Pinus densiflora var. zhangwuensis
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA751417 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15371578_1.fastq.gz | Fastqsanger.gz | |||
| SRR15371579_1.fastq.gz | Fastqsanger.gz | |||
| SRR15371579_2.fastq.gz | Fastqsanger.gz |
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Project description:Pinus densiflora var. densiflora Raw sequence reads
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Project description:Pinus densiflora var. zhangwuensis S.J.Zhang, C.X.Li & X.Y.Yuan, a tree species with promising afforestation potential in northern China. Here, we assembled and annotated the complete chloroplast (cp) genome of P. densiflora var. zhangwuensis using the Oxford Nanopore sequencing technology. The cp genome was 119,725 bp in length, exhibiting a typical quadripartite structure with a large single-copy (LSC: 65,552 bp) and a small single-copy (SSC: 53,183 bp) separated by a pair of inverted repeats regions (IRA and IRB: each of 495 bp) region. The overall GC content is 37.3%. The genome was predicted to encode 112 distinct genes, including 72 protein-coding, 36 tRNA, and four rRNA genes. Maximum-likelihood (ML) phylogenetic for cp genome sequences of 18 Pinaceae species revealed that P. densiflora var. zhangwuensis was closely related to Pinus sylvestris.
| S-EPMC8635610 | biostudies-literature
Project description:Haplotype-resolved assembly and resequencing analysis highlight crucial components of pine genome evolution and allelic imbalance in Pinus densiflora
| PRJNA1089250 | ENA
Project description:The purpose of this study was to determine the effects that different container conditions have on Pinus densiflora seedling growth. Under greenhouse cultivation, there were no statistical differences observed in plant height and the number of branches; however, significant differences in root collar diameter and root status were observed. In control container growth conditions, the roots grew in an abnormal spiral shape, while in negative phototropism container growth conditions the roots grew in a vertical shape. In outdoor cultivation, seedlings in various container growth conditions showed significant differences. The seedlings that were grown in negative phototropism container growth conditions showed the greatest increases in height, number of branches, root collar diameter, and root growth. This study determined that seedling roots in negative phototropism container growth conditions grew vertically, thus displaying successful rooting when they were transplanted outdoors. This resulted in favorable measurements in height, number of branches, root collar diameter, and root growth.
| S-EPMC7277831 | biostudies-literature
Project description:Carbon (C) sequestration capacity in forest ecosystems is generally constrained by soil nitrogen (N) availability. Consequently, N fertilization is seen as a promising tool for enhancing ecosystem-level C sequestration in N-limited forests. We examined the responses of ecosystem C (vegetation and soil) and soil N dynamics to 3 years of annual nitrogen-phosphorus-potassium (N3P4K1 = 11.3 g N, 15.0 g P, 3.7 g K m-2 year-1) or PK fertilization (P4K1), observed over 4 years in a 40-year-old Pinus densiflora forest with poor N nutrition in South Korea. PK fertilization without N was performed to test for PK limitation other than N. Neither tree growth nor soil C fluxes responded to annual NPK or PK fertilization despite an increase in soil mineral N fluxes following NPK fertilization. NPK fertilization increased the rate of N immobilization and 80% of the added N was recovered from mineral soil in the 0-5 cm layer, suggesting that relatively little of the added N was available to trees. These results indicate that N fertilization does not always enhance C sequestration even in forests with poor N nutrition and should therefore be applied with caution.
| S-EPMC9988963 | biostudies-literature
Project description:BackgroundPines are widely distributed in the Northern Hemisphere and have a long evolutionary history. The availability of transcriptome data has facilitated comparative transcriptomics for studying the evolutionary patterns associated with the different geographical distributions of species in the Pinus phylogeny.ResultsThe transcriptome of Pinus kesiya var. langbianensis was sequenced using the Illumina HiSeq 2000 platform, and a total of 68,881 unigenes were assembled by Trinity. Transcriptome sequences of another 12 conifer species were downloaded from public databases. All of the pairwise orthologues were identified by comparative transcriptome analysis in 13 conifer species, from which the rate of diversification was calculated and a phylogenetic tree inferred. All of the fast-evolving positive selection sequences were identified, and some salt-, drought-, and abscisic acid-resistance genes were discovered.ConclusionsmRNA sequences of P. kesiya var. langbianensis were obtained by transcriptome sequencing, and a large number of simple sequence repeat and short nucleotide polymorphism loci were detected. These data can be used in molecular marker-assisted selected in pine breeding. Divergence times were estimated in the 13 conifer species using comparative transcriptomic analysis. A number of positive selection genes were found to be related to environmental factors. Salt- and abscisic acid-related genes exhibited different selection patterns between coastal and inland Pinus. Our findings help elucidate speciation patterns in the Pinus lineage.
| S-EPMC6171231 | biostudies-literature
Project description:Skin aging is caused by exposure to various external factors. Ultraviolet B (UVB) irradiation induces oxidative stress, photoaging, and inflammation in skin cells. Pinus densiflora Sieb. et Zucc. (red pine) has various antimicrobial and antioxidant activities. However, the anti-inflammatory effects of red pine on skin have rarely been reported. The protective effects of malonic acid (MA) isolated from Pinus densiflora were investigated against UVB-induced damage in an immortalized human keratinocyte cell line (HaCaT). MA increased levels of the antioxidant enzymes superoxide dismutase 1 (SOD-1) and heme oxygenase 1 (HO-1) via activation of nuclear factor-erythroid 2-related factor-2 (Nrf2), resulting in a reduction in UVB-induced reactive oxygen species (ROS) levels. Additionally, the inhibition of ROS increased HaCaT cell survival rate. Thus, MA downregulated the expression of ROS-induced nuclear factor-κB, as well as inflammation-related cytokines (interleukin-6, cyclooxygenase-2, and tumor necrosis factor-α). Furthermore, MA significantly suppressed the mitogen-activated protein kinase/activator protein 1 signaling pathway and reduced the expression of matrix metalloproteinases (MMPs; MMP-1, MMP-3, and MMP-9). In contrast, MA treatment increased the expression of collagen synthesis regulatory genes (COL1A1 and COL3A1) via regulation of Smad2/3 signal induction through transforming growth factor-β. In conclusion, MA protected against UVB-induced photoaging via suppression of skin inflammation and induction of collagen biosynthesis.
| S-EPMC7961482 | biostudies-literature
Project description:Physiological response and transcriptome changes were observed to investigate the effects on the growth, metabolism and genetic changes of Pinus densiflora grown for a long time in an environment with an elevated atmospheric CO2 concentration. Pine trees were grown at ambient (400 ppm) and elevated (560 ppm and 720 ppm) CO2 concentrations for 10 years in open-top chambers. The content of nonstructural carbohydrates was significantly increased in elevated CO2. It was notable that the contents of chlorophylls significantly decreased at an elevated CO2. The activities of antioxidants were significantly increased at an elevated CO2 concentration of 720 ppm. We analyzed the differences in the transcriptomes of Pinus densiflora at ambient and elevated CO2 concentrations and elucidated the functions of the differentially expressed genes (DEGs). RNA-Seq analysis identified 2415 and 4462 DEGs between an ambient and elevated CO2 concentrations of 560 ppm and 720 ppm, respectively. Genes related to glycolysis/gluconeogenesis and starch/sucrose metabolism were unchanged or decreased at an elevated CO2 concentration of 560 ppm and tended to increase at an elevated CO2 concentration of 720 ppm. It was confirmed that the expression levels of genes related to photosynthesis and antioxidants were increased at an elevated CO2 concentration of 720 ppm.
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