Genomic Analysis of the Glutathione S-Transferase Family in Pear (Pyrus communis) and Functional Identification of PcGST57 in Anthocyanin Accumulation

Anthocyanin accumulation in vacuoles results in red coloration in pear peels. Glutathione S-transferase (GST) proteins have emerged as important regulators of anthocyanin accumulation. Here, a total of 57 PcGST genes were identified in the European pear ‘Bartlett’ (Pyrus communis) through comprehensive genomic analysis. Phylogenetic analysis showed that PcGST genes were divided into 10 subfamilies. The gene structure, chromosomal localization, collinearity relationship, cis-elements in the promoter region, and conserved motifs of PcGST genes were analyzed. Further research indicated that glutamic acid (Glu) can significantly improve anthocyanin accumulation in pear peels. RNA sequencing (RNA-seq) analysis showed that Glu induced the expression of most PcGST genes, among which PcGST57 was most significantly induced. Further phylogenetic analysis indicated that PcGST57 was closely related to GST genes identified in other species, which were involved in anthocyanin accumulation. Transcript analysis indicated that PcGST57 was expressed in various tissues, other than flesh, and associated with peel coloration at different developmental stages. Silencing of PcGST57 by virus-induced gene silencing (VIGS) inhibited the expression of PcGST57 and reduced the anthocyanin content in pear fruit. In contrast, overexpression of PcGST57 improved anthocyanin accumulation. Collectively, our results demonstrated that PcGST57 was involved in anthocyanin accumulation in pear and provided candidate genes for red pear breeding.

Functional Identification of MicroRNA-Centered Complexes in C. Elegans.

microRNAs (miRNAs) are crucial for normal development and physiology. To identify factors that might coordinate with miRNAs to regulate gene expression, we used 2’-O methylated oligonucleotides to precipitate Caenorhabditis elegans let-7, miR-58, and miR-2 miRNAs and the associated proteins. A total of 211 proteins were identified through mass-spectrometry analysis of miRNA co-precipitates, which included previously identified interactors of key miRNA pathway components. Gene ontology analysis of the identified interactors revealed an enrichment for RNA binding proteins, suggesting that we captured proteins that may be involved in mRNA lifecycle. To determine which miRNA interactors are important for miRNA activity, we used RNAi to deplete putative miRNA co-factors in animals with compromised miRNA activity and looked for alterations of the miRNA mutant phenotypes. Depletion of 25 of 39 tested genes modified the miRNA mutant phenotypes in three sensitized backgrounds. Modulators of miRNA phenotypes ranged from RNA binding proteins RBD-1 and CEY-1 to metabolic factors such as DLST-1 and ECH-5, among others. The observed functional interactions suggest widespread coordination of these proteins with miRNAs to ultimately regulate gene expression. This study provides a foundation for future investigations aimed at deciphering the molecular mechanisms of miRNA-mediated gene regulation.

Genome-wide identification and expression analysis of the coronatine-insensitive 1 (COI1) gene family in response to biotic and abiotic stresses in Saccharum

Background The coronatine insensitive 1 (COI1) gene is the core member of jasmonate signaling pathway, which is closely related to plant biotic and abiotic resistance. However, there have been no reports on COI1 in sugarcane (Sacharum spp.). Hence, systematically investigating the characteristics of the COI1 multigene family in sugarcane can provide a means to study and manipulate the jasmonic acid signaling pathway. Results A total of 156 COI1 proteins were obtained from the genomes of 19 land plants, while none were obtained from five algae species. A phylogenetic tree demonstrated that these COI1 proteins were classified into four groups, while 31 proteins of SsCOI1 from Saccharum spontaneum, SbCOI1 from Sorghum bicolor, and ShCOI1 from Saccharum spp. hybrid cultivar R570 clustered into three groups. Synteny analysis and duplication patterns revealed that COI1 genes expanded through various genome replication events and could have experienced strong purifying selective pressure during evolution in S. spontaneum, S. bicolor, and R570. An investigation of cis-acting elements suggests that COI1 genes may be involved in plant growth and development and response to various stresses. Expression analysis implied that 21 SsCOI1 genes were constitutively expressed, and had positive responses to drought, cold, and Sporisorium scitamineum stresses with different expression patterns. Among them, seven SsCOI1 haplotype genes may play different roles in response to methyl jasmonate. Furthermore, the ShCOI1–4, ShCOI1–5, and ShCOI1–6 genes were cloned from Saccharum spp. hybrid cultivar ROC22. Real-time quantitative PCR (RT-qPCR) analysis demonstrated that these three ShCOI1 genes had divergent expression profiles in response to salicylic acid, abscisic acid, polyethylene glycol, cold, and S. scitamineum. Conclusions These results suggest that COI1 genes may act in sugarcane growth, development, and response to various stresses via different regulatory mechanisms, which laying a foundation for the functional identification of the sugarcane COI1 gene.

Functional Identification of ICE Transcription Factors in Rubber Tree

ICE (inducer of CBF expression) is a positive regulator of cold signaling pathway in plants. Identification of ICE transcription factors is important for the sustainable development of the natural rubber planting industry in nontraditional regions where sudden cold waves often occur. In this study, five ICE genes were isolated from genome of rubber tree (Hevea brasiliensis Muell. Arg.) for analysing tolerance to cold stress. They shared an ICE-specific region in the highly conserved bHLH-ZIP domain and were localized in the nucleus. The HbICEs were different in transcript abundance and expression patterns in response to cold and drought stresses and among different rubber tree clones. Generally, the expression level of HbICEs was significantly higher in the cold-tolerant rubber tree clones than that in the cold-sensitive rubber tree clones. Overexpression of HbICE1, HbICE2, and HbICE4 significantly enhanced the cold tolerance of transgenic Arabidopsis and tobacco, which showed a significant increase in chlorophyll content and decrease in relative water content and conductivity at the early stage of cold stress in comparison with wild-type plants. Furthermore, overexpression of HbICE2 and HbICE4, but also HbICE1 enhanced drought tolerance in transgenic Arabidopsis. The cold tolerance of rubber tree clones is positively controlled by the expression level of HbICE1, HbICE2, and HbICE4.

Online public opinion evaluation through the functional resonance analysis method and deep analysis

A conventional model of public opinion analysis is no longer suitable when the internet is the primary arena of information dissemination. Thus, a more practical approach is urgently needed to deal with this dynamic and complicated phenomenon of propagating public opinion. This paper proposes that the outbreak of internet public opinion and its negative impacts, such as the occurrence of major security incidents, are a result of coupling and the complex interaction of many factors. The Functional Resonance Analysis Method model is composed of those factors and considers the stages of network information dissemination, the unique propagation rule, and textual sentiment resonance on the internet. Moreover, it is the first public opinion governance method that simultaneously highlights the complex system, functional identification, and functional resonance. It suggests a more effective method to shorten the dissipation time of negative public opinion and is a considerable improvement over previous models for risk-prediction. Based on resonance theory and deep learning, this study establishes public opinion resonance functions, which made it possible to analyze public opinion triggers and build a simulation model to explore the patterns of public opinion development through long-term data capture. The simulation results of the Functional Resonance Analysis Method suggest that the resonance in the model is consistent with the evolution of public opinion in real situations and that the components of the resonance of public opinion can be separated into eleven subjective factors and three objective factors. In addition, managing the subjective factors can significantly accelerate the dissipation of negative opinions.

Functional Identification of 9-cis-epoxycarotenoid Dioxygenase Genes in Double Dormant Plant-herbaceous Peony

Seed dormancy and germination is a complex process, which is affected by external environmental conditions and internal factors independently or mutually. Phytohormones play an important regulatory role in this process. ABA was the main phytohormone affecting herbaceous peony seed dormancy release. However, the mechanism of ABA in the dormancy release of herbaceous peony needs to be further explored. Here, transcriptome data was screened from the perspective of ABA metabolism, and significantly differentially expressed PlNCED1 and PlNCED2 were obtained. We found that their expression trends were positively correlated with ABA content. Among them, PlNCED2 had a stronger regulatory effect on ABA content and was more sensitive to exogenous ABA. Overexpression and silencing of PlNCEDs in callus could affect the expression of PlCYP707As and the content of endogenous ABA. Through the observation of seed germination of Arabidopsis thaliana (A. thaliana), we found PlNCED1 and PlNCED2 promoted seed dormancy, and the promotion effect of PlNCED2 was more obvious. In general, PlNCED1 and PlNCED2 participated in the dormancy release of herbaceous peony seeds by regulating the accumulation of endogenous ABA. Our work can reveal the molecular mechanism and related theories of ABA involved in herbaceous peony seed dormancy release.