PmiREN: a comprehensive encyclopedia of plant miRNAs

WP-MOD: A multi-omics and taxonomy database for woody plants

Woody plants, including trees, shrubs, and woody vines, are vital components of terrestrial ecosystems and are critical for maintaining biodiversity, regulating climate, and supporting human livelihoods. Over the past decade, the accumulation of high-throughput sequencing data, multi-omics data, and taxonomic information on woody plants has increased significantly, highlighting the need for an integrative database. Here, we present the Woody Plant Multi-Omics Database (WP-MOD, https://www.woodyplant.com), a comprehensive and user-friendly platform designed to meet the growing need for specialized resources in woody plant research. The WP-MOD integrates extensive taxonomic information and multi-omics data from 373 species across 35 orders and provides a centralized resource for the analysis and exploration of woody plant biology. The database includes high-quality reference genomes and reanalyzed data from RNA sequencing, small RNA sequencing, chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin sequencing, and bisulfite sequencing, along with 17 tools for sequence and omics analysis. The WP-MOD supports both genetic and molecular research and contributes to the conservation and sustainable management of woody plants. We believe that the WP-MOD will be an essential tool for plant science researchers.

Identification and characterization of Eco-miR 169-EcNF-YA13 gene regulatory network reveal their role in conferring tolerance to dehydration and salinity stress in finger millet

The finger millet (Eleusine coracana (L.) Gaertn) genome, comprised 166 conserved microRNAs (miRNAs) belonging to 39 families and three novel miRNAs. The miR169 is one of the most conserved miRNA families, while Eco_N1 is a species-specific miRNA prevalent in finger millet. Its members regulate the expression of genes encoding the Nuclear Factor-Y subunit A (NF-YA) via transcript cleavage. However, the role of miRNA genes in regulating the expression of NF-YA transcription factors in finger millet needs to be deciphered. The present study characterized 166 conserved and novel miRNAs (Eco_N1, Eco_N2 and Eco_N3). Further, secondary structures were predicted, and the potential miR genes targeting the NF-YA transcription factors regulating abiotic stress tolerance were analysed. Twenty-three Eco-miR169 members and one Eco_N1 miRNA targeting EcNF-YA13 were identified in the finger millet genome. The presence of relevant cis-elements such as ABRE (abscisic acid-responsive elements), DRE (dehydration-responsive element), and MYB (myeloblastosis) indicates that the target of Eco-miR169 might be involved in abiotic stress responses. The tissue-specific RNA-seq transcriptomic expression pattern of Eco-miR169 showed variable fold of expression in seedlings compared to the control. At the same time, the expression of EcNF-YA13 (target genes of Eco-miR169 members and Eco_N1) presented a downregulated trend under salinity and dehydration conditions compared to the control. Tissue-specific RNA-seq followed by expression analysis confirmed the antagonistic effect of Eco-miR genes on EcNF-YA13. In a nutshell, the results of this study could be utilized as a platform for further exploration and characterization of finger millet Eco-miR169-EcNF-YA13gene regulatory network.

Role of non-coding RNAs in quality improvement of horticultural crops: computational tools, databases, and algorithms for identification and analysis

Horticultural crops, including fruits, vegetables, flowers, and herbs, are essential for food security and economic sustainability. Advances in biotechnology, including genetic modification and omics approaches, have significantly improved these crops'traits. While initial transgenic efforts focused on protein-coding genes, recent research highlights the crucial roles of non-coding RNAs (ncRNAs) in plant growth, development, and gene regulation. ncRNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), influence key biological processes through transcriptional and post-transcriptional regulation. This review explores the classification, functions, and regulatory mechanisms of ncRNAs, emphasizing their potential in enhancing horticultural crop quality. This growing understanding offers promising avenues for enhancing crop performance and developing new horticultural varieties with improved traits. Additionally, we elucidate the role of ncRNA databases and predictive bioinformatics tools into modern horticultural crop improvement strategies.

Evolution of Plant Conserved microRNAs After Whole-Genome Duplications

MicroRNAs (miRNAs) are a specialized class of small silencing RNAs that regulate gene expression in numerous biological processes in eukaryotes. While the evolutionary dynamics of protein-coding genes after plant whole-genome duplications (WGDs) has been extensively studied, the patterns of evolution for conserved MIRNAs (miRNA genes) post-WGDs are less understood. In this study, we systematically investigated miRNAs and their targets in 6 plant species with varying WGD histories. Our findings reveal that WGDs significantly contribute to the expansion of conserved miRNA families. Notably, through homologous analyses of conserved miRNA families, we discovered that beyond the loci derived from WGDs and other duplication events, some conserved miRNA families have independently gained new loci and/or lost syntenic loci in specific lineage or species through evolution. Additionally, our analyses of sequence divergence in conserved miRNAs showed that the mature sequences of miRNA duplicates gradually diverge following WGDs, with this sequence divergence being correlated with that of their adjacent protein-coding genes after recent WGDs. Furthermore, expression and functional divergence analyses of duplicated targets in different miRNA-target interaction scenarios suggest that conserved miRNAs may play crucial roles in regulating the expression of duplicated genes and related regulatory networks following WGDs. In summary, our analyses reveal universal evolutionary patterns of plant conserved miRNAs following WGDs and provide evidence that some miRNA copies in conserved families originated independently during evolution.

Cell-Type Specific miRNA Regulatory Network Responses to ABA Stress Revealed by Time Series Transcriptional Atlases in Arabidopsis

In plants, microRNAs (miRNAs) participate in complex gene regulatory networks together with the transcription factors (TFs) in response to biotic and abiotic stresses. To date, analyses of miRNAs-induced transcriptome remodeling are at the whole plant or tissue levels. Here, Arabidopsis's ABA-induced single-cell RNA-seq (scRNA-seq) is performed at different stages of time points-early, middle, and late. Single-cell level primary miRNAs (pri-miRNAs) atlas supported the rapid, dynamic, and cell-type specific miRNA responses under ABA treatment. MiRNAs respond rapidly and prior to target gene expression dynamics, and these rapid response miRNAs are highly cell-type specific, especially in mesophyll and vascular cells. MiRNA-TF-mRNA regulation modules are identified by identifying miRNA-contained feed-forward loops (M-FFLs) in the regulatory network, and regulatory networks with M-FFLs have higher co-expression and clustering coefficient (CC) values than those without M-FFLs, suggesting the hub role of miRNAs in regulatory networks. The cell-type-specific M-FFLs are regulated by these hub miRNAs rather than TFs through sc-RNA-seq network analysis. MiR858a-FBH3-MYB module inhibited the expression of MYB63 and MYB20, which related to the formation of plant secondary wall and the production of lignin, through M-FFL specifically in vascular. These results can provide prominent insights into miRNAs' dynamic and cell-type-specific roles in plant development and stress responses.

Expression profile and characterization of respiratory burst oxidase homolog genes in rice under MeJA, SA and Xoo treatments

Respiratory burst oxidase homologs (Rboh) genes is essential for synthesizing reactive oxygen species, which play a crucial role in environmental stress response. The Rboh gene family has been studied in model plants such as Arabidopsis. Nevertheless, Rboh remained largely unexplored in Rice (Oryza sativa L.). Here, we performed characterization of the Rboh genes family in rice (OsRboh) under Xanthomonas oryzae pv. oryzae (Xoo), salicylic acid (SA), and methyl jasmonate (MeJA) treatments. Nine OsRboh genes were retrieved distributed across six chromosomes (1, 5, 8, 9, 11, 12).These genes vary in amino acid sequence length (728-1034), isoelectric point (9.05-9.84), and molecular weight (8.341-115.014 kDa). Analysis of gene structure, motifs and conserved domains showed that OsRboh genes have similar protein sequences and functions. The promoter region of OsRboh genes was found to contain mainly cis-acting elements associated with light, jasmonic acid (JA), abscisic acid (ABA), and SA responsiveness. Predictions of functional protein-protein interaction showed that OsRboh genes were associated with MAPK signaling, plant-pathogen interaction, and other mRNA surveillance pathways. Prediction of miRNA targets and post-translational modification sites indicated that OsRboh genes may be regulated by miRNA and protein phosphorylation. Phylogenetic analysis showed that OsRboh genes were distributed into 7 clusters. Furthermore, 9 OsRboh genes were differentially expressed in different tissues (roots, stems, and leaves). OsRbohA, OsRbohB, and OsRbohD are significant genes in rice defense responses, showing unique and increased expression profiles under (Xoo-PXO99), (MeJA), and (SA) treatments. These genes important function in triggering defense mechanisms is further stressed by the high (> 20-fold) changes in expression they exhibit under these treatments. These findings enhance our understanding of rice OsRboh genes functions and contribute to stress tolerance improvement strategies.

Deciphering the impact of microRNAs in plant biology: a review of computational insights and experimental validation

Exploring the complex world of microRNA (miRNA) biogenesis and functions in plants is essential for understanding their diverse regulatory mechanisms. This review highlights the processes involved in miRNA biogenesis and their crucial roles in growth and development of plant, stress responses, and nutrient homeostasis. miRNAs play a central role in various developmental processes, including the transition from the juvenile to adult stage, the growth of shoot apical meristem, leaf and floral morphogenesis, and the determination of flowering time. By presenting the current state of research, we focus on the vital role of computational tools and databases in deciphering the regulatory networks controlled by miRNAs, which helps us navigate the intricate world of plant biology. Furthermore, it stresses the importance of experimental validation techniques in confirming computational predictions, ensuring that miRNA research is reliable and robust. As the field continues to grow, this review emphasizes the urgent need for integrated approaches, to deepen our knowledge of plant miRNA biology and its implications. These insights will pave the way for advancements in crop improvement, stress resilience, and biotechnological innovations.

Genome-wide identification and characterization of cation-proton antiporter (CPA) gene family in rice (Oryza sativa L.) and their expression profiles in response to phytohormones

The cation-proton antiporter (CPA) superfamily plays pivotal roles in regulating cellular ion and pH homeostasis in plants. To date, the regulatory functions of CPA family members in rice (Oryza sativa L.) have not been elucidated. In this study, we use rice public data and information techniques, 29 OsCPA candidate genes were identified in the rice japonica variety (referred to as OsCPA) and phylogenetically categorized into K+ efflux antiporter (KEA), Na+/H+ exchanger (NHX), and cation/H+ exchanger (CHX) groups containing 4, 7, and 18 OsCPA genes. The OsCPA proteins were predominantly localized in the plasma membrane and unevenly scattered on 11 chromosomes. The structural analysis of OsCPA proteins revealed higher similarities within groups. Prediction of selection pressure, collinearity, and synteny analysis indicated that all duplicated OsCPA genes had undergone strong purifying selection throughout their evolution. The cis-acting regulatory elements (CAREs) analysis identified 56 CARE motifs responsive to light, tissue, hormones, and stresses. Additionally, 124 miRNA families were identified in the gene promoters, and OsNHX7 was targeted by the highest number of miRNAs (43 miRNAs). Gene Ontology analysis demonstrated the numerous functions of OsCPA genes associated with biological processes (57.14%), cellular components (7.94%), and molecular functions (34.92%). A total of 12 transcription factor families (TFFs), including 40 TFs were identified in gene promoters, with the highest numbers of TFFs (5TFFs) linked to OsCHX13, and OsCHX15. Protein-protein interaction analysis suggested maximum functional similarities between rice and Arabidopsis CPA proteins. Based on expression analysis, OsKEA1, OsKEA2, OsNHX3, and OsNHX7 were frequently expressed in rice tissues. Furthermore, OsNHX3, OsNHX4, OsNHX6, OsNHX7, OsCHX8, and OsCHX17 in abscisic acid, OsKEA1, OsNHX3, and OsCHX8 in gibberellic acid, OsKEA1, OsKEA3, OsNHX1, and OsNHX3 in indole-3-acetic acid treatment were demonstrated as potential candidates in response to hormone. These findings highlight potential candidates for further characterization of OsCPA genes, which may aid in the development of rice varieties.

ncPlantDB: a plant ncRNA database with potential ncPEP information and cell type-specific interaction

The field of plant non-coding RNAs (ncRNAs) has seen significant advancements in recent years, with many ncRNAs recognized as important regulators of gene expression during plant development and stress responses. Moreover, the coding potential of these ncRNAs, giving rise to ncRNA-encoded peptides (ncPEPs), has emerged as an essential area of study. However, existing plant ncRNA databases lack comprehensive information on ncRNA-encoded peptides (ncPEPs) and cell type-specific interactions. To address this gap, we present ncPlantDB (https://bis.zju.edu.cn/ncPlantDB), a comprehensive database integrating ncRNA and ncPEP data across 43 plant species. ncPlantDB encompasses 353 140 ncRNAs, 3799 ncPEPs and 4 647 071 interactions, sourced from established databases and literature mining. The database offers unique features including translational potential data, cell-specific interaction networks derived from single-cell RNA sequencing and Ribo-seq analyses, and interactive visualization tools. ncPlantDB provides a user-friendly interface for exploring ncRNA expression patterns at the single-cell level, facilitating the discovery of tissue-specific ncRNAs and potential ncPEPs. By integrating diverse data types and offering advanced analytical tools, ncPlantDB serves as a valuable resource for researchers investigating plant ncRNA functions, interactions, and their potential coding capacity. This database significantly enhances our understanding of plant ncRNA biology and opens new avenues for exploring the complex regulatory networks in plant genomics.

MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models

We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA genes (5160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB's phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely available at mirgenedb.org.

PmiR-Select® - a computational approach to plant pre-miRNA identification in genomes

Precursors of microRNAs (pre-miRNAs) are less used in silico to mine miRNAs. This study developed PmiR-Select® based on covariance models (CMs) to identify new pre-miRNAs, detecting conserved secondary structural features across RNA sequences and eliminating the redundancy. The pipeline preceded PmiR-Select® filtered 20% plant pre-miRNAs (from 38589 to 8677) from miRBase. The second filter reduced pre-miRNAs by 7% (from 8677 to 8045) through length limit to pre-miRNAs (70-300 nt) and miRNAs (20-24 nt). The 80% redundancy threshold was statistically the best, eliminating 55% pre-miRNAs (from 8045 to 3608). Angiosperms retained the highest number of pre-miRNAs and their families (2981 and 2202), followed by gymnosperms (362 and 271), bryophytes (183 and 119), and algae (82 and 78). Thirty-seven conserved pre-miRNA families happened among plant land clades, but none with algae. The PmiR-Select® was applied to the rice genome, producing 8536 pre-miRNAs from 36 families. The 80% redundancy threshold retained 3% pre-miRNAs (n = 264) from 36 families, valuable experimental and computational research resources. 14% (n = 1216) of 8536 were new pre-miRNAs from 19 new families in rice. Only 16 new sequences from six families overlapped (39 to 54% identities) with rice pre-miRNAs and five species on miRBase. The validation against mature miRNAs identified 8086 pre-miRNAs from 13 families. Eleven ones have already been recorded, but two new and abundant pre-miRNAs [miR437 (n = 296) and miR1435 (n = 725)] scattered in all 12-rice chromosomes. PmiR-Select® identified pre-miRNAs, decreased the redundancy, and discovered new miRNAs. These findings pave the way to delineating benchtop and computational experiments.

Host Response of Arabidopsis thaliana Interaction with Fungal Endophytes Involves microRNAs

Plant and fungus interaction is a complex process involving many molecular factors determining the nature of relationship. The enigmatic methodology by which fungal endophytes are able to colonise a plant harmoniously is still inexplicable. Small RNAs have been identified as major regulatory elements under various biotic interactions. However, their role in endophytic plant-fungal interactions remain to be elucidated. Therefore, transcript expression data available on Gene Expression Omnibus for Arabidopsis thaliana was utilised for miRNAs identification under endophytism. The analysis predicted 15 miRNAs with differential expression of which the ath-miRNA398b modulation was significant. Application of psRNAtarget, C-mii, pmiREN, and TarDB provided a pool of 357 target genes for these miRNAs. Protein-protein interaction analysis identified major hub proteins, including BTB/POZ domain-containing protein, beta-Xylosidase-2 (AtBXL2), and Copper/Zinc Superoxide Dismutase-2 (AtSOD2). The quantitative real-time PCR validated the computational prediction and expression for selected target genes AtSOD2, AtBXL2, and AtRCA along with ath-miRNA398b under endophytism. Overall, results indicate that miRNAs have a significant role in regulating Arabidopsis thaliana-endophytic fungal interaction.

MicroRNA analysis reveals 2 modules that antagonistically regulate xylem tracheary element development in Arabidopsis

Tracheary elements (TEs) are vital in the transport of various substances and contribute to plant growth. The differentiation of TEs is complex and regulated by a variety of microRNAs (miRNAs). However, the dynamic changes in miRNAs during each stage of TE differentiation remain unclear, and the miRNA regulatory network is not yet complete. This study employed Vascular cell Induction culture System Using Arabidopsis Leaves to profile the miRNome during TE differentiation in Arabidopsis (Arabidopsis thaliana) and established comprehensive miRNA co-expression networks functioning at the different stages of TE differentiation. Two negatively correlated modules exist in the miRNA networks, each exhibiting strong intra-module positive correlation and strong inter-module negative correlation. Thus, the 2 modules may play opposite roles in TE differentiation and vascular development. Indeed, we found that miR408 promotes cambium formation and TE differentiation, consistent with miR408 as a key node in the networks of fate determination and the initiation of TE differentiation. Additionally, we found that miR163 inhibits secondary cell wall formation and TE differentiation, corresponding to miR163 as a key node in the TE maturation network. Moreover, we discovered that the miRNA co-expression network in poplar (Populus tomentosa) xylem development is also composed of 2 negatively correlated modules that contain miRNAs orthologous to those in Arabidopsis. Therefore, the 2 negatively correlated modules of the miRNA co-expression network are likely conserved and fundamental to xylem TE differentiation. These results provide insights into microRNA regulation in plant development.

Characterization of tae-miR156(s) and their response to abiotic stress in wheat (Triticum aestivum L.)

The microRNA156 (miR156) has been widely studied in plants, however, the characterization of the miR156 family of genes in wheat and their expression patterns under abiotic stress are not completely clear. In this study, a total of 20 miR156 family members, referred to as tae-miR156a to tae-miR156t, were identified in wheat with their loci mapped to various chromosomes. These members were divided into five subgroups: miR156a/b/c/d/e/f, miR156g/h/i, miR156j/k, miR156l/m/n/o/p/q, and miR156r/s/t. They were highly conserved during evolution. The prediction of cis-elements in the tae-MIR156(s) promoter region revealed that the tae-MIR156(s) had diverse cis-acting elements; of these, 15 tae-MIR156(s) and 6 tae-MIR156(s) were found to be drought-responsive elements and cold-responsive elements, respectively. And the prediction target genes of tae-miR156(s) are mainly SPL transcription factor genes. Expression analysis based on quantitative real-time polymerase chain reaction (qRT‒PCR) showed that miR156(s) have different expression levels in the various wheat tissues, and the subgroups' response to abiotic stress varied. Among them, miR156g/h/i were strongly induced in the root of cold and heat stress, and miR156a/b/c/d/e/f were significantly increased in roots after drought stress, whereas miR156r/s/t were highly inhibited in leaves and roots after salt stress. These findings imply that tae-miR156(s) are involved in stress response in wheat, and they provide new fundamental knowledge for further analysis of the function of miR156 and its regulatory mechanism in response to abiotic stress.

In silico identification and characterization of microRNAs from rotifers, cladocerans, and copepods

MicroRNAs (miRNAs) are short non-coding RNA molecules that regulate post-transcription and influence various biological processes across species. Despite various studies of miRNAs in vertebrates, plants, and other organisms, miRNA data in aquatic invertebrates are insufficient. In this study, we identified miRNAs from four aquatic invertebrate species that are widely used in aquatic toxicology: the rotifer Brachionus koreanus, the water flea Daphnia magna, the cyclopoid copepod Paracyclopina nana, and the harpacticoid copepod Tigriopus japonicus, using next-generation sequencing and in silico analysis. We identified total 188, 41, 47, and 100 miRNAs from each species, and target genes were predicted based on 3'-untranslated region information. Target prediction and functional annotation results provided the biological processes of these miRNAs in various development-related mechanisms, signaling transduction, and metabolism-related pathways. Moreover, the network between the miRNAs and their targets concerning defense-related and antioxidant genes suggests the suitability of miRNAs as biomarkers in ecotoxicological studies.

Comprehensive identification of GASA genes in sunflower and expression profiling in response to drought

Drought stress poses a critical threat to global crop yields and sustainable agriculture. The GASA genes are recognized for their pivotal role in stress tolerance and plant growth, but little is known about how they function in sunflowers. The investigation aimed to identify and elucidate the role of HaGASA genes in conferring sunflowers with drought tolerance. Twenty-seven different HaGASA gene family members were found in this study that were inconsistently located across eleven sunflower chromosomes. Phylogeny analysis revealed that the sunflower HaGASA genes were divided into five subgroups by comparing GASA genes with those from Arabidopsis, peanut, and soybean, with members within each subgroup displaying similar conserved motifs and gene structures. In-silico evaluation of cis-regulatory elements indicated the existence of specific elements associated with stress-responsiveness being the most abundant, followed by hormone, light, and growth-responsive elements. Transcriptomic data from the NCBI database was utilized to assess the HaGASA genes expression profile in different sunflower varieties under drought conditions. The HaGASA genes expression across ten sunflower genotypes under drought stress, revealed 14 differentially expressed HaGASA genes, implying their active role in the plant's stress response. The expression in different organs revealed that HaGASA2, HaGASA11, HaGASA17, HaGASA19, HaGASA21 and HaGASA26 displayed maximum expression in the stem. Our findings implicate HaGASA genes in mediating sunflower growth maintenance and adaptation to abiotic stress, particularly drought. The findings, taken together, provided a basic understanding of the structure and potential functions of HaGASA genes, setting the framework for further functional investigations into their roles in drought stress mitigation and crop improvement strategies.

The microRNA408-plantacyanin module balances plant growth and drought resistance by regulating reactive oxygen species homeostasis in guard cells

The conserved microRNA (miRNA) miR408 enhances photosynthesis and compromises stress tolerance in multiple plants, but the cellular mechanism underlying its function remains largely unclear. Here, we show that in Arabidopsis (Arabidopsis thaliana), the transcript encoding the blue copper protein PLANTACYANIN (PCY) is the primary target for miR408 in vegetative tissues. PCY is preferentially expressed in the guard cells, and PCY is associated with the endomembrane surrounding individual chloroplasts. We found that the MIR408 promoter is suppressed by multiple abscisic acid (ABA)-responsive transcription factors, thus allowing PCY to accumulate under stress conditions. Genetic analysis revealed that PCY elevates reactive oxygen species (ROS) levels in the guard cells, promotes stomatal closure, reduces photosynthetic gas exchange, and enhances drought resistance. Moreover, the miR408-PCY module is sufficient to rescue the growth and drought tolerance phenotypes caused by gain- and loss-of-function of MYB44, an established positive regulator of ABA responses, indicating that the miR408-PCY module relays ABA signaling for regulating ROS homeostasis and drought resistance. These results demonstrate that miR408 regulates stomatal movement to balance growth and drought resistance, providing a mechanistic understanding of why miR408 is selected during land plant evolution and insights into the long-pursued quest of breeding drought-tolerant and high-yielding crops.

A multispecies study reveals the diversity and potential regulatory role of long noncoding RNAs in cucurbits

Plant long noncoding RNAs (lncRNAs) exhibit features such as tissue-specific expression, spatiotemporal regulation, and stress responsiveness. Although diverse studies support the regulatory role of lncRNAs in model plants, our knowledge about lncRNAs in crops is limited. We employ a custom pipeline on a dataset of over 1000 RNA-seq samples across nine representative species of the family Cucurbitaceae to predict 91 209 nonredundant lncRNAs. The lncRNAs were characterized according to three confidence levels and classified by their genomic context into intergenic, natural antisense, intronic, and sense-overlapping. Compared with protein-coding genes, lncRNAs were, on average, expressed at low levels and displayed significantly higher specificity when considering tissue, developmental stages, and stress responsiveness. The evolutionary analysis indicates higher positional conservation than sequence conservation, probably linked to the conserved modular motifs within syntenic lncRNAs. Moreover, a positive correlation between the expression of intergenic/natural antisense lncRNAs and their closest/parental gene was observed. For those intergenic, the correlation decreases with the distance to the neighboring gene, supporting that their potential cis-regulatory effect is within a short-range. Furthermore, the analysis of developmental studies showed that a conserved NAT-lncRNA family is differentially expressed in a coordinated way with their cognate sense protein-coding genes. These genes code for proteins associated with phloem development, thus providing insights about the potential involvement of some of the identified lncRNAs in a developmental process. We expect that this extensive inventory will constitute a valuable resource for further research lines focused on elucidating the regulatory mechanisms mediated by lncRNAs in cucurbits.

ANAgdb: a multi-omics and taxonomy database for ANA-grade

BACKGROUND

The ANA-grade, encompassing early-diverging angiosperm lineages, Amborellales, Nymphaeales, and Austrobaileyales, represents a fundamental phase in the evolutionary history of flowering plants. Since the completion of key assembly of the Amborella genome, the continuous influx of omics data from the lineage underscores the need for a specialized database.

RESULTS

Here, we introduce the ANA-grade Genome Database (ANAgdb, https://anagenome.cn/ ), which integrates multi-omics data including 11 genomes, 167 transcriptomes, and 10 miRNAomes, as well as extensive taxonomic details specific to the ANA-grade. Designed with an array of user-friendly tools, ANAgdb not only facilitates the effective storage, querying, and analysis of data but also enables the integration and dissemination of crucial genomic and taxonomic information.

CONCLUSION

By integrating the comprehensive resources and tools, ANAgdb aims to significantly advance research in phylogenomics and taxonomic studies, providing a robust platform for researchers to explore the genetic and morphological diversities of these ancient plant lineages.

Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures

The orthotospovirus capsicum chlorosis virus (CaCV) is an important pathogen affecting capsicum plants. Elevated temperatures may affect disease progression and pose a potential challenge to capsicum production. To date, CaCV-resistant capsicum breeding lines have been established; however, the impact of an elevated temperature of 35 °C on this genetic resistance remains unexplored. Thus, this study aimed to investigate how high temperature (HT) influences the response of CaCV-resistant capsicum to the virus. Phenotypic analysis revealed a compromised resistance in capsicum plants grown at HT, with systemic necrotic spots appearing in 8 out of 14 CaCV-infected plants. Molecular analysis through next-generation sequencing identified 105 known and 83 novel microRNAs (miRNAs) in CaCV-resistant capsicum plants. Gene ontology revealed that phenylpropanoid and lignin metabolic processes, regulated by Can-miR408a and Can- miR397, are likely involved in elevated-temperature-mediated resistance-breaking responses. Additionally, real-time PCR validated an upregulation of Can-miR408a and Can-miR397 by CaCV infection at HT; however, only the Laccase 4 transcript, targeted by Can-miR397, showed a tendency of negative correlation with this miRNA. Overall, this study provides the first molecular insights into how elevated temperature affects CaCV resistance in capsicum plants and reveals the potential role of miRNA in temperature-sensitive tospovirus resistance.

RiceMetaSys: Drought-miR, a one-stop solution for drought responsive miRNAs-mRNA module in rice

MicroRNAs are key players involved in stress responses in plants and reports are available on the role of miRNAs in drought stress response in rice. This work reports the development of a database, RiceMetaSys: Drought-miR, based on the meta-analysis of publicly available sRNA datasets. From 28 drought stress-specific sRNA datasets, we identified 216 drought-responsive miRNAs (DRMs). The major features of the database include genotype-, tissue- and miRNA ID-specific search options and comparison of genotypes to identify common miRNAs. Co-localization of the DRMs with the known quantitative trait loci (QTLs), i.e., meta-QTL regions governing drought tolerance in rice pertaining to different drought adaptive traits, narrowed down this to 37 promising DRMs. To identify the high confidence target genes of DRMs under drought stress, degradome datasets and web resource on drought-responsive genes (RiceMetaSys: DRG) were used. Out of the 216 unique DRMs, only 193 had targets with high stringent parameters. Out of the 1081 target genes identified by Degradome datasets, 730 showed differential expression under drought stress in at least one accession. To retrieve complete information on the target genes, the database has been linked with RiceMetaSys: DRG. Further, we updated the RiceMetaSys: DRGv1 developed earlier with the addition of DRGs identified from RNA-seq datasets from five rice genotypes. We also identified 759 putative novel miRNAs and their target genes employing stringent criteria. Novel miRNA search has all the search options of known miRNAs and additionally, it gives information on their in silico validation features. Simple sequence repeat markers for both the miRNAs and their target genes have also been designed and made available in the database. Network analysis of the target genes identified 60 hub genes which primarily act through abscisic acid pathway and jasmonic acid pathway. Co-localization of the hub genes with the meta-QTL regions governing drought tolerance narrowed down this to 16 most promising DRGs. Database URL: http://14.139.229.201/RiceMetaSys_miRNA Updated database of RiceMetaSys URL: http://14.139.229.201/RiceMetaSysA/Drought/.

Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize (Zea mays L.)

Deep sowing is an efficient strategy for maize to ensure the seedling emergence rate under adverse conditions such as drought or low temperatures. However, the genetic basis of deep-sowing tolerance-related traits in maize remains largely unknown. In this study, we performed a genome-wide association study on traits related to deep-sowing tolerance, including mesocotyl length (ML), coleoptile length (CL), plumule length (PL), shoot length (SL), and primary root length (PRL), using 255 maize inbred lines grown in three different environments. We identified 23, 6, 4, and 4 quantitative trait loci (QTLs) associated with ML, CL, PL, and SL, respectively. By analyzing candidate genes within these QTLs, we found a γ-tubulin-containing complex protein, ZmGCP2, which was significantly associated with ML, PL, and SL. Loss of function of ZmGCP2 resulted in decreased PL, possibly by affecting the cell elongation, thus affecting SL. Additionally, we identified superior haplotypes and allelic variations of ZmGCP2 with a longer PL and SL, which may be useful for breeding varieties with deep-sowing tolerance to improve maize cultivation.

Species-Specific miRNAs Contribute to the Divergence between Deciduous and Evergreen Species in Ilex

MicroRNAs (miRNAs) are pivotal regulators of gene expression, playing crucial roles in plant developmental processes and environmental responses. However, the function of miRNAs in influencing deciduous traits has been little explored. Here, we utilized sRNA-seq on two deciduous species, Ilex polyneura (Hand.-Mazz.) S. Y. Hu and Ilex asprella Champ. ex Benth., along with an evergreen species, Ilex latifolia Thunb., to identify and annotate miRNAs within these species. Our analysis revealed 162 species-specific miRNAs (termed SS-miRNAs) from 120 families, underscoring the fundamental roles and potential influence of SS-miRNAs on plant phenotypic diversity and adaptation. Notably, three SS-miRNAs in I. latifolia were found to target crucial genes within the abscission signaling pathway. Analysis of cis-regulatory elements suggested a novel regulatory relationship that may contribute to the evergreen phenotype of I. latifolia by modulating the abscission process in a light-independent manner. These findings propose a potential mechanism by which SS-miRNAs can influence the conserved abscission pathway, contributing to the phenotypic divergence between deciduous and evergreen species within the genus Ilex.

Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network

Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utilize expression data to identify the most physiologically relevant targets. Although these methods are effective, they typically require a large sample size and high-depth sequencing to detect potential miRNA-target pairs, thereby limiting their applicability in improving plant breeding. In this study, we propose a novel miRNA-target prediction framework named kmerPMTF (k-mer-based prediction framework for plant miRNA-target). Our framework effectively extracts the latent semantic embeddings of sequences by utilizing k-mer splitting and a deep self-supervised neural network. We construct multiple similarity networks based on k-mer embeddings and employ graph convolutional networks to derive deep representations of miRNAs and targets and calculate the probabilities of potential associations. We evaluated the performance of kmerPMTF on four typical plant datasets: Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, and Prunus persica. The results demonstrate its ability to achieve AUPRC values of 84.9%, 91.0%, 80.1%, and 82.1% in 5-fold cross-validation, respectively. Compared with several state-of-the-art existing methods, our framework achieves better performance on threshold-independent evaluation metrics. Overall, our study provides an efficient and simplified methodology for identifying plant miRNA-target associations, which will contribute to a deeper comprehension of miRNA regulatory mechanisms in plants.

Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.

Convergent and divergent evolution of microRNA-mediated regulation in metazoans

The evolution of microRNAs (miRNAs) has been studied extensively to understand their roles in gene regulation and evolutionary processes. This review focuses on how miRNA-mediated regulation has evolved in bilaterian animals, highlighting both convergent and divergent evolution. Since animals and plants display significant differences in miRNA biogenesis and target recognition, the 'independent origin' hypothesis proposes that miRNA pathways in these groups independently evolved from the RNA interference (RNAi) pathway, leading to modern miRNA repertoires through convergent evolution. However, recent evidence raises the alternative possibility that the miRNA pathway might have already existed in the last common ancestor of eukaryotes, and that the differences in miRNA pathway and miRNA repertoires among animal and plant lineages arise from lineage-specific innovations and losses of miRNA pathways, miRNA acquisition, and loss of miRNAs after eukaryotic divergence. The repertoire of miRNAs has considerably expanded during bilaterian evolution, primarily through de novo creation and duplication processes, generating new miRNAs. Although ancient functionally established miRNAs are rarely lost, many newly emerged miRNAs are transient and lineage specific, following a birth-death evolutionary pattern aligning with the 'out-of-the-testis' and 'transcriptional control' hypotheses. Our focus then shifts to the convergent molecular evolution of miRNAs. We summarize how miRNA clustering and seed mimicry contribute to this phenomenon, and we review how miRNAs from different sources converge to degrade maternal messenger RNAs (mRNAs) during animal development. Additionally, we describe how miRNAs evolve across species due to changes in sequence, seed shifting, arm switching, and spatiotemporal expression patterns, which can result in variations in target sites among orthologous miRNAs across distant strains or species. We also provide a summary of the current understanding regarding how the target sites of orthologous miRNAs can vary across strains or distantly related species. Although many paralogous miRNAs retain their seed or mature sequences after duplication, alterations can occur in the seed or mature sequences or expression patterns of paralogous miRNAs, leading to functional diversification. We discuss our current understanding of the functional divergence between duplicated miRNAs, and illustrate how the functional diversification of duplicated miRNAs impacts target site evolution. By investigating these topics, we aim to enhance our current understanding of the functions and evolutionary dynamics of miRNAs. Additionally, we shed light on the existing challenges in miRNA evolutionary studies, particularly the complexity of deciphering the role of miRNA-mediated regulatory network evolution in shaping gene expression divergence and phenotypic differences among species.

Genome-wide identification and characterization of protein phosphatase 2C (PP2C) gene family in sunflower (Helianthus annuus L.) and their expression profiles in response to multiple abiotic stresses

Plant protein phosphatase 2C (PP2C) plays vital roles in responding to various stresses, stimulating growth factors, phytohormones, and metabolic activities in many important plant species. However, the PP2C gene family has not been investigated in the economically valuable plant species sunflower (Helianthus annuus L.). This study used comprehensive bioinformatics tools to identify and characterize the PP2C gene family members in the sunflower genome (H. annuus r1.2). Additionally, we analyzed the expression profiles of these genes using RNA-seq data under four different stress conditions in both leaf and root tissues. A total of 121 PP2C genes were identified in the sunflower genome distributed unevenly across the 17 chromosomes, all containing the Type-2C phosphatase domain. HanPP2C genes are divided into 15 subgroups (A-L) based on phylogenetic tree analysis. Analyses of conserved domains, gene structures, and motifs revealed higher structural and functional similarities within various subgroups. Gene duplication and collinearity analysis showed that among the 53 HanPP2C gene pairs, 48 demonstrated segmental duplications under strong purifying selection pressure, with only five gene pairs showing tandem duplications. The abundant segmental duplication was observed compared to tandem duplication, which was the major factor underlying the dispersion of the PP2C gene family in sunflowers. Most HanPP2C proteins were localized in the nucleus, cytoplasm, and chloroplast. Among the 121 HanPP2C genes, we identified 71 miRNAs targeting 86 HanPP2C genes involved in plant developmental processes and response to abiotic stresses. By analyzing cis-elements, we identified 63 cis-regulatory elements in the promoter regions of HanPP2C genes associated with light responsiveness, tissue-specificity, phytohormone, and stress responses. Based on RNA-seq data from two sunflower tissues (leaf and root), 47 HanPP2C genes exhibited varying expression levels in leaf tissue, while 49 HanPP2C genes showed differential expression patterns in root tissue across all stress conditions. Transcriptome profiling revealed that nine HanPP2C genes (HanPP2C12, HanPP2C36, HanPP2C38, HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73) exhibited higher expression in leaf tissue, and five HanPP2C genes (HanPP2C13, HanPP2C47, HanPP2C48, HanPP2C54, and HanPP2C95) showed enhanced expression in root tissue in response to the four stress treatments, compared to the control conditions. These results suggest that these HanPP2C genes may be potential candidates for conferring tolerance to multiple stresses and further detailed characterization to elucidate their functions. From these candidates, 3D structures were predicted for six HanPP2C proteins (HanPP2C47, HanPP2C48, HanPP2C53, HanPP2C54, HanPP2C59, and HanPP2C73), which provided satisfactory models. Our findings provide valuable insights into the PP2C gene family in the sunflower genome, which could play a crucial role in responding to various stresses. This information can be exploited in sunflower breeding programs to develop improved cultivars with increased abiotic stress tolerance.

Genome-wide analysis of plant specific YABBY transcription factor gene family in carrot (Dacus carota) and its comparison with Arabidopsis

YABBY gene family is a plant-specific transcription factor with DNA binding domain involved in various functions i.e. regulation of style, length of flowers, and polarity development of lateral organs in flowering plants. Computational methods were utilized to identify members of the YABBY gene family, with Carrot (Daucus carota) 's genome as a foundational reference. The structure of genes, location of the chromosomes, protein motifs and phylogenetic investigation, syntony and transcriptomic analysis, and miRNA targets were analyzed to unmask the hidden structural and functional characteristics YABBY gene family in Carrots. In the following research, it has been concluded that 11 specific YABBY genes irregularly dispersed on all 9 chromosomes and proteins assembled into five subgroups i.e. AtINO, AtCRC, AtYAB5, AtAFO, and AtYAB2, which were created on the well-known classification of Arabidopsis. The wide ranges of YABBY genes in carrots were dispersed due to segmental duplication, which was detected as prevalent when equated to tandem duplication. Transcriptomic analysis showed that one of the DcYABBY genes was highly expressed during anthocyanin pigmentation in carrot taproots. The cis-regulatory elements (CREs) analysis unveiled elements that particularly respond to light, cell cycle regulation, drought induce ability, ABA hormone, seed, and meristem expression. Furthermore, a relative study among Carrot and Arabidopsis genes of the YABBY family indicated 5 sub-families sharing common characteristics. The comprehensive evaluation of YABBY genes in the genome provides a direction for the cloning and understanding of their functional properties in carrots. Our investigations revealed genome-wide distribution and role of YABBY genes in the carrots with best-fit comparison to Arabidopsis thaliana.

Augmenting tomato functional genomics with a genome-wide induced genetic variation resource

Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.

Genome-wide in-silico analysis of ethylene biosynthesis gene family in Musa acuminata L. and their response under nutrient stress

Ethylene is a gaseous phytohormone involved in plants' growth and developmental processes, including seed germination, root initiation, fruit ripening, flower and leaf senescence, abscission, and stress responses. Ethylene biosynthesis (EB) gene analysis in response to nitrogen (N) and potassium (K) stress has not yet been conducted in Musa acuminata (banana) roots. The genome mining of banana (Musa acuminata L.) revealed 14 putative 1-aminocyclopropane-1-carboxylate synthase (ACS), 10 1-aminocyclopropane-1-carboxylate oxidase (ACO), and 3 Ethylene overproducer 1 (ETO1) genes. ACS, ACO, and ETO1 proteins possessed amino acid residues ranging from 422-684, 636-2670, and 893-969, respectively, with molecular weight (Mw) ranging from 4.93-7.55 kD, 10.1-8.3 kD and 10.1-10.78 kD. The number of introns present in ACS, ACO, and ETO1 gene sequences ranges from 0-14, 1-6, and 0-6, respectively. The cis-regulatory element analysis revealed the presence of light-responsive, abscisic acid, seed regulation, auxin-responsive, gibberellin element, endosperm-specific, anoxic inducibility, low-temperature responsiveness, salicylic acid responsiveness, meristem-specific and stress-responsive elements. Comprehensive phylogenetic analyses ACS, ACO, and ETO1 genes of Banana with Arabidopsis thaliana revealed several orthologs and paralogs assisting in understanding the putative functions of these genes. The expression profile of Musa acuminata genes in root under normal and low levels of nitrogen and potassium shows that MaACS14 and MaACO6 expressed highly at normal nitrogen supply. MaACS1 expression was significantly upregulated at low potassium levels, whereas, MaACO6 gene expression was significantly downregulated. The functional divergence and site-specific selective pressures on specific gene sequences of banana have been investigated. The bioinformatics-based genome-wide assessment of the family of banana attempted in the present study could be a significant step for deciphering novel ACS, ACO, and ETO1 genes based on genome-wide expression profiling.

Genome wide identification and characterization of the amino acid transporter (AAT) genes regulating seed protein content in chickpea (Cicer arietinum L.)

Amino acid transporters (AATs), besides, being a crucial component for nutrient partitioning system are also vital for growth and development of the plants and stress resilience. In order to understand the role of AAT genes in seed quality proteins, a comprehensive analysis of AAT gene family was carried out in chickpea leading to identification of 109 AAT genes, representing 10 subfamilies with random distribution across the chickpea genome. Several important stress responsive cis-regulatory elements like Myb, ABRE, ERE were detected in the promoter region of these CaAAT genes. Most of the genes belonging to the same sub-families shared the intron-exon distribution pattern owing to their conserved nature. Random distribution of these CaAAT genes was observed on plasma membrane, vacuolar membrane, Endoplasmic reticulum and Golgi membranes, which may be associated to distinct biochemical pathways. In total 92 out 109 CaAAT genes arise as result of duplication, among which segmental duplication was more prominent over tandem duplication. As expected, the phylogenetic tree was divided into 2 major clades, and further sub-divided into different sub-families. Among the 109 CaAAT genes, 25 were found to be interacting with 25 miRNAs, many miRNAs like miR156, miR159 and miR164 were interacting only with single AAT genes. Tissues specific expression pattern of many CaAAT genes was observed like CaAAP7 and CaAVT18 in nodules, CaAAP17, CaAVT5 and CaCAT9 in vegetative tissues while CaCAT10 and CaAAP23 in seed related tissues as per the expression analysis. Mature seed transcriptome data revealed that genotypes having high protein content (ICC 8397, ICC 13461) showed low CaAATs expression as compared to the genotypes having low protein content (FG 212, BG 3054). Amino acid profiling of these genotypes revealed a significant difference in amount of essential and non-essential amino acids, probably due to differential expression of CaAATs. Thus, the present study provides insights into the biological role of AAT genes in chickpea, which will facilitate their functional characterization and role in various developmental stages, stress responses and involvement in nutritional quality enhancement.

Conserved structured domains in plant non-coding RNA enod40, their evolution and recruitment of sequences from transposable elements

Plant long noncoding RNA enod40 is involved in the regulation of symbiotic associations with bacteria, in particular, in nitrogen-fixing root nodules of legumes, and with fungi in phosphate-acquiring arbuscular mycorrhizae formed by various plants. The presence of enod40 genes in plants that do not form such symbioses indicates its other roles in cell physiology. The molecular mechanisms of enod40 RNA function are poorly understood. Enod40 RNAs form several structured domains, conserved to different extents. Due to relatively low sequence similarity, identification of enod40 sequences in plant genomes is not straightforward, and many enod40 genes remain unannotated even in complete genomes. Here, we used comparative structure analysis and sequence similarity searches in order to locate enod40 genes and determine enod40 RNA structures in nitrogen-fixing clade plants and in grasses. The structures combine conserved features with considerable diversity of structural elements, including insertions of structured domain modules originating from transposable elements. Remarkably, these insertions contain sequences similar to tandem repeats and several stem-loops are homologous to microRNA precursors.

Non-coding RNAs (ncRNAs) in plant: Master regulators for adapting to extreme temperature conditions

Unusual daily temperature fluctuations caused by climate change and climate variability adversely impact agricultural crop production. Since plants are immobile and constantly receive external environmental signals, such as extreme high (heat) and low (cold) temperatures, they have developed complex molecular regulatory mechanisms to cope with stressful situations to sustain their natural growth and development. Among these mechanisms, non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), small-interfering RNAs (siRNAs), and long-non-coding RNAs (lncRNAs), play a significant role in enhancing heat and cold stress tolerance. This review explores the pivotal findings related to miRNAs, siRNAs, and lncRNAs, elucidating how they functionally regulate plant adaptation to extreme temperatures. In addition, this review addresses the challenges associated with uncovering these non-coding RNAs and understanding their roles in orchestrating heat and cold tolerance in plants.

Small RNA profiling reveals that an ovule-specific microRNA, cja-miR5179, targets a B-class MADS-box gene in Camellia japonica

BACKGROUND AND AIMS

The functional specialization of microRNA and its target genes is often an important factor in the establishment of spatiotemporal patterns of gene expression that are essential to plant development and growth. In different plant lineages, understanding the functional conservation and divergence of microRNAs remains to be explored.

METHODS

To identify small regulatory RNAs underlying floral patterning, we performed a tissue-specific profiling of small RNAs in various floral organs from single and double flower varieties (flowers characterized by multiple layers of petals) in Camellia japonica. We identified cja-miR5179, which belongs to a deeply conserved microRNA family that is conserved between angiosperms and basal plants but frequently lost in eudicots. We characterized the molecular function of cja-miR5179 and its target - a B-function MADS-box gene - through gene expression analysis and transient expression assays.

KEY RESULTS

We showed that cja-miR5179 is exclusively expressed in ovule tissues at the early stage of floral development. We found that cja-miR5179 targets the coding sequences of a DEFICIENS-like B-class gene (CjDEF) mRNA, which is located in the K motif of the MADS-box domain; and the target sites of miR5179/MADS-box were consistent in Camellia and orchids. Furthermore, through a petal transient-expression assay, we showed that the BASIC PENTACYSTEINE proteins bind to the GA-rich motifs in the cja-miR5179 promoter region and suppresses its expression.

CONCLUSIONS

We propose that the regulation between miR5179 and a B-class MADS-box gene in C. japonica has a deep evolutionary origin before the separation of monocots and dicots. During floral development of C. japonica, cja-miR5179 is specifically expressed in the ovule, which may be required for the inhibition of CjDEF function. This work highlights the evolutionary conservation as well as functional divergence of small RNAs in floral development.

Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses

Glycolate oxidase (GLO) is an FMN-containing enzyme localized in peroxisomes and performs in various molecular and biochemical mechanisms. It is a key player in plant glycolate and glyoxylate accumulation pathways. The role of GLO in disease and stress resistance is well-documented in various plant species. Although studies have been conducted regarding the role of GLO genes from spinach on a microbial level, the direct response of GLO genes to various stresses in short-season and leafy plants like lettuce has not been published yet. The genome of Lactuca sativa cultivar 'Salinas' (v8) was used to identify GLO gene members in lettuce by performing various computational analysis. Dual synteny, protein-protein interactions, and targeted miRNA analyses were conducted to understand the function of GLO genes. The identified GLO genes showed further clustering into two groups i.e., glycolate oxidase (GOX) and hydroxyacid oxidase (HAOX). Genes were observed to be distributed unevenly on three chromosomes, and syntenic analysis revealed that segmental duplication was prevalent. Thus, it might be the main reason for GLO gene diversity in lettuce. Almost all LsGLO genes showed syntenic blocks in respective plant genomes under study. Protein-protein interactions of LsGLO genes revealed various functional enrichments, mainly photorespiration, and lactate oxidation, and among biological processes oxidative photosynthetic carbon pathway was highly significant. Results of in-depth analyses disclosed the interaction of GLO genes with other members of the glycolate pathway and the activity of GLO genes in various organs and developmental stages in lettuce. The extensive genome evaluation of GLO gene family in garden lettuce is believed to be a reference for cloning and studying functional analyses of GLO genes and characterizing other members of glycolate/glyoxylate biosynthesis pathway in various plant species.

MicroRNA 4407 modulates nodulation in soybean by repressing a root-specific ISOPENTENYLTRANSFERASE (GmIPT3)

MicroRNAs (miRNAs) are important regulators of plant biological processes, including soybean nodulation. One miRNA, miR4407, was identified in soybean roots and nodules. However, the function of miR4407 in soybean is still unknown. MiR4407, unique to soybean, positively regulates lateral root emergence and root structures and represses a root-specific ISOPENTENYLTRANSFERASE (GmIPT3). By altering the expression of miR4407 and GmIPT3, we investigated the role of miR4407 in lateral root and nodule development. Both miR4407 and GmIPT3 are expressed in the inner root cortex and nodule primordia. Upon rhizobial inoculation, miR4407 was downregulated while GmIPT3 was upregulated. Overexpressing miR4407 reduced the number of nodules in transgenic soybean hairy roots while overexpressing the wild-type GmIPT3 or a miR4407-resistant GmIPT3 mutant (mGmIPT3) significantly increased the nodule number. The mechanism of miR4407 and GmIPT3 functions was also linked to autoregulation of nodulation (AON), where miR4407 overexpression repressed miR172c and activated its target, GmNNC1, turning on AON. Exogenous CK mimicked the effects of GmIPT3 overexpression on miR172c, supporting the notion that GmIPT3 regulates nodulation by enhancing root-derived CK. Overall, our data revealed a new miRNA-mediated regulatory mechanism of nodulation in soybean. MiR4407 showed a dual role in lateral root and nodule development.

Global transcriptome analysis reveals fungal disease responsive core gene regulatory landscape in tea

Fungal infections are the inevitable limiting factor for productivity of tea. Transcriptome reprogramming recruits multiple regulatory pathways during pathogen infection. A comprehensive meta-analysis was performed utilizing previously reported, well-replicated transcriptomic datasets from seven fungal diseases of tea. The study identified a cumulative set of 18,517 differentially expressed genes (DEGs) in tea, implicated in several functional clusters, including the MAPK signaling pathway, transcriptional regulation, and the biosynthesis of phenylpropanoids. Gene set enrichment analyses under each pathogen stress elucidated that DEGs were involved in ethylene metabolism, secondary metabolism, receptor kinase activity, and various reactive oxygen species detoxification enzyme activities. Expressional fold change of combined datasets highlighting 2258 meta-DEGs shared a common transcriptomic response upon fungal stress in tea. Pervasive duplication events caused biotic stress-responsive core DEGs to appear in multiple copies throughout the tea genome. The co-expression network of meta-DEGs in multiple modules demonstrated the coordination of appropriate pathways, most of which involved cell wall organization. The functional coordination was controlled by a number of hub genes and miRNAs, leading to pathogenic resistance or susceptibility. This first-of-its-kind meta-analysis of host-pathogen interaction generated consensus candidate loci as molecular signatures, which can be associated with future resistance breeding programs in tea.

Evaluation of efficacy of non-coding RNA in abiotic stress management of field crops: Current status and future prospective

Abiotic stresses are responsible for the major losses in crop yield all over the world. Stresses generate harmful ROS which can impair cellular processes in plants. Therefore, plants have evolved antioxidant systems in defence against the stress-induced damages. The frequency of occurrence of abiotic stressors has increased several-fold due to the climate change experienced in recent times and projected for the future. This had particularly aggravated the risk of yield losses and threatened global food security. Non-coding RNAs are the part of eukaryotic genome that does not code for any proteins. However, they have been recently found to have a crucial role in the responses of plants to both abiotic and biotic stresses. There are different types of ncRNAs, for example, miRNAs and lncRNAs, which have the potential to regulate the expression of stress-related genes at the levels of transcription, post-transcription, and translation of proteins. The lncRNAs are also able to impart their epigenetic effects on the target genes through the alteration of the status of histone modification and organization of the chromatins. The current review attempts to deliver a comprehensive account of the role of ncRNAs in the regulation of plants' abiotic stress responses through ROS homeostasis. The potential applications ncRNAs in amelioration of abiotic stresses in field crops also have been evaluated.

Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine

The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families. These models are available in our tool MirMachine, which annotates conserved microRNAs within genomes. We successfully applied MirMachine to a range of animal species, including those with large genomes and genome duplications and extinct species, where small RNA sequencing is hard to achieve. We further describe a microRNA score of expected microRNAs that can be used to assess the completeness of genome assemblies. MirMachine closes a long-persisting gap in the microRNA field by facilitating automated genome annotation pipelines and deeper studies into the evolution of genome regulation, even in extinct organisms.

Cadmium induced a non-coding RNA microRNA535 mediates Cd accumulation in rice

Identifying key regulators related to cadmium (Cd) tolerance and accumulation is the main factor for genetic engineering to improve plants for bioremediation and ensure crop food safety. MicroRNAs (miRNAs), as fine-tuning regulators of genes, participate in various abiotic stress processes. MiR535 is an ancient conserved non-coding small RNA in land plants, positively responding to Cd stress. We investigated the effects of knocking out (mir535) and overexpressing miR535 (mir535 and OE535) under Cd stress in rice plants in this study. The mir535 plants showed better Cd tolerance than wild type (WT), whereas the OE535 showed the opposite effect. Cd accumulated approximately 71.9% and 127% in the roots of mir535 and OE535 plants, respectively, compared to WT, after exposure to 2 µmol/L Cd. In brown rice, the total Cd accumulation of OE535 and mir535 was about 78% greater and 35% lower than WT. When growing in 2 mg/kg Cd of soil, the Cd concentration was significantly lower in mir535 and higher in OE535 than in the WT; afterward, we further revealed the most possible target gene SQUAMOSA promoter binding-like transcription factor 7(SPL7) and it negatively regulates Nramp5 expression, which in turn regulates Cd metabolism. Therefore, the CRISPR/Cas9 technology may be a valuable strategy for creating new rice varieties to ensure food safety.

The Progression in Developing Genomic Resources for Crop Improvement

Sequencing technologies have rapidly evolved over the past two decades, and new technologies are being continually developed and commercialized. The emerging sequencing technologies target generating more data with fewer inputs and at lower costs. This has also translated to an increase in the number and type of corresponding applications in genomics besides enhanced computational capacities (both hardware and software). Alongside the evolving DNA sequencing landscape, bioinformatics research teams have also evolved to accommodate the increasingly demanding techniques used to combine and interpret data, leading to many researchers moving from the lab to the computer. The rich history of DNA sequencing has paved the way for new insights and the development of new analysis methods. Understanding and learning from past technologies can help with the progress of future applications. This review focuses on the evolution of sequencing technologies, their significant enabling role in generating plant genome assemblies and downstream applications, and the parallel development of bioinformatics tools and skills, filling the gap in data analysis techniques.

Overexpression of Sly-miR398b Compromises Disease Resistance against Botrytis cinerea through Regulating ROS Homeostasis and JA-Related Defense Genes in Tomato

MicroRNAs (miRNAs) have been shown to be critical components in plant immunity. MicroRNA398 (miR398) is a highly conserved miRNA in all land plants and plays crucial roles in diverse biotic stress responses. However, the role of miR398 has not yet been characterized in tomato resistance against Botrytis cinerea. In this report, the transcript levels of sly-miR398b were strongly decreased in B. cinerea-infected leaves and the overexpression of sly-miR398b resulted in enhanced susceptibility. The attenuated expression of cytosol Cu/Zn-SOD (CSD1), chloroplast Cu/Zn-SOD (CSD2), and guaiacol peroxidase (GPOD), as well as the decreased activities of superoxide dismutase (SOD) and GPOD, collectively led to increased hydrogen peroxide (H₂O₂) accumulation in sly-miR398b overexpressing plants. Furthermore, sly-miR398b was induced by methyl jasmonate (MeJA) treatment. The overexpression of sly-miR398b suppressed the expression of TomLoxD, LapA, and PR-STH2 in response to B. cinerea and MeJA treatment. Our data demonstrate that sly-miR398b overexpression negatively regulates the resistance to B. cinerea in tomato by inducing the accumulation of reactive oxygen species (ROS) and downregulating the expression of MeJA-responsive defense genes.

Genome-wide identification and expression profiling of two-component system (TCS) genes in Brassica oleracea in response to shade stress

The Two-component system (TCS) consists of Histidine kinases (HKs), Phosphotransfers (HPs), and response regulator (RR) proteins. It has an important role in signal transduction to respond to a wide variety of abiotic stresses and hence in plant development. Brassica oleracea (cabbage) is a leafy vegetable, which is used for food and medicinal purposes. Although this system was identified in several plants, it had not been identified in Brassica oleracea yet. This genome-wide study identified 80 BoTCS genes consisting of 21 HKs, 8 HPs, 39 RRs, and 12 PRRs. This classification was done based on conserved domains and motif structure. Phylogenetic relationships of BoTCS genes with Arabidopsis thaliana, Oryza sativa, Glycine max, and Cicer arietinum showed conservation in TCS genes. Gene structure analysis revealed that each subfamily had conserved introns and exons. Both tandem and segmental duplication led to the expansion of this gene family. Almost all of the HPs and RRs were expanded through segmental duplication. Chromosomal analysis showed that BoTCS genes were dispersed across all nine chromosomes. The promoter regions of these genes were found to contain a variety of cis-regulatory elements. The 3D structure prediction of proteins also confirmed the conservation of structure within subfamilies. MicroRNAs (miRNAs) involved in the regulation of BoTCSs were also predicted and their regulatory roles were also evaluated. Moreover, BoTCSs were docked with abscisic acid to evaluate their binding. RNA-seq-based expression analysis and validation by qRT-PCR showed significant variation of expression for BoPHYs, BoERS1.1, BoERS2.1, BoERS2.2, BoRR10.2, and BoRR7.1 suggesting their importance in stress response. These genes showing unique expression can be further used in manipulating the plant's genome to make the plant more resistant the environmental stresses which will ultimately help in the increase of plant's yield. More specifically, these genes have altered expression in shade stress which clearly indicates their importance in biological functions. These findings are important for future functional characterization of TCS genes in generating stress-responsive cultivars.

Long non-coding RNA and microRNA landscape of two major domesticated cotton species

Allotetraploid cotton plants Gossypium hirsutum and Gossypium barbadense have been widely cultivated for their natural, renewable textile fibres. Even though ncRNAs in domesticated cotton species have been extensively studied, systematic identification and annotation of lncRNAs and miRNAs expressed in various tissues and developmental stages under various biological contexts are limited. This influences the comprehension of their functions and future research on these cotton species. Here, we report high confidence lncRNAs and miRNA collection from G. hirsutum accession and G. barbadense accession using large-scale RNA-seq and small RNA-seq datasets incorporated into a user-friendly database, CoNCRAtlas. This database provides a wide range and depth of lncRNA and miRNA annotation based on the systematic integration of extensive annotations such as expression patterns derived from transcriptome data analysis in thousands of samples, as well as multi-omics annotations. We assume this comprehensive resource will accelerate evolutionary and functional studies in ncRNAs and inform future breeding programs for cotton improvement. CoNCRAtlas is accessible at http://www.nipgr.ac.in/CoNCRAtlas/.

The Potential of CRISPR/Cas Technology to Enhance Crop Performance on Adverse Soil Conditions

Worldwide food security is under threat in the actual scenery of global climate change because the major staple food crops are not adapted to hostile climatic and soil conditions. Significant efforts have been performed to maintain the actual yield of crops, using traditional breeding and innovative molecular techniques to assist them. However, additional strategies are necessary to achieve the future food demand. Clustered regularly interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology, as well as its variants, have emerged as alternatives to transgenic plant breeding. This novelty has helped to accelerate the necessary modifications in major crops to confront the impact of abiotic stress on agriculture systems. This review summarizes the current advances in CRISPR/Cas applications in crops to deal with the main hostile soil conditions, such as drought, flooding and waterlogging, salinity, heavy metals, and nutrient deficiencies. In addition, the potential of extremophytes as a reservoir of new molecular mechanisms for abiotic stress tolerance, as well as their orthologue identification and edition in crops, is shown. Moreover, the future challenges and prospects related to CRISPR/Cas technology issues, legal regulations, and customer acceptance will be discussed.

Genome-Wide Characterization and Expression Analysis of Transcription Factor Families in Desert Moss Syntrichia caninervis under Abiotic Stresses

Transcription factor (TF) families play important roles in plant stress responses. S. caninervis is a new model moss for plant desiccation tolerance studies. Here, we report a high-confidence identification and characterization of 591 TFs representing 52 families that covered all chromosomes in S. caninervis. GO term and KEGG pathway analysis showed that TFs were involved in the regulation of transcription, DNA-templated, gene expression, binding activities, plant hormone signal transduction, and circadian rhythm. A number of TF promoter regions have a mixture of various hormones-related cis-regulatory elements. AP2/ERF, bHLH, MYB, and C2H2-zinc finger TFs were the overrepresented TF families in S. caninervis, and the detailed classification of each family is performed based on structural features. Transcriptome analysis revealed the transcript abundances of some ScAP2/ERF, bHLH, MYB, and C2H2 genes were accumulated in the treated S. caninervis under cold, dehydration, and rehydration stresses. The RT-qPCR results strongly agreed with RNA-seq analysis, indicating these TFs might play a key role in S. caninervis response to abiotic stress. Our comparative TF characterization and classification provide the foundations for functional investigations of the dominant TF genes involved in S. caninervis stress response, as well as excellent stress tolerance gene resources for plant stress resistance breeding.

Network of miR396-mRNA in Tissue Differentiation in Moso Bamboo (Phyllostachys edulis)

MiR396 plays an essential role in various developmental processes. However, the miR396-mRNA molecular network in bamboo vascular tissue differentiation during primary thickening has not been elucidated. Here, we revealed that three of the five members from the miR396 family were overexpressed in the underground thickening shoots collected from Moso bamboo. Furthermore, the predicted target genes were up/down-regulated in the early (S2), middle (S3) and late (S4) developmental samples. Mechanistically, we found that several of the genes encoding protein kinases (PKs), growth-regulating factors (GRF), transcription factors (TFs), and transcription regulators (TRs) were the potential targets of miR396 members. Moreover, we identified QLQ (Gln, Leu, Gln) and WRC (Trp, Arg, Cys) d omains in five PeGRF homologs and a Lipase_3 domain and a K_trans domain in another two potential targets, where the cleavage targets were identified via degradome sequencing (p < 0.05). The sequence alignment indicated many mutations in the precursor sequence of miR396d between Moso bamboo and rice. Our dual-luciferase assay revealed that ped-miR396d-5p binds to a PeGRF6 homolog. Thus, the miR396-GRF module was associated with Moso bamboo shoot development. Fluorescence in situ hybridization localized miR396 in the vascular tissues of the leaves, stems, and roots of pot Moso bamboo seedlings at the age of two months. Collectively, these experiments revealed that miR396 functions as a regulator of vascular tissue differentiation in Moso bamboo. Additionally, we propose that miR396 members are targets for bamboo improvement and breeding.

PmliHFM: Predicting Plant miRNA-lncRNA Interactions with Hybrid Feature Mining Network

Due to the crucial role of interactions between microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in biological processes, the study of their biological functions is necessary. So far, the various computational methods have been employed to make predictions of the miRNA-lncRNA interaction, which compensate for the inadequacy of biological experiments. However, the existing methods do not consider the differences between miRNA and lncRNA in feature extraction. In this paper, we propose a hybrid feature mining network, named PmliHFM, for predicting plant miRNA-lncRNA interactions. Firstly, miRNA and lncRNA with different sequence lengths are encoded by different encodings, which can reduce the loss of information caused by using the same coding approach. Then, a hybrid feature mining network is designed to adapt to different encoding methods and extract more useful feature information than a single network. Finally, an ensemble module is utilized to integrate the training results of the hybrid feature mining network, while a prediction module is employed to determine whether there are interactions. By testing on multiple test sets, PmliHFM outperforms several state-of-the-art approaches. The results show that the AUC of PmliHFM achieves 0.8[Formula: see text], 3.1[Formula: see text] and 0.4[Formula: see text] improvement respectively on three balanced datasets, and achieves 2.1[Formula: see text] and 1.8[Formula: see text] improvement respectively on two imbalanced datasets. These experiments demonstrate the feasibility of the proposed method.

Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling

The mantled phenotype is an abnormal somaclonal variant arising from the oil palm cloning process and severe phenotypes lead to oil yield losses. Hypomethylation of the Karma retrotransposon within the B-type MADS-box EgDEF1 gene has been associated with this phenotype. While abnormal Karma-EgDEF1 hypomethylation was detected in mantled clones, we examined the methylation state of Karma in ortets that gave rise to high mantling rates in their clones. Small RNAs (sRNAs) were proposed to play a role in Karma hypomethylation as part of the RNA-directed DNA methylation process, hence differential expression analysis of sRNAs between the ortet groups was conducted. While no sRNA was differentially expressed at the Karma-EgDEF1 region, three sRNA clusters were differentially regulated in high-mantling ortets. The first two down-regulated clusters were possibly derived from long non-coding RNAs while the third up-regulated cluster was derived from the intron of a DnaJ chaperone gene. Several predicted mRNA targets for the first two sRNA clusters conversely displayed increased expression in high-mantling relative to low-mantling ortets. These predicted mRNA targets may be associated with defense or pathogenesis response. In addition, several differentially methylated regions (DMRs) were identified in Karma and its surrounding regions, mainly comprising subtle CHH hypomethylation in high-mantling ortets. Four of the 12 DMRs were located in a region corresponding to hypomethylated areas at the 3'end of Karma previously reported in mantled clones. Further investigations on these sRNAs and DMRs may indicate the predisposition of certain ortets towards mantled somaclonal variation.

Sly-miR398 Participates in Cadmium Stress Acclimation by Regulating Antioxidant System and Cadmium Transport in Tomato (Solanum lycopersicum)

Cadmium (Cd) pollution is one of the major threats in agricultural production, and can cause oxidative damage and growth limitation in plants. MicroRNA398 (miR398) is involved in plant resistance to different stresses, and the post-transcriptional regulation of miR398 on CSDs plays a key role. Here, we report that miR398 was down-regulated in tomato in response to Cd stress. Simultaneously, CSD1 and SOD were up-regulated, with CSD2 unchanged, suggesting CSD1 is involved in miR398-induced regulation under Cd stress. In addition, the role of miR398 in Cd tolerance in tomato was evaluated using a transgenic line overexpressing MIR398 (miR398#OE) in which the down-expression of miR398 was disrupted. The results showed that Cd stress induced more significant growth inhibition, oxidative damage, and antioxidant enzymes disorder in miR398#OE than that in wild type (WT). Moreover, higher Cd concentration in the shoot and xylem sap, and net Cd influx rate, were observed in miR398#OE, which could be due to the increased Cd uptake genes (IRT1, IRT2, and NRAMP2) and decreased Cd compartmentalization gene HMA3. Overall, our results indicate that down-regulated miR398 plays a protective role in tomato against Cd stress by modulating the activity of antioxidant enzymes and Cd uptake and translocation.