER: S-EPMC7720952 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Complete chloroplast genome of the Meconopsis quintuplinervia (Papaveraceae), a traditional medicine of Tibetan.

Project description:As a medicinal herb of Tibetan, Meconopsis quintuplinervia is often utilized for treating pneumonia. In this study, the complete chloroplast genome of M. quintuplinervia was determined by next-generation sequencing technology. The overall genome was 154,997 bp in size, including a large single copy (LSC), a small single copy (SSC) and two inverted repeat (IR) regions, which were 85,153 bp, 17,876 bp, and 25,984 bp in length, respectively. The circular chloroplast genome owned 129 genes, comprising 84 protein-coding genes, 8 ribosomal RNA genes (four rRNA species), and 37 transfer RNA genes. The GC contents of the entire sequence, LSC, SSC, and IR region were 38.5%, 37.1%, 32.8%, and 43%, separately. The maximum likelihood tree revealed that M. quintuplinervia was closely related to M. racemosa with strong support value.

| S-EPMC7687438 | biostudies-literature

Characterization of the complete chloroplast genome of the prickly blue poppy Meconopsis horridula Hook. f. & Thomson (Ranunculales: Papaveraceae).

Project description:The prickly blue poppy (Meconopsis horridula Hook. f. & Thomson) is a traditional Tibetan medicinal herb with high values. In this study, its chloroplast genome was determined to be 153,761 bp in length with an A + T-biased base composition, and comprises a pair of inverted repeat (IR) regions (26,030 bp), separated by a large single-copy (LSC) region (83,803 bp) and a small single-copy (SSC) region (17,898 bp). A total of 113 gene species were annotated, with 20 of them being completely or partially duplicated and 18 of them harboring one or two introns. Phylogenetic analysis suggests that M. horridula is closely related to Meconopsis racemosa Maxim.

| S-EPMC7954420 | biostudies-literature

Complete chloroplast genome sequences of two species used for Tibetan medicines, Meconopsis punicea vig. and M. henrici vig. (Papaveraceae).

Project description:Meconopsis Vig. is a genus possessing important medicinal and ornamental values in the Papaveraceae. Many species in this genus are commonly used in traditional Tibetan medicines over thousands of years. In this study, we sequenced complete chloroplast (cp) genome sequences of two species, namely Meconopsis punicea and M. henrici to investigate their phylogenetic relationships in Papaveraceae. Total lengths of the chloroplast genomes were 153,281 bp and 153,388 bp, respectively. Both of the two genomes had typical quadripartite structure, LSC region (83,999 bp and 83,698 bp) and SSC region (17,730 bp and 17,822 bp) were separated by a pair of IRs (25,776 bp and 26,107 bp), respectively. Moreover, they were composed of 112 genes, including 78 protein coding genes, 30 tRNA genes, three rRNA genes and one pseudogene. Phylogenetic analysis based on complete chloroplast genomes showed that M. henrici had closer relationship with M. racenosa than M. punicea; meanwhile, Meconopsis was closely related to Papaver in Papaveraceae.

| S-EPMC7721039 | biostudies-literature

Characterization of the complete chloroplast genome of Saussurea integrifolia (Compositae).

Project description:The complete chloroplast genome sequence of Saussurea integrifolia, a flowering plant occurring in Hengduan Mountains with high altitudes, is determined in this study. The plastome is 152,584 bp in length, with one large single-copy region of 83,497 bp, one small single-copy region of 18,646 bp, and two inverted repeat (IR) regions of 25,221 bp. It contains 123 genes, including 86 protein-coding genes, 8 ribosomal RNA, and 36 transfer RNA. Phylogenetic tree shows that this species is a sister to Arctium lappa. The published plastome within Saussurea provides significant insight for elucidating the phylogenetic relationship of taxa within tribe Compositae.

| S-EPMC7707334 | biostudies-literature

Meconopsis integrifolia

Project description:The complete chloroplast genome of Meconopsis integrifolia

| PRJNA728396 | ENA

Meconopsis integrifolia

Project description:Meconopsis integrifolia overview

| PRJNA820095 | ENA

Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome.

Project description:Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost or pseudogenized throughout the chloroplast genomes of various Corydalis species. Analysis of five protein-coding genes revealed simple sequence repeats and repetitive sequences that can be potential molecular markers for species identification. Phylogenetic analysis revealed three subgenera in Corydalis. Subgenera Cremnocapnos and Sophorocapnos represented the Type 2 and 3 genome structures, respectively. Subgenus Corydalis included all types except type 3, suggesting that chloroplast genome structural diversity increased during its differentiation. Despite the explosive diversification of this subgenus, most endemic species collected from the Korean Peninsula shared only one type of genome structure, suggesting recent divergence. These findings will greatly improve our understanding of the chloroplast genome of Corydalis and may help develop effective molecular markers.

| S-EPMC10513226 | biostudies-literature

The complete chloroplast genome of Papaver setigerum and comparative analyses in Papaveraceae.

Project description:Papaver setigerum is an annual herb that is closely related to the opium poppy, P. somniferum. Genetic resources for P. setigerum are scarce. In the present study, we assembled the complete chloroplast (cp) genome of P. setigerum based on genome skimming data, and we conducted comparative cp genome analyses to study the evolutionary pattern in Papaveraceae. The cp genome of P. setigerum is 152,862 bp in length with a typical quadripartite structure. Comparative analyses revealed no gene rearrangement in the Papaveraceae family, although differences were evident in genome size, gene losses, as well as inverted repeats (IR) region expansion and contraction. The rps15 gene has been lost from the genomes of Meconopsis racemosa, Coreanomecon hylomeconoides, P. orientale, P. somniferum, and P. setigerum, and the ycf15 gene is found only in C. hylomeconoides. Moreover, 13 cpDNA markers, including psbA-trnH, rps16-trnQ, trnS-trnG, trnC-petN, trnE-trnT, trnL-trnF, trnF-ndhJ, petA-psbJ, ndhF-rpl32, rpl32-trnL, ccsA-ndhD, ndhE-ndhG, and rps15-ycf1, were identified with relatively high levels of variation within Papaver, which will be useful for species identification in this genus. Among those markers, psbA-trnH is the best one to distinguish P. somniferum and P. setigerum.

| S-EPMC7433754 | biostudies-literature

Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation.

Project description:The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.

| S-EPMC10888623 | biostudies-literature

Complete chloroplast genome of a Chinese endemic species Corydalis trisecta Franch. (Papaveraceae).

Project description:Corydalis trisecta Franch. is an endemic plant found in China. In this study, we presented the first complete chloroplast genome of C. trisecta, which was assembled and characterized based on Illumina pair-end sequencing data. The complete chloroplast genome was 161,410?bp in length, with a GC content of 41.4% in total. Its structure contained a large single copy (LSC) region of 89,127?bp and a small single copy (SSC) region of 16,993?bp, which were separated by a pair of extremely inverted repeats (IRs) of 27,645?bp each, with GC content 39.8, 87.2, and 45.2%, respectively. The phylogenetic analysis indicated that C. triscta was sister to Lamprocapons spectabilis in Papaveraceae.

| S-EPMC7687375 | 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