Insights into the cotton anther development through association analysis of transcriptomic and small RNA sequencing

Regulation of endogenous hormone and miRNA in leaves of alfalfa (Medicago sativa L.) seedlings under drought stress by endogenous nitric oxide

BACKGROUND

Alfalfa (Medicago sativa. L) is one of the best leguminous herbage in China and even in the world, with high nutritional and ecological value. However, one of the drawbacks of alfalfa is its sensitivity to dry conditions, which is a global agricultural problem. The objective of this study was to investigate the regulatory effects of endogenous nitric oxide (NO) on endogenous hormones and related miRNAs in alfalfa seedling leaves under drought stress. The effects of endogenous NO on endogenous hormones such as ABA, GA3, SA, and IAA in alfalfa leaves under drought stress were studied. In addition, high-throughput sequencing technology was used to identify drought-related miRNAs and endogenous NO-responsive miRNAs in alfalfa seedling leaves under drought stress.

RESULT

By measuring the contents of four endogenous hormones in alfalfa leaves, it was found that endogenous NO could regulate plant growth and stress resistance by inducing the metabolism levels of IAA, ABA, GA3, and SA in alfalfa, especially ABA and SA in alfalfa. In addition, small RNA sequencing technology and bioinformatics methods were used to analyze endogenous NO-responsive miRNAs under drought stress. It was found that most miRNAs were enriched in biological pathways and molecular functions related to hormones (ABA, ETH, and JA), phenylpropane metabolism, and plant stress tolerance.

CONCLUSION

In this study, the analysis of endogenous hormone signals and miRNAs in alfalfa leaves under PEG and PEG + cPTIO conditions provided an important basis for endogenous NO to improve the drought resistance of alfalfa at the physiological and molecular levels. It has important scientific value and practical significance for endogenous NO to improve plant drought resistance.

Genome-Wide Analysis of the Phospholipase D Family in Five Cotton Species, and Potential Role of GhPLD2 in Fiber Development and Anther Dehiscence

Phospholipase D (PLD) and its hydrolysis product phosphatidic acid play an important role in the regulation of several cellular processes, including root growth, pollen tube elongation, and microtubule reorganization. Here, we systematically identified and analyzed the membership, characterization, and evolutionary relationship of PLDs in five species of cotton. The results of the transcriptomic analysis suggested that the evaluated PLD genes showed high expression levels in anther tissue and during the fiber initiation and elongation periods. Quantitative real-time polymerase chain reaction showed differential expression of GhPLD genes in the anthers of photoperiod sensitive male sterility mutant 5 (psm5). Previous research on multiple stable quantitative trait loci also suggests the role of PLD genes in the fiber development. Further analyses showed that GhPLD2 protein is localized to the plasma membrane. The virus-induced gene silencing of GhPLD2 in cotton seedlings repressed its expression by 40-70%, which led to a reduction in reactive oxygen species (ROS) levels, 22% anther indehiscence, and disrupted fiber initiation and elongation. Thus, we inferred that GhPLD2 may promote ROS production, which, in turn, may regulate anther dehiscence and fiber development.

Barley Anther and Meiocyte Transcriptome Dynamics in Meiotic Prophase I

In flowering plants, successful germinal cell development and meiotic recombination depend upon a combination of environmental and genetic factors. To gain insights into this specialized reproductive development program we used short- and long-read RNA-sequencing (RNA-seq) to study the temporal dynamics of transcript abundance in immuno-cytologically staged barley (Hordeum vulgare) anthers and meiocytes. We show that the most significant transcriptional changes in anthers occur at the transition from pre-meiosis to leptotene-zygotene, which is followed by increasingly stable transcript abundance throughout prophase I into metaphase I-tetrad. Our analysis reveals that the pre-meiotic anthers are enriched in long non-coding RNAs (lncRNAs) and that entry to meiosis is characterized by their robust and significant down regulation. Intriguingly, only 24% of a collection of putative meiotic gene orthologs showed differential transcript abundance in at least one stage or tissue comparison. Argonautes, E3 ubiquitin ligases, and lys48 specific de-ubiquitinating enzymes were enriched in prophase I meiocyte samples. These developmental, time-resolved transcriptomes demonstrate remarkable stability in transcript abundance in meiocytes throughout prophase I after the initial and substantial reprogramming at meiosis entry and the complexity of the regulatory networks involved in early meiotic processes.

Integrative expression network analysis of microRNA and gene isoforms in sacred lotus

Background

Gene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant.

Results

Through RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes.

Conclusions

Taken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.

Small RNA and Transcriptome Sequencing Reveals miRNA Regulation of Floral Thermogenesis in Nelumbo nucifera

The sacred lotus (Nelumbo nucifera Gaertn.) can produce heat autonomously and maintain a relatively stable floral chamber temperature for several days when blooming. Floral thermogenesis is critical for flower organ development and reproductive success. However, the regulatory role of microRNA (miRNA) underlying floral thermogenesis in N. nucifera remains unclear. To comprehensively understand the miRNA regulatory mechanism of thermogenesis, we performed small RNA sequencing and transcriptome sequencing on receptacles from five different developmental stages. In the present study, a total of 172 known miRNAs belonging to 39 miRNA families and 126 novel miRNAs were identified. Twenty-nine thermogenesis-related miRNAs and 3024 thermogenesis-related mRNAs were screened based on their expression patterns. Of those, seventeen differentially expressed miRNAs (DEMs) and 1765 differentially expressed genes (DEGs) had higher expression during thermogenic stages. The upregulated genes in the thermogenic stages were mainly associated with mitochondrial function, oxidoreductase activity, and the energy metabolism process. Further analysis showed that miR156_2, miR395a_5, miR481d, and miR319p may play an important role in heat-producing activity by regulating cellular respiration-related genes. This study provides comprehensive miRNA and mRNA expression profile of receptacle during thermogenesis in N. nucifera, which advances our understanding on the regulation of floral thermogenesis mediated by miRNA.

Different MicroRNA Families Involved in Regulating High Temperature Stress Response during Cotton (Gossypium hirsutum L.) Anther Development

MicroRNAs (miRNAs) are small molecule RNAs widely involved in responses to plant abiotic stresses. We performed small RNA sequencing of cotton anthers at four developmental stages under normal and high temperature (NT and HT, respectively) conditions to investigate the stress response characteristics of miRNA to HT. A total of 77 miRNAs, including 33 known miRNAs and 44 novel miRNAs, were identified, and 41 and 28 miRNAs were differentially expressed under NT and HT stress conditions, respectively. The sporogenous cell proliferation (SCP), meiotic phase (MP), microspore release period (MRP), and pollen maturity (PM) stages had 10 (including 12 miRNAs), four (including six miRNAs), four (including five miRNAs), and seven (including 11 miRNAs) HT stress-responsive miRNA families, respectively, which were identified after removing the changes in genotype-specific miRNAs under NT condition. Seven miRNA families (miR2949, miR167, and miR160 at the SCP stage; miR156 and miR172 at the MP stage; miR156 at the MRP stage; and miR393 and miR3476 at the PM stage), which had expression abundance of more than 10% of the total expression abundance, served as the main regulators responding to HT stress with positive or negative regulation patterns. These miRNAs orchestrated the expression of the corresponding target genes and led to different responses in the HT-tolerant and the HT-sensitive lines. The results revealed that the HT stress response of miRNAs in cotton anthers were stage-specific and differed with the development of anthers. Our study may enhance the understanding of the response of miRNAs to HT stress in cotton anthers and may clarify the mechanism of plant tolerance to HT stress.

Discovering and Constructing ceRNA-miRNA-Target Gene Regulatory Networks during Anther Development in Maize

The “competing endogenous RNA (ceRNA) hypothesis” has recently been proposed for a new type of gene regulatory model in many organisms. Anther development is a crucial biological process in plant reproduction, and its gene regulatory network (GRN) has been gradually revealed during the past two decades. However, it is still unknown whether ceRNAs contribute to anther development and sexual reproduction in plants. We performed RNA and small RNA sequencing of anther tissues sampled at three developmental stages in two maize lines. A total of 28,233 stably transcribed loci, 61 known and 51 potentially novel microRNAs (miRNAs) were identified from the transcriptomes. Predicted ceRNAs and target genes were found to conserve in sequences of recognition sites where their corresponding miRNAs bound. We then reconstructed 79 ceRNA-miRNA-target gene regulatory networks consisting of 51 known miRNAs, 28 potentially novel miRNAs, 619 ceRNA-miRNA pairs, and 869 miRNA-target gene pairs. More than half of the regulation pairs showed significant negative correlations at transcriptional levels. Several well-studied miRNA-target gene pairs associated with plant flower development were located in some networks, including miR156-SPL, miR159-MYB, miR160-ARF, miR164-NAC, miR172-AP2, and miR319-TCP pairs. Six target genes in the networks were found to be orthologs of functionally confirmed genes participating in anther development in plants. Our results provide an insight that the ceRNA-miRNA-target gene regulatory networks likely contribute to anther development in maize. Further functional studies on a number of ceRNAs, miRNAs, and target genes will facilitate our deep understanding on mechanisms of anther development and sexual plants reproduction.

MicroRNAome Profile of Euphorbia kansui in Response to Methyl Jasmonate

miRNAs play vital regulatory roles in different plant developmental stages and in plant response to biotic and abiotic stresses. However, information is limited on the miRNA regulatory mechanism to methyl jasmonate (MeJA). In this study, we used the microRNAome profile to illustrate the relevant regulatory mechanisms of Euphorbia kansui in response to methyl jasmonate (MeJA) through Illumina RNA-Seq. As a result, we identified 875 miRNAs corresponding to 11,277 target mRNAs, among them, 168 known miRNA families representing 6019 target mRNAs sequences were obtained. 452 miRNA-mRNA pairs presented an anti-correlationship (Cor < −0.50 and p-value of correlation ≤ 0.05). The miRNA with a fold change ≥ 2 and a p (p-Value) < 0.05 in pairwise comparison were identified as significant differentially expressed miRNAs (DEMs). The DEMs in MeJA treatment of 0, 24, 36 and 48 h were compared by using Short Time Expression Miner (STEM) cluster and 4 significant gene profiles (p-value ≤ 0.02) were identified. Through the kyoto encyclopedia of genes and genomes (KEGG) pathway and gene ontology (GO) enrichment analysis on all miRNA targets, we identified 33 mRNAs in terpenoid biosynthesis, which were regulated by miRNAs under MeJA treatment, so the miRNA maybe involved in the response of E. kansui plant to exogenous MeJA and the results would provide very useful information on illustrating the regulatory mechanism of E. kansui and also provide an overall view of the miRNAs response to MeJA stress of a non-model plant.