Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.

The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling

Transcriptome and metabolome profiling reveals key pathways and metabolites involved in defense against Verticillium dahliae in upland cotton

Circular RNA (circRNA) is a type of non-coding RNA with multiple biological functions. Whole circRNA genomes in plants have been identified, and circRNAs have been demonstrated to be widely present and highly expressed in various plant tissues and organs. CircRNAs are highly stable and conserved in plants, and exhibit tissue specificity and developmental stage specificity. CircRNAs often interact with other biomolecules, such as miRNAs and proteins, thereby regulating gene expression, interfering with gene function, and affecting plant growth and development or response to environmental stress. CircRNAs are less studied in plants than in animals, and their regulatory mechanisms of biogenesis and molecular functions are not fully understood. A variety of circRNAs in plants are involved in regulating growth and development and responding to environmental stress. This review focuses on the biogenesis and regulatory mechanisms of circRNAs, as well as their biological functions during growth, development, and stress responses in plants, including a discussion of plant circRNA research prospects. Understanding the generation and regulatory mechanisms of circRNAs is a challenging but important topic in the field of circRNAs in plants, as it can provide insights into plant life activities and their response mechanisms to biotic or abiotic stresses as well as new strategies for plant molecular breeding and pest control. 

Advances in CircRNAs in the Past Decade: Review of CircRNAs Biogenesis, Regulatory Mechanisms, and Functions in Plants

Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.

Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies

<title>Abstract</title> Background Sunflower (<italic>Helianthus annuus</italic>) is one of the most important oilseed crops worldwide. To reveal the molecular mechanism of biosynthesis and accumulation of major fatty acid components in sunflower, and to clarify the primary and secondary relationships between temperature, genes, and fatty acid synthesis in sunflower. In this study, as our study materials, we chose the sunflower inbred lines J9 and P50 with high and low oleic acids, respectively. Sampling at the same period of sowing at different periods (S-test) and sampling at different periods of sowing at the same time (A-test) were used to determine the fatty acid fractions and contents of different samples of seeds after pollination, respectively; and RNA-Seq technology was utilized to sequence the different samples to obtain the gene expression data related to fatty acid synthesis for each sample. Results Five main fatty acids were detected, including Oleic acid, linoleic acid, stearic acid, linolenic acid, palmitic acid, and the relative contents of oleic acid and linoleic acid were negatively correlated, while the relative contents of linolenic acid and palmitic acid were lower and showed a continuous decreasing trend during seed development. The crucial turning point in sunflower fatty acid synthesis occurs at 20 days after flowering (DAF), and fatty acid fractions and contents of high oleic sunflower lines were little affected by temperature, while low oleic lines were susceptible to temperature. A total of 81,676 unigenes were obtained by transcriptome sequencing. There were 15885 and 18220 genes obtained in the S dataset and A dataset, respectively, were annotated in the GO and KEGG functional databases. Based on the KEGG database, a total of 19 pathways associated with lipid metabolism, with a cumulative enrichment of 29 DEGs. Through the analysis of metabolic pathways, a total of 42 differentially expressed genes (DEGs) directly related to sunflower fatty acid metabolism were identified. These DEGs belong to 22 different types of enzymes, including PIGT, KCS, ACC, SAD, MFP, ACX, ACP, and FAB, which are key genes involved in the biosynthesis of unsaturated fatty acids and oil accumulation in sunflowers. Conclusions We predicted that PIGT, KCS, ACC, SAD, MFP, ACX, ACP, and FAB were the key enzymes, regulating their genes in the fatty acid biosynthesis and oil accumulation in sunflower seed. This study provides the first comprehensive genomic resources characterizing sunflowers seed gene expression at the transcriptional level. These data lay the foundation for elucidating the molecular mechanisms of fatty acid biosynthesis and oil accumulation for sunflower. 

Transcriptome analysis reveals the potential molecular mechanism involved in fatty acids biosynthesis of Sunflower

Identification and functional prediction of CircRNAs of developing seeds in high oleic acid sunflower (Helianthus annuus L.)

Helianthus annuus L. seeds possess high nutritional value and more stable oleic acid oil. Initial analysis of sunflower seed for oleic acid content during seed development revealed rapid oleic acid accumulation by 17 days after flowering (DAF), with high oleic acid levels persisting until after 27 DAF. Subsequent transcriptome sequencing analysis of high ('L-1-OL-1') and low ('86-1') oleic acid oil-producing sunflower cultivars enabled gene expression profile comparisons. Further analysis on differentially expressed genes (DEGs) in seed from different group at 17 and 27 days revealed 5971 (2751 up, 3220 down), 4906 (2518 up, 2388 down), 12761 (5807 up, 6954 down), and 9883 (3803 up, 6080 down) DEGs for D8617d vs D8627d, D8617d vs L17d, D8627d vs L27d, and L17d vs L27d, respectively. DEGs annotation detected the key fatty acid biosynthesis genes and transcription factors with potential roles in lipid metabolism. Furthermore, quantitative real time PCR (RT-PCR ） results of 12 DEGs involved in fatty acid metabolism were positively correlated with their expression patterns using RNA-Seq implying a good reliability of results produced by this method. The results in this research may pave theoretical basis for researching molecular mechanisms of sunflower lipid metabolism.

Comparative transcriptomic analyses of high and low oleic acid content sunflower ( helianthus annuus l.) seed development

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Identification and functional prediction of CircRNAs of developing seeds in high oleic acid sunflower (Helianthus annuus L.)

Comparative transcriptomic analyses of high and low oleic acid content sunflower ( helianthus annuus l.) seed development