Identification of microRNAs and their target genes related to needle discoloration of evergreen tree Chinese cedar (Cryptomeria fortunei) in cold winters

Research advances of coloring mechanism regulated by MicroRNAs in plants

In plants, microRNAs (miRNAs) are a class of important small RNAs involved in their growth and development, and play a very significant role in regulating their tissue coloring. In this paper, the mechanisms on miRNA regulation of plant coloring are mainly reviewed from three aspects: macroscopic physiological and molecular foundations related to tissue coloring, miRNA biosynthesis and function, and specific analysis of miRNA regulation studies on leaf color, flower color, fruit color, and other tissue color formation in plants. Furthermore, we also systematically summarize the miRNA regulatory mechanisms identified on pigments biosynthesis and color formation in plants, and the regulatory mechanisms of these miRNAs mentioned on the existing researches can be divided into four main categories: directly targeting the related transcription factors, directly targeting the related structural genes, directly targeting the related long noncoding RNAs (LncRNAs) and miRNA-mediated production of trans-acting small interfering RNAs (ta-siRNAs). Together, these research results aim to provide a theoretical reference for the in-depth study of plant coloring mechanism and molecular breeding study of related plants in the future.

The ncRNAs Involved in the Regulation of Abiotic Stress-Induced Anthocyanin Biosynthesis in Plants

Plants have evolved complicated defense and adaptive systems to grow in various abiotic stress environments such as drought, cold, and salinity. Anthocyanins belong to the secondary metabolites of flavonoids with strong antioxidant activity in response to various abiotic stress and enhance stress tolerance. Anthocyanin accumulation often accompanies the resistance to abiotic stress in plants to scavenge reactive oxygen species (ROS). Recent research evidence showed that many regulatory pathways such as osmoregulation, antioxidant response, plant hormone response, photosynthesis, and respiration regulation are involved in plant adaption to stress. However, the molecular regulatory mechanisms involved in controlling anthocyanin biosynthesis in relation to abiotic stress response have remained obscure. Here, we summarize the current research progress of specific regulators including small RNAs, and lncRNAs involved in the molecular regulation of abiotic stress-induced anthocyanin biosynthesis. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by microRNAs (miRNAs), long non-coding RNAs (lncRNAs), transcription factors, and stress response factors is also discussed. Understanding molecular mechanisms of anthocyanin biosynthesis for ROS scavenging in various abiotic stress responses will benefit us for resistance breeding in crop plants.

Physiological and gene expression changes of Cryptomeria fortunei Hooibrenk families under heat stress

Heat stress is one of the major abiotic stresses affecting plant growth and productivity. Cryptomeria fortunei (Chinese cedar) is an excellent timber and landscaping tree species in southern China thanks to its beautiful appearance, straight texture and ability to purify the air and improve the environment. In this study, we first screened 8 excellent C. fortunei families (#12, #21, #37, #38, #45, #46, #48, #54) in a second generation seed orchard. We then analyzed the electrolyte leakage (EL) and lethal temperature at 50% (LT₅₀) values under heat stress, to identify the families with the best heat resistance (#48) and the lowest heat resistance (#45) and determine the physiological and morphological response of different threshold-resistance of C. fortune to heat stress. The relative conductivity of the C. fortunei families showed an increasing trend with increasing temperature, following an "S" curve, and the half-lethal temperature ranges between 39°C and 43.2°C. The activities of SOD and POD fluctuated in the early stage of stress but decreased after 37°C. We observed the changes in the cell ultrastructure at 43°C, and the mesophyll cell structure of #48 was less damaged than that of #45. Eight heat resistance gene, including CfAPX1, CfAPX2, CfHSP11, CfHSP21, CfHSP70, CfHSFA1a, CfHSFB2a and CfHSFB4, were all up-regulated in #45 and #48, and there were significant differences between #45 and #48 under different heat stress treatments. We found a significant difference in heat tolerance between #45 and #48, such that #48 shows higher heat tolerance capability and could be exploited in breeding programs. We conclude that the strongly heat-resistant family had a more stable physiological state and a wider range of heat stress adaptations.

Understory vegetation diversity, soil properties and microbial community response to different thinning intensities in Cryptomeria japonica var. sinensis plantations

Introduction

Soil microorganisms are the key factors in elucidating the effects of thinning on tree growth performance, but the effects of vegetation and soil on the species composition and function of soil microorganisms after thinning are still not well elaborated.

Methods

The effects of thinning on understory vegetation diversity, soil physicochemical properties and soil microbial community composition were investigated in a thinning trial plantation of Cryptomeria japonica var. sinensis, including four thinning intensities (control: 0%, LIT: 20%, MIT: 30% and HIT: 40%), and the relationships of the microbial community structure with the understory vegetation diversity and soil properties were assessed.

Results

The results showed that thinning had a greater effect on the diversity of the shrub layer than the herb layer. The soil bulk density and the contents of soil organic matter, total potassium and nitrogen increased with increasing thinning intensities. The Shannon and Chao indices of soil bacteria and fungi were significantly lower in the LIT, MIT and HIT treatments than in the control. Thinning can significantly increase the abundance of Proteobacteria and Actinobacteria, and higher thinning intensities led to a higher relative abundance of Ascomycota and a lower relative abundance of Basidiomycota, Rozellomycota, and Mortierellomycota. Redundancy analysis indicated that soil physicochemical properties rather than understory vegetation diversity were the main drivers of microbial communities, and fungi were more sensitive to soil properties than bacteria. Functional prediction showed that thinning significantly reduced the potential risk of human diseases and plant pathogens, and the nitrogen fixation capacity of bacteria was the highest in the HIT treatment. Thinning significantly increased the relative abundance of cellulolysis and soil saprotrophs in bacteria and fungi.

Conclusion

The findings provide important insights into the effects of thinning on C. japonica var. sinensis plantation ecosystems, which is essential for developing thinning strategies to promote their ecological and economic benefits.

Further Mining and Characterization of miRNA Resource in Chinese Fir (Cunninghamia lanceolata)

In this study, we aimed to expand the current miRNA data bank of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) regarding its potential value for further genetic and genomic use in this species. High-throughput small RNA sequencing successfully captured 140 miRNAs from a Chinese fir selfing family harboring vigor and depressed progeny. Strikingly, 75.7% (n = 106) of these miRNAs have not been documented previously, and most (n = 105) of them belong to the novel set with 6858 putative target genes. The new datasets were then integrated with the previous information to gain insight into miRNA genetic architecture in Chinese fir. Collectively, a relatively high proportion (62%, n = 110) of novel miRNAs were found. Furthermore, we identified one MIR536 family that has not been previously documented in this species and four overlapped miRNA families (MIR159, MIR164, MIR171_1, and MIR396) from new datasets. Regarding the stability, we calculated the secondary structure free energy and found a relatively low R2 value (R2 < 0.22) between low minimal folding free energy (MFE) of pre-miRNAs and MFE of its corresponding mature miRNAs in most datasets. When in view of the conservation aspect, the phylogenetic trees showed that MIR536 and MIR159 sequences were highly conserved in gymnosperms.

LncRNA H19 alleviates sepsis-induced acute lung injury by regulating the miR-107/TGFBR3 axis

OBJECTIVE

Acute lung injury (ALI) increases sepsis morbidity and mortality. LncRNA H19 plays a critical role in sepsis. miR-107 is highly-expressed and TGFβ type III receptor (TGFBR3) is poorly-expressed in sepsis, yet their roles in sepsis development require further investigation. This study aimed to investigate the mechanism of H19 in alleviating sepsis-induced ALI through the miR-107/TGFBR3 axis.

METHODS

Mice were intravenously injected with Ad-H19 adenovirus vector or control vector one week before establishing the mouse model of cecal ligation and puncture (CLP). Pulmonary microvascular endothelial cells (PMVECs) were transfected with oe-H19 or oe-NC plasmids and then stimulated by lipopolysaccharide (LPS). Lung injury was assessed via hematoxylin-eosin staining, measurement of wet-to-dry (W/D) ratio, and TUNEL staining. Levels of H19, miR-107, and TGFBR3 were determined by RT-qPCR. Apoptosis of PMVECs was evaluated by flow cytometry. Levels of Bax and Bcl-2 in lung tissues and PMVECs were measured using Western blot. Total protein concentration and the number of total cells, neutrophils, and macrophages in bronchoalveolar lavage fluid (BALF) were quantified. Levels of TNF-α, IL-1β, IL-6, and IL-10 in BALF, lung tissues, and PMVECs were measured by ELISA. Cross-linking relationships among H19, miR-107 and TGFBR3 were verified by dual-luciferase and RIP assays.

RESULTS

H19 was poorly-expressed in CLP-operated mice. H19 overexpression attenuated sepsis-induced ALI, which was manifested with complete alveolar structure, decreased lung injury score and lung W/D ratio, and inhibited apoptosis in CLP-operated mice, which was manifested with decreased number of TUNEL-positive cells and Bax level and increased Bcl-2 level. CLP-operated mice had increased concentration of total protein and number of total cells, neutrophils, and macrophages in BALF, which was nullified by H19 overexpression. H19 overexpression declined levels of TNF-α, IL-1β, and IL-6 and elevated IL-10 levels. H19 inhibited LPS-induced PMVEC apoptosis and pro-inflammatory cytokine production. H19 targeted TGFBR3 as the ceRNA of miR-107. miR-107 overexpression or silencing TGFBR3 partially averted the inhibition of H19 overexpression on LPS-induced PMVEC apoptosis and pro-inflammatory cytokine production.

CONCLUSION

LncRNA H19 inhibited LPS-induced PMVEC apoptosis and pro-inflammatory cytokine production and attenuated sepsis-induced ALI by targeting TGFBR3 as the ceRNA of miR-107.

Integrative analyses of morphology, physiology, and transcriptional expression profiling reveal miRNAs involved in culm color in bamboo

Culm color variation is an interesting phenomenon that contributes to the breeding of new varieties of ornamental plants during domestication. De-domesticated variation is considered ideal for identifying and interpreting the molecular mechanisms of plant mutations. However, the variation in culm color of bamboo remains unknown. In the present study, yellow and green culms generated from the same rhizome of Phyllostachys vivax cv. Aureocaulis (P. vivax) were used to elucidate the molecular mechanism of culm color formation. Phenotypic and physiological data showed that environmental suitability was higher in green culms than in yellow culms. High-throughput sequencing analysis showed 295 differentially expressed genes (DEGs) and 22 differentially expressed miRNAs (DEMs) in two different colored bamboo culms. There were 103 DEM-DEG interaction pairs, of which a representative "miRNA-mRNA" regulatory module involved in photosynthesis and pigment metabolism was formed by 14 DEM-DEG pairs. The interaction of the three key pairs was validated by qPCR and dual-luciferase assays. This study provides new insights into the molecular mechanism of miRNAs involved in P. vivax culm color formation, which provides evidence for plant de-domestication and is helpful for revealing the evolutionary mechanism of bamboo.