Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete chloroplast genome sequences of Corydalis edulis and Corydalis shensiana (Papaveraceae).

ABSTRACT: Corydalis DC., the largest genus of Papaveraceae, was recognized as one of the most taxonomically challenging plant taxa. Due to the lack of genetic information used in previous studies, species discrimination and taxonomic assignment in Corydalis have not been fully solved. Here, the complete chloroplast genomes were reported for Corydalis edulis Maxim. and Corydalis shensiana Liden, with their genome sizes being 154,395 and 155,938 bp, respectively. Both of the chloroplast genomes comprise two inverted repeat (IR) regions, separated by a large single-copy (LSC) region and a small single-copy (SSC) region, and encode 130 genes, including 85 protein-coding genes, 8 ribosomal RNA genes, 37 transfer RNA genes. Our study will provide novel insight into the molecular phylogeny and classification of Corydalis.

SUBMITTER: Liu YY

PROVIDER: S-EPMC7872545 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

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

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

Characterization of the complete chloroplast genome of Corydalis inopinata Prain ex Fedde (Papaveraceae).

Project description:The complete chloroplast genome of Corydalis inopinata Prain ex Fedde was assembled and characterized in this study. The chloroplast genome was 181,335 bp in length, consisting of a large single-copy (LSC) region of 91,727 bp, a small single-copy (SSC) region of 1502 bp, and a pair of inverted repeat (IR) regions of 44,053 bp. It encoded 110 unique genes, including 68 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 9 pseudogenes. Phylogenetic analyses by maximum likelihood (ML) and Bayesian inference (BI) revealed that C. inopinata was closely related to C. conspersa Maxim. with full support in the present sampling. The complete plastid genome provided in this work would be useful for elucidating the taxonomy, phylogeny, and evolution of C. inopinata and other related species.

| S-EPMC7782898 | biostudies-literature

Highly variable chloroplast genome from two endangered Papaveraceae lithophytes Corydalis tomentella and Corydalis saxicola.

Project description:The increasingly wide application of chloroplast (cp) genome super-barcode in taxonomy and the recent breakthrough in cp genetic engineering make the development of new cp gene resources urgent and significant. Corydalis is recognized as the most genotypes complicated and taxonomically challenging plant taxa in Papaveraceae. However, there currently are few reports about cp genomes of the genus Corydalis. In this study, we sequenced four complete cp genomes of two endangered lithophytes Corydalis saxicola and Corydalis tomentella in Corydalis, conducted a comparison of these cp genomes among each other as well as with others of Papaveraceae. The cp genomes have a large genome size of 189,029-190,247 bp, possessing a quadripartite structure and with two highly expanded inverted repeat (IR) regions (length: 41,955-42,350 bp). Comparison between the cp genomes of C. tomentella, C. saxicola, and Papaveraceae species, five NADH dehydrogenase-like genes (ndhF, ndhD, ndhL, ndhG, and ndhE) with psaC, rpl32, ccsA, and trnL-UAG normally located in the SSC region have migrated to IRs, resulting in IR expansion and gene duplication. An up to 9 kb inversion involving five genes (rpl23, ycf2, ycf15, trnI-CAU, and trnL-CAA) was found within IR regions. The accD gene was found to be absent and the ycf1 gene has shifted from the IR/SSC border to the SSC region as a single copy. Phylogenetic analysis based on the sequences of common CDS showed that the genus Corydalis is quite distantly related to the other genera of Papaveraceae, it provided a new clue for recent advocacy to establish a separate Fumariaceae family. Our results revealed one special cp genome structure in Papaveraceae, provided a useful resources for classification of the genus Corydalis, and will be valuable for understanding Papaveraceae evolutionary relationships.

| S-EPMC8093665 | biostudies-literature

Complete chloroplast genome of Meconopsis integrifolia (Papaveraceae).

Project description: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.

| S-EPMC7720952 | biostudies-literature

Chloroplast genome of Corydalis impatiens (Pall.) Fisch. ex DC. (Papaveraceae), a Tibetan medical herb.

Project description:Corydalis impatiens (Pall.) Fisch. 1821. (Papaveraceae) is a Tibetan medical herb used to reduce pain, treat skin injuries, cure hepatitis, and benefit the circulatory system. In the current study, the chloroplast genome of C. impatiens was sequenced. This complete genome is a circular 197,317 bp sequence consisting of a small single-copy (SSC, 3105 bp) region, a large single-copy (LSC, 89,790 bp) region, and a pair of inverted repeats (IRs, 52,211 bp). This chloroplast genome encodes a total of 127 functional genes, including 81 protein-coding, 38 transfer RNA, and eight ribosomal RNA genes. Furthermore, this chloroplast genome contains six pseudogenes, including a pair of ndhB a pair of ndhD, one ndhC, and one ndhK. The phylogenetic relationship within the genus Corydalis was inferred with the maximum-likelihood method, and the result showed that C. impatiens was most closely related to C. conspersa.

| S-EPMC9347461 | 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

Characterization of the complete chloroplast genome of Corydalis bungeana Turcz.

Project description:Corydalis bungeana Turcz. is a perennial herb belonging to the family Papaveraceae. Its chloroplast genome was sequenced and characterized. The cp genome of C. bungeana is 167,629 bp long with a GC content of 36.52%. A total of 144 genes were identified in this cp genome, including 79 protein-coding genes, 31 tRNAs and four rRNAs. A phylogenetic tree based on the complete nucleic acid sequence indicated that C. bungeana was classified into Corydaleae and had a close relationship with Lamprocapnos spectabilis.

| S-EPMC8204951 | biostudies-literature

The complete chloroplast genome sequence of Casimiroa edulis.

Project description:The first complete chloroplast genome (cpDNA) sequence of Casimiroa edulis was determined from Illumina HiSeq pair-end sequencing data in this study. The cpDNA is 160,176 bp in length, contains a large single-copy region (LSC) of 87,536 bp and a small single-copy region (SSC) of 18,576 bp, which were separated by a pair of inverted repeats (IR) regions of 27,032 bp. The genome contains 131 genes, including 86 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. The overall GC content of the whole genome is 38.2%, and the corresponding values of the LSC, SSC, and IR regions are 36.5, 33.0, and 42.9%, respectively. Further, phylogenomic analysis showed that C. edulis, Phellodendron amurense, and Zanthoxylum bungeanum clustered in a clade in family Rutaceae.

| S-EPMC7707685 | biostudies-literature

Comparative Chloroplast Genomics of Corydalis Species (Papaveraceae): Evolutionary Perspectives on Their Unusual Large Scale Rearrangements.

Project description:The chloroplast genome (plastome) of angiosperms (particularly photosynthetic members) is generally highly conserved, although structural rearrangements have been reported in a few lineages. In this study, we revealed Corydalis to be another unusual lineage with extensive large-scale plastome rearrangements. In the four newly sequenced Corydalis plastomes that represent all the three subgenera of Corydalis, we detected (1) two independent relocations of the same five genes (trnV-UAC-rbcL) from the typically posterior part of the large single-copy (LSC) region to the front, downstream of either the atpH gene in Corydalis saxicola or the trnK-UUU gene in both Corydalis davidii and Corydalis hsiaowutaishanensis; (2) relocation of the rps16 gene from the LSC region to the inverted repeat (IR) region in Corydalis adunca; (3) uniform inversion of an 11-14 kb segment (ndhB-trnR-ACG) in the IR region of all the four Corydalis species (the same below); (4) expansions (>10 kb) of IR into the small single-copy (SSC) region and corresponding contractions of SSC region; and (5) extensive pseudogenizations or losses of 13 genes (accD, clpP, and 11 ndh genes). In addition, we also found that the four Corydalis plastomes exhibited elevated GC content in both gene and intergenic regions and high number of dispersed repeats. Phylogenomic analyses generated a well-supported topology that was consistent with the result of previous studies based on a few DNA markers but contradicted with the morphological character-based taxonomy to some extent. This study provided insights into the evolution of plastomes throughout the three Corydalis subgenera and will be of value for further study on taxonomy, phylogeny, and evolution of Corydalis.

| S-EPMC7873532 | 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