Genome-wide prediction of cauliflower miRNAs and lncRNAs and their roles in post-transcriptional gene regulation

Study on the changes of miRNAs and their target genes in regulating anthocyanin synthesis during purple discoloration of cauliflower curd under low temperature stress

Introduction

Cauliflower is widely cultivated all over the world is attributed to its palatable flavor, high levels of anti-cancer compounds, and diverse array of nutrients. Exposure to extremely cold stress during production can result in a more frequent occurrence of purple discoloration in cauliflower curds. In response to cold stress, plants naturally produce anthocyanins to eliminate reactive oxygen species (ROS) generated as a defense mechanism.

Methods

This research involved conducting mRNA sequencing analysis on cauliflower curds both before and after exposure to cold stress treatment.

Results

It was determined that the up-regulation of anthocyanin biosynthesis-related genes CHS, CHI, DFR, ANS, UGFT, PAP1/2, and MYBL2 occurred significantly in response to cold stress, resulting in a significant increase in total anthocyanin content. Subsequently, miRNA sequencing was employed to identify miRNAs in cauliflower curds, followed by differential expression analysis. The results showed that Bna-miR289 and Ath-miR157a may play a key role in regulating the accumulation of anthocyanin in cauliflower curds. Furthermore, we utilized degradome sequencing data to predict the target genes of the identified miRNAs, resulting in the identification of BolK_3g48940.1, BolK_9g11680.1, BolK_7g41780.1, BolK_3g68050.1, and BolK_3g729700.1 as targets. Subsequently, the expression patterns of the miRNAs and their target genes were validated using qRT-PCR, the results showed that Ath-miR157a and its target genes BolK_3g68050.1 and BolK_3g72970.1 may be the key to the purple of cauliflower curds under cold stress.

Discussion

Our preliminary findings identified key miRNAs and their target genes that may be involved in regulating anthocyanin synthesis, thereby enhancing the cold tolerance of cauliflower through mRNA, miRNA, and degradome sequencing. Overall, our study sheds light on the activation of anthocyanin synthesis in flower curds under cold stress conditions as a mechanism to enhance resilience to adverse environmental conditions.

Comparative proteomic analysis provides insights into wood formation in immature xylem at different ages in Eucalyptus urophylla × Eucalyptus grandis

Introduction

Wood formation is a crucial developmental stage in the life cycle of a woody plant; this process has substantial scientific research implications and practical applications. However, the mechanisms underlying woody plant development, especially the process of wood formation, remain poorly understood. As eucalyptus is one of the fastest growing tree species in the world, understanding the mechanism of wood formation in eucalyptus will greatly promote the development of molecular breeding technology for forest trees.

Results

In this study, we investigated the proteomic profile of immature xylem at four different ages of Eucalyptus urophylla × Eucalyptus grandis (E. urograndis) using iTARQ technology. We identified 5236 proteins and 492 differentially abundant proteins (DAPs). The expression profiles of the DAPs corresponding to coding genes associated with wood formation were assessed using qRT-PCR. From the different expression profiles, it is inferred that the genes encoding kinesin, CDKD3, EXPA13, EXPA2, XTH27, EGases, UGT76E2, LAC, CCoAMT, CesA3, PAL, and CAD may undergo posttranscriptional regulation (PTR). Additionally, the genes encoding EIN2, ETR, MC4-like, and XCP may undergo posttranslational modifications (PTMs).

Conclusions

We investigated changes in wood formation-related proteins at the protein abundance level in the immature xylem of E. urograndis, thereby elucidating potential regulatory mechanisms of key proteins involved in eucalyptus wood formation. This study may provide theoretical guidance for further research on molecular breeding techniques and genetic improvement related to the cultivation of rapidly growing and high-quality trees.

Deciphering miRNA-lncRNA-mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan

Pigeon pea (Cajanus cajan) is widely cultivated for its nutritional and medicinal value yet remains an orphan crop as productivity has not been improved because of a lack of genome and non-coding genome information. Non-coding RNAs, like miRNAs and long non-coding RNAs (lncRNAs), are involved in regulation of growth, metabolism, development, and stress response, and have a critical role in post-transcriptional gene regulation (PTGR). We attempted to elucidate the roles of miRNAs and lncRNAs in pigeon pea through experimental validation of computationally predicted miRNAs and lncRNAs and targets of miRNAs on mRNAs. We experimentally validated 20 miRNAs and 11 lncRNAs. We predicted cleavage sites of three miRNA targets: serine/threonine-protein kinase, polygalacturonase, beta-galactosidase. We identified 469 targets of 265 miRNAs and their functional annotations using computational methods. We built a miRNA-mRNA-lncRNA network model, with the miRNAs targeting both mRNAs and lncRNAs, to obtain information on the interplay of these three molecules. A confirmed interaction through experimental validation was established between miRNA, namely cca-miR1535a targeting the mRNA for beta-galactosidase, as well as the lncRNA cca-lnc-020033. Our findings increase knowledge of the non-coding genome of pigeon pea and their roles in PTGR and in improving agronomic traits of this pulse crop.

MicroRNAs in Medicinal Plants

Medicinal plant microRNAs (miRNAs) are an endogenous class of small RNA central to the posttranscriptional regulation of gene expression. Biosynthetic research has shown that the mature miRNAs in medicinal plants can be produced from either the standard messenger RNA splicing mechanism or the pre-ribosomal RNA splicing process. The medicinal plant miRNA function is separated into two levels: (1) the cross-kingdom level, which is the regulation of disease-related genes in animal cells by oral intake, and (2) the intra-kingdom level, which is the participation of metabolism, development, and stress adaptation in homologous or heterologous plants. Increasing research continues to enrich the biosynthesis and function of medicinal plant miRNAs. In this review, peer-reviewed papers on medicinal plant miRNAs published on the Web of Science were discussed, covering a total of 78 species. The feasibility of the emerging role of medicinal plant miRNAs in regulating animal gene function was critically evaluated. Staged progress in intra-kingdom miRNA research has only been found in a few medicinal plants, which may be mainly inhibited by their long growth cycle, high demand for growth environment, immature genetic transformation, and difficult RNA extraction. The present review clarifies the research significance, opportunities, and challenges of medicinal plant miRNAs in drug development and agricultural production. The discussion of the latest results furthers the understanding of medicinal plant miRNAs and helps the rational design of the corresponding miRNA/target genes functional modules.