Determination of the MiRNAs Related to Bean Pyralid Larvae Resistance in Soybean Using Small RNA and Transcriptome Sequencing

Identification of an SCF Ubiquitin Ligase Complex that Contributes to Resistance Against Valsa Canker in Apple

E3 ubiquitin ligases play a critical role in plant disease resistance. Among them, the Skp1-Cullin-F-box protein (SCF) ubiquitin ligase complex is the largest family and regulates the ubiquitination of a wide range of proteins. Apple Valsa canker (AVC) is a fungal disease of apple trees caused by the fungus Valsa mali, which can lead to significant economic losses. However, the function of the SCF complex in apple resistance to this disease is still largely unknown. In this study, we identified an SCF ubiquitin ligase complex that can enhance resistance to Valsa canker in apple. Disease evaluation experiments demonstrated that MdSkp1 increased apple resistance to AVC. Furthermore, MdSkp1 interacted with an F-box protein, MdSKIP14, and interacted with a cullin-1 protein, MdCUL1, to form an SCF ubiquitin ligase complex. Additionally, we revealed both MdSKIP14 and MdCUL1 as positive regulators of AVC resistance. In conclusion, our results identified an SCF complex capable of contributing to apple resistance against AVC, providing a theoretical basis for apple disease resistance and the sustainable development of the industry. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome Assembly of Cordia subcordata, a Coastal Protection Species in Tropical Coral Islands

Cordia subcordata trees or shrubs, belonging to the Boraginaceae family, have strong resistance and have adapted to their habitat on a tropical coral island in China, but the lack of genome information regarding its genetic background is unclear. In this study, the genome was assembled using both short/long whole genome sequencing reads and Hi-C reads. The assembled genome was 475.3 Mb, with 468.7 Mb (99.22%) of the sequences assembled into 16 chromosomes. Repeat sequences accounted for 54.41% of the assembled genome. A total of 26,615 genes were predicted, and 25,730 genes were functionally annotated using different annotation databases. Based on its genome and the other 17 species, phylogenetic analysis using 336 single-copy genes obtained from ortholog analysis showed that C. subcordata was a sister to Coffea eugenioides, and the divergence time was estimated to be 77 MYA between the two species. Gene family evolution analysis indicated that the significantly expanded gene families were functionally related to chemical defenses against diseases. These results can provide a reference to a deeper understanding of the genetic background of C. subcordata and can be helpful in exploring its adaptation mechanism on tropical coral islands in the future.

Identification of Cumin (Cuminum cyminum) MicroRNAs through Deep Sequencing and Their Impact on Plant Secondary Metabolism

The pharmacological properties of plants lie in the content of secondary metabolites that are classified into different categories based on their biosynthesis, structures, and functions. MicroRNAs (miRNAs) are small non-coding RNA molecules that play crucial post-transcriptional regulatory roles in plants, including development and stress-response signaling; however, information about their involvement in secondary metabolism is still limited. Cumin is one of the most popular seeds from the plant Cuminum cyminum, with extensive applications in herbal medicine and cooking; nevertheless, no previous studies focus on the miRNA profile of cumin. In this study, the miRNA profile of C. cyminum and its association with the biosynthesis of secondary metabolites were determined using NGS technology. The sequencing data yielded 10,956,054 distinct reads with lengths ranging from 16 to 40 nt, of which 349 miRNAs were found to be conserved and 39 to be novel miRNAs. Moreover, this work identified 1959 potential target genes for C. cyminum miRNAs. It is interesting to note that several conserved and novel miRNAs have been found to specifically target important terpenoid backbone, flavonoid biosynthesis, and lipid/fatty acid pathways enzymes. We believe this investigation will aid in elucidating the implications of miRNAs in plant secondary metabolism.

Multi-omics assisted breeding for biotic stress resistance in soybean

Biotic stress is a critical factor limiting soybean growth and development. Soybean responses to biotic stresses such as insects, nematodes, fungal, bacterial, and viral pathogens are governed by complex regulatory and defense mechanisms. Next-generation sequencing has availed research techniques and strategies in genomics and post-genomics. This review summarizes the available information on marker resources, quantitative trait loci, and marker-trait associations involved in regulating biotic stress responses in soybean. We discuss the differential expression of related genes and proteins reported in different transcriptomics and proteomics studies and the role of signaling pathways and metabolites reported in metabolomic studies. Recent advances in omics technologies offer opportunities to reshape and improve biotic stress resistance in soybean by altering gene regulation and/or other regulatory networks. We suggest using 'integrated omics' to precisely understand how soybean responds to different biotic stresses. We also discuss the potential challenges of integrating multi-omics for the functional analysis of genes and their regulatory networks and the development of biotic stress-resistant cultivars. This review will help direct soybean breeding programs to develop resistance against different biotic stresses.

Kaempferol Inhibits Hepatic Stellate Cell Activation by Regulating miR-26b-5p/Jag1 Axis and Notch Pathway

Kaempferol, a natural flavonoid molecule, has demonstrated anti-inflammatory, antimicrobial and antioxidant activities. Recent studies have shown the beneficial effects of kaempferol on liver fibrosis. Notch pathway has been reported to be involved in the aberrant activation of hepatic stellate cells (HSCs). However, whether Notch pathway plays a key role in the anti-fibrotic effects of kaempferol is largely unknown. In this study, kaempferol significantly suppressed liver fibrosis in CCl₄ mice, with reduced collagen deposition as well as restored liver function. In vitro, kaempferol enhanced the suppression of HSC activation, with a decrease in α-SMA as well as collagen level. It was found that Notch pathway played an important role in kaempferol-reduced the activation of HSCs. Jag1, a ligand of Notch pathway, was obviously inhibited by kaempferol. Overexpression of Jag1 effectively abolished kaempferol-induced HSC inactivation. Furthermore, Jag1 was demonstrated as a target of microRNA-26b-5p (miR-26b-5p). Interestingly, miR-26b-5p inhibitor prevented HSC activation inhibition caused by kaempferol. Further studies indicated that kaempferol inhibited Notch pathway via miR-26b-5p and Jag1, leading to HSC inactivation. Collectively, we demonstrate that kaempferol could inhibit HSC activation, at least in part, via miR-26b-5p-mediated Jag1 axis and Notch pathway. Kaempferol may serve as a promising drug in the application of treating liver fibrosis.

Methylome and transcriptome analyses of soybean response to bean pyralid larvae

BACKGROUND

Bean pyralid is one of the major leaf-feeding insects that affect soybean crops. DNA methylation can control the networks of gene expressions, and it plays an important role in responses to biotic stress. However, at present the genome-wide DNA methylation profile of the soybean resistance to bean pyralid has not been reported so far.

RESULTS

Using whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analyzed the highly resistant material (Gantai-2-2, HRK) and highly susceptible material (Wan82-178, HSK), under bean pyralid larvae feeding 0 h and 48 h, to clarify the molecular mechanism of the soybean resistance and explore its insect-resistant genes. We identified 2194, 6872, 39,704 and 40,018 differentially methylated regions (DMRs), as well as 497, 1594, 9596 and 9554 differentially methylated genes (DMGs) in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48 comparisons, respectively. Through the analysis of global methylation and transcription, 265 differentially expressed genes (DEGs) were negatively correlated with DMGs, there were 34, 49, 141 and 116 negatively correlated genes in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48, respectively. The MapMan cluster analysis showed that 114 negatively correlated genes were clustered in 24 pathways, such as protein biosynthesis and modification; primary metabolism; secondary metabolism; cell cycle, cell structure and component; RNA biosynthesis and processing, and so on. Moreover, CRK40; CRK62; STK; MAPK9; L-type lectin-domain containing receptor kinase VIII.2; CesA; CSI1; fimbrin-1; KIN-14B; KIN-14 N; KIN-4A; cytochrome P450 81E8; BEE1; ERF; bHLH25; bHLH79; GATA26, were likely regulatory genes involved in the soybean responses to bean pyralid larvae. Finally, 5 DMRs were further validated that the genome-wide DNA data were reliable through PS-PCR and 5 DEGs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. The results showed an excellent agreement with deep sequencing.

CONCLUSIONS

Genome-wide DNA methylation profile of soybean response to bean pyralid was obtained for the first time. Several specific DMGs which participated in protein kinase, cell and organelle, flavonoid biosynthesis and transcription factor were further identified to be likely associated with soybean response to bean pyralid. Our data will provide better understanding of DNA methylation alteration and their potential role in soybean insect resistance.

Identification and characterization of miRNAs associated with sterile flower buds in the tea plant based on small RNA sequencing

Background

miRNAs are a type of conserved, small RNA molecule that regulate gene expression and play an important role in the growth and development of plants. miRNAs are involved in seed germination, root development, shoot apical meristem maintenance, leaf development, and flower development by regulating various target genes. However, the role of miRNAs in the mechanism of tea plant flower sterility remains unclear. Therefore, we performed miRNA sequencing on the flowers of fertile male parents, female parents, and sterile offspring.

Results

A total of 55 known miRNAs and 90 unknown miRNAs were identified. In the infertile progeny, 37 miRNAs were differentially expressed; 18 were up-regulated and 19 were down-regulated. miR156, miR157, miR164, miR167, miR169, miR2111 and miR396 family members were down-regulated, and miR160, miR172 and miR319 family members were up-regulated. Moreover, we predicted that the 37 differentially expressed miRNAs target a total of 363 genes, which were enriched in 31 biological functions. We predicted that miR156 targets 142 genes, including ATD1A, SPL, ACA1, ACA2, CKB22 and MADS2.

Conclusion

We detected a large number of differentially expressed miRNAs in the sterile tea plant flowers, and their target genes were involved in complex biological processes. Among these miRNAs, the down-regulation of miR156 may be one of the factor in the formation of sterile floral buds in tea plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41065-021-00188-8.

High-Throughput Sequencing and Expression Analysis Suggest the Involvement of Pseudomonas putida RA-Responsive microRNAs in Growth and Development of Arabidopsis

Beneficial soil microorganisms largely comprise of plant growth-promoting rhizobacteria (PGPR), which adhere to plant roots and facilitate their growth and development. Pseudomonas putida (RA) strain MTCC5279 is one such PGPR that exhibits several characteristics of plant growth promotion, such as P-solubilization, and siderophores and IAA production. Plant–PGPR interactions are very complex phenomena, and essentially modulate the expression of numerous genes, consequently leading to changes in the physiological, biochemical, cellular and molecular responses of plants. Therefore, in order to understand the molecular bases of plant–PGPR interactions, we carried out the identification of microRNAs from the roots of Arabidopsis upon P. putida RA-inoculation, and analyses of their expression. MicroRNAs (miRNAs) are 20- to 24-nt non-coding small RNAs known to regulate the expression of their target genes. Small RNA sequencing led to the identification of 293 known and 67 putative novel miRNAs, from the control and RA-inoculated libraries. Among these, 15 known miRNAs showed differential expression upon RA-inoculation in comparison to the control, and their expressions were corroborated by stem-loop quantitative real-time PCR. Overall, 28,746 and 6931 mRNAs were expected to be the targets of the known and putative novel miRNAs, respectively, which take part in numerous biological, cellular and molecular processes. An inverse correlation between the expression of RA-responsive miRNAs and their target genes also strengthened the crucial role of RA in developmental regulation. Our results offer insights into the understanding of the RA-mediated modulation of miRNAs and their targets in Arabidopsis, and pave the way for the further exploitation and characterization of candidate RA-responsive miRNA(s) for various crop improvement strategies directed towards plant sustainable growth and development.

Small RNA Mobility: Spread of RNA Silencing Effectors and its Effect on Developmental Processes and Stress Adaptation in Plants

Plants are exposed every day to multiple environmental cues, and tight transcriptome reprogramming is necessary to control the balance between responses to stress and processes of plant growth. In this context, the silencing phenomena mediated by small RNAs can drive transcriptional and epigenetic regulatory modifications, in turn shaping plant development and adaptation to the surrounding environment. Mounting experimental evidence has recently pointed to small noncoding RNAs as fundamental players in molecular signalling cascades activated upon exposure to abiotic and biotic stresses. Although, in the last decade, studies on stress responsive small RNAs increased significantly in many plant species, the physiological responses triggered by these molecules in the presence of environmental stresses need to be further explored. It is noteworthy that small RNAs can move either cell-to-cell or systemically, thus acting as mobile silencing effectors within the plant. This aspect has great importance when physiological changes, as well as epigenetic regulatory marks, are inspected in light of plant environmental adaptation. In this review, we provide an overview of the categories of mobile small RNAs in plants, particularly focusing on the biological implications of non-cell autonomous RNA silencing in the stress adaptive response and epigenetic modifications.