Genome-Wide Identification and Expression Analysis of the YTH Domain-Containing RNA-Binding Protein Family in Cinnamomum camphora.

N6-methyladenosine (m6A) is one of the most abundant chemical modifications on mRNA in eukaryotes. RNA-binding proteins containing the YT521-B (YTH) domain play crucial roles in post-transcriptional regulation of plant growth, development, and stress response by reading the m6A mark. However, the YTH domain-containing RNA-binding protein family has not been studied in a valuable and medicinal tree such as Cinnamomum camphora (C. camphora) yet. In this study, we identified 10 YTH genes in C. camphora, located on eight out of 12 chromosomes. Phylogenetic analysis revealed that these genes can be classified into two major classes, YTHDF (CcDF) and YTHDC (CcDC). Closely related CcYTHs within the same class exhibited a similar distribution of conserved motifs and domain organization, suggesting functional similarities among these closely related CcYTHs. All CcYTH proteins possessed a highly conserved YTH domain, with CcDC1A containing an additional CCCH domain. The liquid-liquid phase separation (LLPS) predictions indicate that CcDC1A, CcDF1A, CcDF1C, CcDF3C, CcDF4C, and CcDF5C may undergo phase transitions. Quantitative expression analysis revealed that tissue-specific expression was observed fo CcYTHs. Notably, there were two genes, CcDF1A and CcDF5C; both exhibited significantly higher expression levels in various tissues than other genes, indicating that the m6A-YTH regulatory network in C. camphora might be quite distinct from that in most plants such as Arabidopsis thaliana (A. thaliana) with only one abundant YTH protein. According to the analysis of the up-stream cis-regulatory elements of these YTH genes, these genes could be closely related to stress, hormones, and development. The following stress response experiments further verified that their expression levels indeed changed under both PEG and NaCl treatments. These findings not only provide a foundation for future functional analysis of CcYTHs in C. camphora, but also provide insights into the functions of epigenetic mark m6A in forest trees.

Temporal and Within-Sporophyte Variations in Triphenyltin Chloride (TPTCL) and Its Degradation Products in Cultivated Undaria pinnatifida.

Undaria pinnatifida can effectively deal with organotin pollution through its excellent accumulation and degradation capabilities found under laboratory conditions. However, nothing is known regarding its accumulation, degradation performance, and related impact factors in the wild farming area. In this study, we monitored triphenyltin chloride (TPTCL) contents and degradation products in different algal parts (blades, stipes, sporophylls, and holdfasts) of cultivated U. pinnatifida from December 2018 to May 2019. Our results showed that sporophytes had an accumulation and degradation capacity for TPTCL. The TPTCL contents and degradation products varied with the algal growth stages and algal parts. TPTCL accumulated in the blades at the growth stage and the blades, stipes, sporophylls, and holdfasts at the mature stage. The TPTCL content among algal parts was blades (74.92 ± 2.52 µg kg-1) > holdfasts (62.59 ± 1.42 µg kg-1) > sporophylls (47.24 ± 1.41 µg kg-1) > stipes (35.53 ± 0.55 µg kg-1). The primary degradation product DPTCL accumulated only in the blades at any stage, with a concentration of 69.30 ± 3.89 µg kg-1. The secondary degradation product MPTCL accumulated in the blades at the growth stage and in the blades, stipe, and sporophyll at the mature stage. The MPTCL content among algal parts was blades (52.80 ± 3.48 µg kg-1) > sporophylls (31.08 ± 1.53 µg kg-1) > stipes (20.44 ± 0.85 µg kg-1). The accumulation pattern of TPTCL and its degradation products seems closely related to nutrient allocation in U. pinnatifida. These results provide the basis for applying cultivated U. pinnatifida in the bioremediation of organotin pollution and the food safety evaluation of edible algae.

Analysis on metabolic functions of rhizosphere microbial communities of Pinus massoniana provenances with different carbon storage by Biolog Eco microplates.

Introduction: Rhizosphere microorganisms are influenced by vegetation. Meanwhile, they respond to vegetation through their own changes, developing an interactive feedback system between microorganisms and vegetation. However, it is still unclear whether the functional diversity of rhizosphere soil microorganisms varies with different carbon storage levels and what factors affect the functional diversity of rhizosphere soil microorganisms. Methods: In this study, the Biolog-Eco microplate technique was used to analyze the metabolic diversity of carbon source of rhizosphere soil microorganisms from 6 Pinus massoniana provenances with three levels of high, medium and low carbon storage. Results: The results showed that the average well color development(AWCD) value of rhizosphere microorganisms was significantly positive correlated with carbon storage level of Pinus massoniana (p < 0.05). The AWCD value, Simpson and Shannon diversity of high carbon sequestrance provenances were 1.40 (144h incubation) 0.96 and 3.24, respectively, which were significantly higher (p < 0.05) than those of other P. massoniana provenances. The rhizosphere microbial AWCD, Shannon and Simpson diversity of the 6 provenances showed the same variation trend (SM>AY>QJ>SX>HF>SW). Similarly, microbial biomass carbon (MBC) content was positively correlated with carbon storage level, and there were significant differences among high, medium and low carbon storage provenances. The PCA results showed that the differences in the carbon source metabolism of rhizosphere microorganisms were mainly reflected in the utilization of amino acids, carboxylic acids and carbohydrates. Pearson correlation analysis showed that soil organic carbon (SOC), total nitrogen (TN) and pH were significantly correlated with rhizosphere AWCD (p < 0.05). Conclusion: Soil properties are important factors affecting rhizosphere microbial carbon source metabolism. The study confirmed that the microorganisms of high carbon storage provenances had relatively high carbon metabolic activity. Among them, the carbon metabolic activity of rhizosphere microorganisms of SM provenance was the highest, which was the preferred provenances in effective ecological service function.

Non-concordant epigenetic and transcriptional responses to acute thermal stress in western mosquitofish (Gambusia affinis).

Climate change is intensifying the frequency and severity of extreme temperatures. Understanding the molecular mechanisms underlying the ability to cope with acute thermal stress is key for predicting species' responses to extreme temperature events. While many studies have focused on the individual roles of gene expression, post-transcriptional processes and epigenetic modifications in response to acute thermal stress, the relative contribution of these molecular mechanisms remains unclear. The wide range of thermal limits of western mosquitofish (Gambusia affinis) provides an opportunity to explore this interplay. Here, we quantified changes in gene expression, alternative splicing, DNA methylation and microRNA (miRNA) expression in muscle tissue dissected from mosquitofish immediately after reaching high (CTmax) or low thermal limit (CTmin). Although the numbers of genes showing expression and splicing changes in response to acute temperature stress were small, we found a possibly larger and non-redundant role of splicing compared to gene expression, with more genes being differentially spliced (DSGs) than differentially expressed (DEGs), and little overlap between DSGs and DEGs. We also identified a small proportion of CpGs showing significant methylation change (i.e. differentially methylated cytosines, DMCs) in fish at thermal limits; however, there was no overlap between DEGs and genes annotated with DMCs in both CTmax and CTmin experiments. The weak interplay between epigenetic modifications and gene expression was further supported by our discoveries of no differentially expressed miRNAs. These findings provide novel insights into the relative role of different molecular mechanisms underlying immediate responses to extreme temperatures and demonstrate non-concordant responses of epigenetic and transcriptional mechanisms to acute temperature stress.