The complete chloroplast genome of Typhonium giganteum (Araceae).
Ontology highlight
ABSTRACT:
SUBMITTER: Kim J
PROVIDER: S-EPMC7782031 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Acorus tatarinowii is a useful traditional Chinese medicine (TCM) and is officially documented in the Chinese Pharmacopeia with the name 'Shi Chang Pu'. It belongs to the Araceae family and is used for the treatment of dementia, epilepsy, amnesia and insomnia. We resequenced complete chloroplast (cp) genome of A. tatarinowii from Fujian, China. The whole genome was 153,453 bp in length, consisting of a pair of inverted repeats (IR 25,795 bp), a large single-copy region (LSC 83,631 bp), and a small single-copy region (SSC 18,232 bp). The complete genome contained 132 genes, including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The overall GC content of the whole genome was 38.7%. A maximum-likelihood phylogenetic analysis showed that A. tatarinowii is sister to A. tatarinowii which was collected in Yunnan, China. The complete chloroplast genome of A. tatarinowii will help improve and integrate the existing genome data of monocots and provide insights into the phylogenetic relationship among basal angiosperms, monocots and dicots.
| S-EPMC7782871 | biostudies-literature
Project description:This work determined and analyzed the complete chloroplast genome sequence of Amorphophallus konjac K. Koch ex N.E.Br 1858 from Yunnan, China. The genome size was 167,470 bp, of which contains a large single-copy region (LSC 93,443 bp), a small single-copy region (SSC 21,575 bp), and a pair of inverted repeat regions (IR 26,226 bp). The chloroplast genome has 131 genes, including 86 protein-coding genes, 37 tRNAs, and eight rRNAs. A previous study reported deletion of accD, psbE, and trnG-GCC genes in the A. konjac chloroplast genome. Our study supports the conservative structure of A. konjac and does not support the gene deletion mentioned above. Phylogenetic analysis indicated that A. konjac shares a close relationship with another A. konjac (collected from Guizhou) and A. titanium by forming a clade in the genus Amorphophallus. Our results provide some useful information to the evolution of the family Araceae.
| S-EPMC10776074 | biostudies-literature
Project description:Epipremnum aureum is an important foliage plant in the Araceae family. In this study, we have sequenced the complete chloroplast genome of E. aureum by using Illumina Hiseq sequencing platforms. This genome is a double-stranded circular DNA sequence of 164,831 bp that contains 35.8% GC. The two inverted repeats (IRa and IRb; 26,606 bp) are spaced by a small single-copy region (22,868 bp) and a large single-copy region (88,751 bp). The chloroplast genome has 131 (113 unique) functional genes, including 86 (79 unique) protein-coding genes, 37 (30 unique) tRNA genes, and eight (four unique) rRNA genes. Tandem repeats comprise the majority of the 43 long repetitive sequences. In addition, 111 simple sequence repeats are present, with mononucleotides being the most common type and di- and tetranucleotides being infrequent events. Positive selection pressure on rps12 in the E. aureum chloroplast has been demonstrated via synonymous and nonsynonymous substitution rates and selection pressure sites analyses. Ycf15 and infA are pseudogenes in this species. We constructed a Maximum Likelihood phylogenetic tree based on the complete chloroplast genomes of 38 species from 13 families. Those results strongly indicated that E. aureum is positioned as the sister of Colocasia esculenta within the Araceae family. This work may provide information for further study of the molecular phylogenetic relationships within Araceae, as well as molecular markers and breeding novel varieties by chloroplast genetic-transformation of E. aureum in particular.
| S-EPMC5846728 | biostudies-literature
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
Project description:Symplocarpus renifolius is a member of Araceae family that is extraordinarily diverse in appearance. Previous studies on chloroplast genomes in Araceae were focused on duckweeds (Lemnoideae) and root crops (Colocasia, commonly known as taro). Here, we determined the chloroplast genome of Symplocarpus renifolius and compared the factors, such as genes and inverted repeat (IR) junctions and performed phylogenetic analysis using other Araceae species. The chloroplast genome of S. renifolius is 158,521 bp and includes 113 genes. A comparison among the Araceae chloroplast genomes showed that infA in Lemna, Spirodela, Wolffiella, Wolffia, Dieffenbachia and Colocasia has been lost or has become a pseudogene and has only been retained in Symplocarpus. In the Araceae chloroplast DNA (cpDNA), psbZ is retained. However, psbZ duplication occurred in Wolffia species and tandem repeats were noted around the duplication regions. A comparison of the IR junction in Araceae species revealed the presence of ycf1 and rps15 in the small single copy region, whereas duckweed species contained ycf1 and rps15 in the IR region. The phylogenetic analyses of the chloroplast genomes revealed that Symplocarpus are a basal group and are sister to the other Araceae species. Consequently, infA deletion or pseudogene events in Araceae occurred after the divergence of Symplocarpus and aquatic plants (duckweeds) in Araceae and duplication events of rps15 and ycf1 occurred in the IR region.
| S-EPMC5704237 | biostudies-literature
Project description:Background and aimsSince the advent of molecular phylogenetics, numerous attempts have been made to infer the evolutionary trajectories of chromosome numbers on DNA phylogenies. Ideally, such inferences should be evaluated against cytogenetic data. Towards this goal, we carried out phylogenetic modelling of chromosome number change and fluorescence in situ hybridization (FISH) in a medium sized genus of Araceae to elucidate if data from chromosomal markers would support maximum likelihood-inferred changes in chromosome numbers among close relatives. Typhonium, the focal genus, includes species with 2n = 65 and 2n = 8, the lowest known count in the family.MethodsA phylogeny from nuclear and plastid sequences (96 taxa, 4252 nucleotides) and counts for all included species (15 of them first reported here) were used to model chromosome number evolution, assuming discrete events, such as polyploidization and descending or ascending dysploidy, occurring at different rates. FISH with three probes (5S rDNA, 45S rDNA and Arabidopsis-like telomeres) was performed on ten species with 2n = 8 to 2n = 24.Key resultsThe best-fitting models assume numerous past chromosome number reductions. Of the species analysed with FISH, the two with the lowest chromosome numbers contained interstitial telomeric signals (Its), which together with the phylogeny and modelling indicates decreasing dysploidy as an explanation for the low numbers. A model-inferred polyploidization in another species is matched by an increase in rDNA sites.ConclusionsThe combination of a densely sampled phylogeny, ancestral state modelling and FISH revealed that the species with n = 4 is highly derived, with the FISH data pointing to a Robertsonian fusion-like chromosome rearrangement in the ancestor of this species.
| S-EPMC3936593 | biostudies-literature
Project description:Pistia stratiotes is an invasive aquatic weed in South China. In this study, the first complete chloroplast (cp) genome of P. stratiotes was reported and phylogenetic analysis was conducted with Araceae species based on the cp genome sequences. The genome is a circular molecule of 164,551 bp in length with 36.00% average GC content and includes a large single-copy region (90,705 bp), a small single-copy region (21,886 bp), and two inverted repeat regions (25,980 bp). It contains a total of 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The maximum likelihood tree indicated that P. stratiotes is related to the genus of Alocasia. The cp genome will provide useful molecular data for further phylogenetic and evolutionary analysis of P. stratiotes.
| S-EPMC7510755 | biostudies-literature
Project description:Typhonii rhizoma, a widely used herb in traditional Chinese medicine, has acute irritating toxicity related to Typhonium giganteum lectin (TGL). TGL exhibits acute inflammatory effects, but the underlying molecular mechanisms are largely unknown. This paper is designed to assess the pro-inflammatory response of TGL on RAW 264.7 cells. RAW 264.7 treated with 6.25, 12.5, 25, and 50 µg/mL TGL showed elevated levels of inflammatory factors (TNF-?, IL-1?) and of p-I?B and p-p65, all dose-dependent, indicating that TGL had a substantial inflammatory effect and mobilized the nuclear factor-?B (NF-?B) pathway. All four TGL treatments also induced the up-regulation of reactive oxygen species (ROS) and cytosolic free Ca2+ and down-regulation of mitochondrial membrane potential (MMP). The production of cytokines and p-I?B, p-p65 were reduced by N-acetylcysteine (NAC), an ROS scavenger, which somewhat abrogated ROS production. The results showed the TGL-activated inflammatory signaling pathway NF-?B to be associated with the overproduction of ROS. Moreover, 50 ?g/mL treatment with TGL led to cell apoptosis after 1 h and increased necrosis over time. These results provided potential molecular mechanisms for the observed inflammatory response to TGL including up-regulation of ROS and cytosolic free Ca2+, down-regulation of MMP, the mobilization of the NF-?B pathway, and the subsequent overproduction of pro-inflammatory factors resulting in apoptosis. Long-term stimulation with TGL resulted in strong toxic effects related to inflammation that induced necrosis in macrophages.
| S-EPMC5618208 | biostudies-literature
Project description:Keteleeria cyclolepis complete chloroplast genome Raw sequence reads
| PRJNA723268 | ENA
Project description:Comparative chloroplast genome analyses are mostly carried out at lower taxonomic levels, such as the family and genus levels. At higher taxonomic levels, chloroplast genomes are generally used to reconstruct phylogenies. However, little attention has been paid to chloroplast genome evolution within orders. Here, we present the chloroplast genome of Sedum sarmentosum and take advantage of several available (or elucidated) chloroplast genomes to examine the evolution of chloroplast genomes in Saxifragales. The chloroplast genome of S. sarmentosum is 150,448 bp long and includes 82,212 bp of a large single-copy (LSC) region, 16.670 bp of a small single-copy (SSC) region, and a pair of 25,783 bp sequences of inverted repeats (IRs).The genome contains 131 unique genes, 18 of which are duplicated within the IRs. Based on a comparative analysis of chloroplast genomes from four representative Saxifragales families, we observed two gene losses and two pseudogenes in Paeonia obovata, and the loss of an intron was detected in the rps16 gene of Penthorum chinense. Comparisons among the 72 common protein-coding genes confirmed that the chloroplast genomes of S. sarmentosum and Paeonia obovata exhibit accelerated sequence evolution. Furthermore, a strong correlation was observed between the rates of genome evolution and genome size. The detected genome size variations are predominantly caused by the length of intergenic spacers, rather than losses of genes and introns, gene pseudogenization or IR expansion or contraction. The genome sizes of these species are negatively correlated with nucleotide substitution rates. Species with shorter duration of the life cycle tend to exhibit shorter chloroplast genomes than those with longer life cycles.
| S-EPMC3799696 | biostudies-literature