Comparative Analysis of Transposable Elements in Strawberry Genomes of Different Ploidy Levels.

Transposable elements (TEs) make up a large portion of plant genomes and play a vital role in genome structure, function, and evolution. Cultivated strawberry (Fragaria x ananassa) is one of the most important fruit crops, and its octoploid genome was formed through several rounds of genome duplications from diploid ancestors. Here, we built a pan-genome TE library for the Fragaria genus using ten published strawberry genomes at different ploidy levels, including seven diploids, one tetraploid, and two octoploids, and performed comparative analysis of TE content in these genomes. The TEs comprise 51.83% (F. viridis) to 60.07% (F. nilgerrensis) of the genomes. Long terminal repeat retrotransposons (LTR-RTs) are the predominant TE type in the Fragaria genomes (20.16% to 34.94%), particularly in F. iinumae (34.94%). Estimating TE content and LTR-RT insertion times revealed that species-specific TEs have shaped each strawberry genome. Additionally, the copy number of different LTR-RT families inserted in the last one million years reflects the genetic distance between Fragaria species. Comparing cultivated strawberry subgenomes to extant diploid ancestors showed that F. vesca and F. iinumae are likely the diploid ancestors of the cultivated strawberry, but not F. viridis. These findings provide new insights into the TE variations in the strawberry genomes and their roles in strawberry genome evolution.

Effect of cerium on the production of reactive oxygen species in the root of Arabidopsis thaliana: An in vitro study.

In the current study, the effect of trivalent cerium (Ce3+ ) on the production of reactive oxygen species (ROS) was investigated in the root of Arabidopsis thaliana by an in vitro study. The roots of A. thaliana were exposed with 0, 1, and 5 µmol/L Ce3+ for 12 h in vitro. It was found that the level of H2 O2 , O2 .- , and ·OH was enhanced by 5 µmol/L Ce3+ , but reduced by 1 µmol/L Ce3+ . The activities of peroxidase (POD), catalase (CAT), and superoxidase dismutase (SOD) were enhanced by 1 µmol/L Ce3+ , but reduced by 5 µmol/L Ce3+ . Moreover, we used a laser-scanning confocal microscopy to detect the changes of ROS in the root cells of A. thaliana by using a fluorochrome 2',7'-dichlorofluorescein diacetate (H2 DCF-DA). It showed that the level of ROS was declined in the root cells treated by 1 µmol/L Ce3+ , but the oscillation of ROS was found in the root cells treated with 5 µmol/L Ce3+ . In addition, REEs affect the uptake of mineral elements, which may be related to the oxidative stress in the cells of roots. In all, the data of our study indicated that the appropriate concentration of Ce3+ exhibited an anti-oxidation property and improved the defense system in the root cells of A. thaliana.

The toxicity of neodymium and genome-scale genetic screen of neodymium-sensitive gene deletion mutations in the yeast Saccharomyces cerevisiae.

The wide usage of neodymium (Nd) in industry, agriculture, and medicine has made it become an emerging pollutant in the environment. Increasing Nd pollution has potential hazards to plants, animals, and microorganisms. Thus, it is necessary to study the toxicity of Nd and the mechanism of Nd transportation and detoxification in microorganisms. Through genome-scale screening, we identified 70 yeast monogene deletion mutations sensitive to Nd ions. These genes are mainly involved in metabolism, transcription, protein synthesis, cell cycle, DNA processing, protein folding, modification, and cell transport processes. Furthermore, the regulatory networks of Nd toxicity were identified by using the protein interaction group analysis. These networks are associated with various signal pathways, including calcium ion transport, phosphate pathways, vesicular transport, and cell autophagy. In addition, the content of Nd ions in yeast was detected by an inductively coupled plasma mass spectrometry, and most of these Nd-sensitive mutants showed an increased intracellular Nd content. In all, our results provide the basis for understanding the molecular mechanisms of detoxifying Nd ions in yeast cells, which will be useful for future studies on Nd-related issues in the environment, agriculture, and human health.

The Sensitive Genes in Response to Various Metal Ion Stresses in the Yeast Saccharomyces cerevisiae.

Yeast Saccharomyces cerevisiae is a good eukaryotic model for studying the molecular mechanism of toxic metal ion stress. Numerous studies have been performed on the signal transduction induced by toxic metal ion stress. The physiological process of eukaryotic cells has been studied, and various stress factors have been elucidated by constructing a gene deletion library. The sensitivity and tolerance mechanism of yeast under metal ion stress has been widely studied. The sensitive genes induced by metal ion stress will provide a key foundation for studying the gene function of eukaryotic organisms. In addition, the functions of genes in response to metal ion stress mainly participate in regulating ion homeostasis, high glycerin pathway, vacuole protein separation pathway, cell wall integrity pathway, and cell autophagy. However, the interaction of these signal pathways and the detailed response mechanism need to be further studied. In addition, the technique of genomics and proteomics will help study the detailed molecular mechanism induced by toxic metal ion stress. Thus, the sensitive genes related to various signal pathways under toxic metal ion stress will be reviewed in the yeast S. cerevisiae.

The accumulation and effect of rare earth element neodymium on the root of rice seedlings.

Neodymium (Nd) potentially threatens ecological equilibrium for its wide usage in industries. In this study, the accumulation and effect of Nd on roots were investigated in the rice seedlings (Oryza sativa L.) exposed to different concentrations of Nd (0, 1, 10, 100, and 1000 µM). The toxic effect of Nd on rice growth was observed at the higher concentration, but the positive effects were found at the lower concentration. The accumulation of Nd was present in six different chemical forms, and the insoluble phosphate and oxalate Nd were the major forms of Nd in the roots. In addition, Nd was accumulated in the soluble fractions, organelles, and cell walls of rice seedlings, and the root cell wall was a major Nd sink site. The result of Fourier transform infrared spectrometer spectral analysis indicated that the functional groups of -OH and C-OH were the major binding sites of Nd in the cell wall of roots. Moreover, the level of reactive oxygen species (ROS) and the activity of catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) were significantly increased with the increase of Nd concentration. The enhanced antioxidant capacity also played an important role in Nd detoxification of rice seedlings. In all, the results indicated that forming of inactive oxalate or phosphate and efficient sequestration into the root cell wall was a key process in Nd accumulation and detoxification of rice seedlings.

Gadolinium accumulation, distribution, chemical forms, and influence on the growth of rice seedlings.

The content of gadolinium (Gd) is continuously increased in environment, which potentially threatens human health and ecological equilibrium. However, the phytotoxicity of Gd on plants remains unknown until now. In this study, the accumulation, distribution, and chemical forms of Gd as well as its influence on growth and nutrient balance were systematically studied in rice seedlings after the treatments of different concentrations of Gd (0, 1, 10, 100, and 1000 µM) for 10 days. The results showed that most Gd was accumulated in the roots and only a little percentage of Gd was transported to shoots. The accumulation of Gd was increased in a dose-dependent manner in various chemical forms and subcellular fractions. More than 80% of Gd was in the forms of insoluble oxalates and phosphates. Gd was mainly compartmentalized in the cell wall, and the content of Gd was increased with increasing concentrations of Gd. In addition, hormetic effects of Gd were found on rice growth. The growth of rice was induced by the lower concentration of Gd, but inhibited by the higher concentration of Gd. The results indicated that rice seedlings could cope with Gd toxicity through cell wall compartmentalization as well as forming of precipitates with oxalate and phosphate.