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.

A transcription factor complex in Dictyostelium enables adaptive changes in macropinocytosis during the growth-to-development transition.

Macropinocytosis, an evolutionarily conserved endocytic pathway, mediates nonselective bulk uptake of extracellular fluid. It is the primary route for axenic Dictyostelium cells to obtain nutrients and has also emerged as a nutrient-scavenging pathway for mammalian cells. How cells adjust macropinocytic activity in various physiological or developmental contexts remains to be elucidated. We discovered that, in Dictyostelium cells, the transcription factors Hbx5 and MybG form a functional complex in the nucleus to maintain macropinocytic activity during the growth stage. In contrast, during starvation-induced multicellular development, the transcription factor complex undergoes nucleocytoplasmic shuttling in response to oscillatory cyclic adenosine 3',5'-monophosphate (cAMP) signals, which leads to increased cytoplasmic retention of the complex and progressive downregulation of macropinocytosis. Therefore, by coupling macropinocytosis-related gene expression to the cAMP oscillation system, which facilitates long-range cell-cell communication, the dynamic translocation of the Hbx5-MybG complex orchestrates a population-level adjustment of macropinocytic activity to adapt to changing environmental conditions.

WRKY transcription factors in Arachis hypogaea and its donors: From identification to function prediction.

WRKY transcription factors (TFs) play important roles in plant growth and development and responses to abiotic and biotic stresses. Since the initial isolation of a WRKY TF in Ipomoea batatas in 1994, WRKY TFs have been identified in plants, protozoa, and fungi. Peanut (Arachis hypogaea) is a key oil and protein crop for humans and a forage source for animal consumption. Several Arachis genomes have been sequenced and genome-wide WRKY TFs have been identified. In this review, we summarized WRKY TFs and their functions in A. hypogaea and its donors. We also standardized the nomenclature for Arachis WRKY TFs to ensure uniformity. We determined the evolutionary relationships between Arachis and Arabidopsis thaliana WRKY (AtWRKY) TFs using a phylogenetic analysis. Biological functions and regulatory networks of Arachis WRKY TFs were predicted using AtWRKY TFs. Thus, this review paves the way for studies of Arachis WRKY TFs.

A Smartphone-Based Sensing for Portable and Sensitive Visual Detection of Hg (II) via Nitrogen Doped Carbon Quantum Dots Modified Paper Strip.

The development of portable and cost-effective sensing system for Hg2+ quantitation is highly demanded for environmental monitoring. Herein, an on-site, rapid and portable smartphone readout device based Hg2+ sensing system integrating nitrogen-doped carbon quantum dots (NCDs) modified paper strip was proposed, and the physicochemical properties of NCDs were characterized by high resolution TEM, FTIR, UV-vis absorption spectrum and fluorescence spectral analysis. The modified paper strip was prepared via "ink-jet" printing technology and exhibits sensitive fluorescence response to Hg2+ with fluorescence color of bright blue (at the excitation/emission wavelength of 365/440 nm). This portable smartphone-based sensing platform is highly selective and sensitive to Hg2+ with the limit of detection (LOD) of 10.6 nM and the concentration range of 0-130 nM. In addition, the recoveries of tap water and local lake water were in the range of 89.4% to 109%. The cost-effective sensing system based on smartphone shows a great potential for trace amounts of Hg2+ monitoring in environmental water samples.

LettuceGDB: The community database for lettuce genetics and omics.

As a globally popular leafy vegetable and a representative plant of the Asteraceae family, lettuce has great economic and academic significance. In the last decade, high-throughput sequencing, phenotyping, and other multi-omics data in lettuce have accumulated on a large scale, thus increasing the demand for an integrative lettuce database. Here, we report the establishment of a comprehensive lettuce database, LettuceGDB (https://www.lettucegdb.com/). As an omics data hub, the current LettuceGDB includes two reference genomes with detailed annotations; re-sequencing data from over 1000 lettuce varieties; a collection of more than 1300 worldwide germplasms and millions of accompanying phenotypic records obtained with manual and cutting-edge phenomics technologies; re-analyses of 256 RNA sequencing datasets; a complete miRNAome; extensive metabolite information for representative varieties and wild relatives; epigenetic data on the genome-wide chromatin accessibility landscape; and various lettuce research papers published in the last decade. Five hierarchically accessible functions (Genome, Genotype, Germplasm, Phenotype, and O-Omics) have been developed with a user-friendly interface to enable convenient data access. Eight built-in tools (Assembly Converter, Search Gene, BLAST, JBrowse, Primer Design, Gene Annotation, Tissue Expression, Literature, and Data) are available for data downloading and browsing, functional gene exploration, and experimental practice. A community forum is also available for information sharing, and a summary of current research progress on different aspects of lettuce is included. We believe that LettuceGDB can be a comprehensive functional database amenable to data mining and database-driven exploration, useful for both scientific research and lettuce breeding.

Identification of Species-Specific MicroRNAs Provides Insights into Dynamic Evolution of MicroRNAs in Plants.

MicroRNAs (miRNAs) are an important class of regulatory small RNAs that program gene expression, mainly at the post-transcriptional level. Although sporadic examples of species-specific miRNAs (termed SS-miRNAs) have been reported, a genome-scale study across a variety of distant species has not been assessed. Here, by comprehensively analyzing miRNAs in 81 plant species phylogenetically ranging from chlorophytes to angiosperms, we identified 8048 species-specific miRNAs from 5499 families, representing over 61.2% of the miRNA families in the examined species. An analysis of the conservation from different taxonomic levels supported the high turnover rate of SS-miRNAs, even over short evolutionary distances. A comparison of the intrinsic features between SS-miRNAs and NSS-miRNAs (non-species-specific miRNAs) indicated that the AU content of mature miRNAs was the most striking difference. Our data further illustrated a significant bias of the genomic coordinates towards SS-miRNAs lying close to or within genes. By analyzing the 125,267 putative target genes for the 7966 miRNAs, we found the preferentially regulated functions of SS-miRNAs related to diverse metabolic processes. Collectively, these findings underscore the dynamic evolution of miRNAs in the species-specific lineages.

Miniature Inverted-repeat Transposable Elements Drive Rapid MicroRNA Diversification in Angiosperms.

MicroRNAs (miRNAs) are fast evolving endogenous small RNAs that regulate organism function and behavior in both animals and plants. Although models for de novo miRNA biogenesis have been proposed, the genomic mechanisms driving swift diversification of the miRNA repertoires in plants remain elusive. Here, by comprehensively analyzing 21 phylogenetically representative plant species, ranging from green algae to angiosperms, we systematically identified de novo miRNA events associated with 8,649 miRNA loci. We found that 399 (4.6%), 466 (5.4%), and 1,402 (16.2%) miRNAs were derived from inverted gene duplication events, long terminal repeats of retrotransposons, and miniature inverted-repeat transposable elements (MITEs), respectively. Among the miRNAs of these origins, MITEs, especially those belonging to the Mutator, Tc1/Mariner, and PIF/Harbinger superfamilies, were the predominant genomic source for de novo miRNAs in the 15 examined angiosperms but not in the six non-angiosperms. Our data further illustrated a transposition-transcription process by which MITEs are converted into new miRNAs (termed MITE-miRNAs) whereby properly sized MITEs are transcribed and therefore become potential substrates for the miRNA processing machinery by transposing into introns of active genes. By analyzing the 58,038 putative target genes for the 8,095 miRNAs, we found that the target genes of MITE-miRNAs were preferentially associated with response to environmental stimuli such as temperature, suggesting that MITE-miRNAs are pertinent to plant adaptation. Collectively, these findings demonstrate that molecular conversion of MITEs is a genomic mechanism leading to rapid and continuous changes to the miRNA repertoires in angiosperm.

The carboxy terminal transmembrane domain of SPL7 mediates interaction with RAN1 at the endoplasmic reticulum to regulate ethylene signalling in Arabidopsis.

In Arabidopsis, copper (Cu) transport to the ethylene receptor ETR1 mediated using RAN1, a Cu transporter located at the endoplasmic reticulum (ER), and Cu homeostasis mediated using SPL7, the key Cu-responsive transcription factor, are two deeply conserved vital processes. However, whether and how the two processes interact to regulate plant development remain elusive. We found that its C-terminal transmembrane domain (TMD) anchors SPL7 to the ER, resulting in dual compartmentalisation of the transcription factor. Immunoprecipitation coupled mass spectrometry, yeast-two-hybrid assay, luciferase complementation imaging and subcellular co-localisation analyses indicate that SPL7 interacts with RAN1 at the ER via the TMD. Genetic analysis revealed that the ethylene-induced triple response was significantly compromised in the spl7 mutant, a phenotype rescuable by RAN1 overexpression but not by SPL7 without the TMD. The genetic interaction was corroborated by molecular analysis showing that SPL7 modulates RAN1 abundance in a TMD-dependent manner. Moreover, SPL7 is feedback regulated by ethylene signalling via EIN3, which binds the SPL7 promoter and represses its transcription. These results demonstrate that ER-anchored SPL7 constitutes a cellular mechanism to regulate RAN1 in ethylene signalling and lay the foundation for investigating how Cu homeostasis conditions ethylene sensitivity in the developmental context.

De novo genes in Arachis hypogaea cv. Tifrunner: systematic identification, molecular evolution, and potential contributions to cultivated peanut.

De novo genes are derived from non-coding sequences, and they can play essential roles in organisms. Cultivated peanut (Arachis hypogaea) is a major oil and protein crop derived from a cross between Arachis duranensis and Arachis ipaensis. However, few de novo genes have been documented in Arachis. Here, we identified 381 de novo genes in A. hypogaea cv. Tifrunner based on comparison with five closely related Arachis species. There are distinct differences in gene expression patterns and gene structures between conserved and de novo genes. The identified de novo genes originated from ancestral sequence regions associated with metabolic and biosynthetic processes, and they were subsequently integrated into existing regulatory networks. De novo paralogs and homoeologs were identified in A. hypogaea cv. Tifrunner. De novo paralogs and homoeologs with conserved expression have mismatching cis-acting elements under normal growth conditions. De novo genes potentially have pluripotent functions in responses to biotic stresses as well as in growth and development based on quantitative trait locus data. This work provides a foundation for future research examining gene birth processes and gene function in Arachis and related taxa.

Oligopeptide transporter Slc15A modulates macropinocytosis in Dictyostelium by maintaining intracellular nutrient status.

Macropinocytosis mediates non-selective bulk uptake of extracellular fluid. It is the major route by which axenic Dictyostelium cells obtain nutrients and has emerged as a nutrient-scavenging pathway in mammalian cells. How environmental and cellular nutrient status modulates macropinocytic activity is not well understood. By developing a high-content imaging-based genetic screen in Dictyostelium discoideum we identified Slc15A, an oligopeptide transporter located at the plasma membrane and early macropinosome, as a novel macropinocytosis regulator. We show that deletion of slc15A but not two other related slc15 genes, leads to reduced macropinocytosis, reduced cell growth and aberrantly increased autophagy in cells grown in nutrient-rich medium. Expression of Slc15A protein or supplying cells with free amino acids rescues these defects. In contrast, expression of transport-defective Slc15A or supplying cells with amino acids in their di-peptide forms fails to rescue these defects. Therefore, Slc15A modulates the level of macropinocytosis by maintaining the intracellular availability of key amino acids through extraction of oligopeptides from the early macropinocytic pathway. We propose that Slc15A constitutes part of a positive feedback mechanism coupling cellular nutrient status and macropinocytosis. This article has an associated First Person interview with the first authors of the paper.

PmiREN2.0: from data annotation to functional exploration of plant microRNAs.

Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named 'PmiREN Community' was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.

Genome-Wide Characterization of SPL Gene Family in Codonopsis pilosula Reveals the Functions of CpSPL2 and CpSPL10 in Promoting the Accumulation of Secondary Metabolites and Growth of C. pilosula Hairy Root.

SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors play critical roles in regulating diverse aspects of plant growth and development, including vegetative phase change, plant architecture, anthocyanin accumulation, lateral root growth, etc. In the present study, 15 SPL genes were identified based on the genome data of Codonopsis pilosula, a well-known medicinal plant. Phylogenetic analysis clustered CpSPLs into eight groups (G1-G8) along with SPLs from Arabidopsis thaliana, Solanum lycopersicum, Oryza sativa and Physcomitrella patens. CpSPLs in the same group share similar gene structure and conserved motif composition. Cis-acting elements responding to light, stress and phytohormone widely exist in their promoter regions. Our qRT-PCR results indicated that 15 CpSPLs were differentially expressed in different tissues (root, stem, leaf, flower and calyx), different developmental periods (1, 2 and 3 months after germination) and various conditions (NaCl, MeJA and ABA treatment). Compared with the control, overexpression of CpSPL2 or CpSPL10 significantly promoted not only the growth of hairy roots, but also the accumulation of total saponins and lobetyolin. Our results established a foundation for further investigation of CpSPLs and provided novel insights into their biological functions. As far as we know, this is the first experimental research on gene function in C. pilosula.

MicroRNA775 regulates intrinsic leaf size and reduces cell wall pectin levels by targeting a galactosyltransferase gene in Arabidopsis.

Plants possess unique primary cell walls made of complex polysaccharides that play critical roles in determining intrinsic cell and organ size. How genes responsible for synthesizing and modifying the polysaccharides in the cell wall are regulated by microRNAs (miRNAs) to control plant size remains largely unexplored. Here we identified 23 putative cell wall-related miRNAs, termed as CW-miRNAs, in Arabidopsis thaliana and characterized miR775 as an example. We showed that miR775 post-transcriptionally silences GALT9, which encodes an endomembrane-located galactosyltransferase belonging to the glycosyltransferase 31 family. Over-expression of miR775 and deletion of GALT9 led to significantly enlarged leaf-related organs, primarily due to increased cell size. Monosaccharide quantification, confocal Raman imaging, and immunolabeling combined with atomic force microscopy revealed that the MIR775A-GALT9 circuit modulates pectin levels and the elastic modulus of the cell wall. We also showed that MIR775A is directly repressed by the transcription factor ELONGATED HYPOCOTYL5 (HY5). Genetic analysis confirmed that HY5 is a negative regulator of leaf size that acts through the HY5-MIR775A-GALT9 repression cascade to control pectin levels. These findings demonstrate that miR775-regulated cell wall remodeling is an integral determinant of intrinsic leaf size in A. thaliana. Studying other CW-miRNAs would provide more insights into cell wall biology.

The PIF1-miR408-PLANTACYANIN repression cascade regulates light-dependent seed germination.

Light-dependent seed germination is a vital process for many seed plants. A decisive event in light-induced germination is degradation of the central repressor PHYTOCHROME INTERACTING FACTOR 1 (PIF1). The balance between gibberellic acid (GA) and abscisic acid (ABA) helps to control germination. However, the cellular mechanisms linking PIF1 turnover to hormonal balancing remain elusive. Here, employing far-red light-induced Arabidopsis thaliana seed germination as the experimental system, we identified PLANTACYANIN (PCY) as an inhibitor of germination. It is a blue copper protein associated with the vacuole that is both highly expressed in mature seeds and rapidly silenced during germination. Molecular analyses showed that PIF1 binds to the miR408 promoter and represses miR408 accumulation. This in turn posttranscriptionally modulates PCY abundance, forming the PIF1-miR408-PCY repression cascade for translating PIF1 turnover to PCY turnover during early germination. Genetic analysis, RNA-sequencing, and hormone quantification revealed that PCY is necessary and sufficient to maintain the PIF1-mediated seed transcriptome and the low-GA-high-ABA state. Furthermore, we found that PCY domain organization and regulation by miR408 are conserved features in seed plants. These results revealed a cellular mechanism whereby PIF1-relayed external light signals are converted through PCY turnover to internal hormonal profiles for controlling seed germination.

PmiREN: a comprehensive encyclopedia of plant miRNAs.

MicroRNAs (miRNAs) are small non-coding RNA molecules that function as diverse endogenous gene regulators at the post-transcriptional level. In the past two decades, as research effort on miRNA identification, function and evolution has soared, so has the demand for miRNA databases. However, the current plant miRNA databases suffer from several typical drawbacks, including a lack of entries for many important species, uneven annotation standards across different species, abundant questionable entries, and limited annotation. To address these issues, we developed a knowledge-based database called Plant miRNA Encyclopedia (PmiREN, http://www.pmiren.com/), which was based on uniform processing of sequenced small RNA libraries using miRDeep-P2, followed by manual curation using newly updated plant miRNA identification criteria, and comprehensive annotation. PmiREN currently contains 16,422 high confidence novel miRNA loci in 88 plant species and 3,966 retrieved from miRBase. For every miRNA entry, information on precursor sequence, precursor secondary structure, expression pattern, clusters and synteny in the genome, potential targets supported by Parallel Analysis of RNA Ends (PARE) sequencing, and references is attached whenever possible. PmiREN is hierarchically accessible and has eight built-in search engines. We believe PmiREN is useful for plant miRNA cataloguing and data mining, therefore a resource for data-driven miRNA research in plants.

Evolutionary balance between LRR domain loss and young NBS-LRR genes production governs disease resistance in Arachis hypogaea cv. Tifrunner.

BACKGROUND: Cultivated peanut (Arachis hypogaea L.) is an important oil and protein crop, but it has low disease resistance; therefore, it is important to reveal the number, sequence features, function, and evolution of genes that confer resistance. Nucleotide-binding site-leucine-rich repeats (NBS-LRRs) are resistance genes that are involved in response to various pathogens. RESULTS: We identified 713 full-length NBS-LRRs in A. hypogaea cv. Tifrunner. Genetic exchange events occurred on NBS-LRRs in A. hypogaea cv. Tifrunner, which were detected in the same subgenomes and also found in different subgenomes. Relaxed selection acted on NBS-LRR proteins and LRR domains in A. hypogaea cv. Tifrunner. Using quantitative trait loci (QTL), we found that NBS-LRRs were involved in response to late leaf spot, tomato spotted wilt virus, and bacterial wilt in A. duranensis (2 NBS-LRRs), A. ipaensis (39 NBS-LRRs), and A. hypogaea cv. Tifrunner (113 NBS-LRRs). In A. hypogaea cv. Tifrunner, 113 NBS-LRRs were classified as 75 young and 38 old NBS-LRRs, indicating that young NBS-LRRs were involved in response to disease after tetraploidization. However, compared to A. duranensis and A. ipaensis, fewer LRR domains were found in A. hypogaea cv. Tifrunner NBS-LRR proteins, partly explaining the lower disease resistance of the cultivated peanut. CONCLUSIONS: Although relaxed selection acted on NBS-LRR proteins and LRR domains, LRR domains were preferentially lost in A. hypogaea cv. Tifrunner compared to A. duranensis and A. ipaensis. The QTL results suggested that young NBS-LRRs were important for resistance against diseases in A. hypogaea cv. Tifrunner. Our results provid insight into the greater susceptibility of A. hypogaea cv. Tifrunner to disease compared to A. duranensis and A. ipaensis.

The Complete Mitogenome of Pyrrhocoris tibialis (Hemiptera: Pyrrhocoridae) and Phylogenetic Implications.

We determined the complete mitogenome of Pyrrhocoris tibialis (Hemiptera: Heteroptera: Pyrrhocoridae) to better understand the diversity and phylogeny within Pentatomomorpha, which is the second largest infra-order of Heteroptera. Gene content, gene arrangement, nucleotide composition, codon usage, ribosomal RNA (rRNA) structures, and sequences of the mitochondrial transcription termination factor were well conserved in Pyrrhocoroidea. Different protein-coding genes have been subject to different evolutionary rates correlated with the G + C content. The size of control regions (CRs) was highly variable among mitogenomes of three sequenced Pyrrhocoroidea species, with the P. tibialis CR being the largest. All the transfer RNA genes found in Pyrrhocoroidea had the typical clover leaf secondary structure, except for trnS1 (AGN), which lacked the dihydrouridine arm and possessed an unusual anticodon stem (9 bp vs. the normal 5 bp). A total of three different phylogenetic relationships among the five super-families of Pentatomomorpha were obtained using three analytical methods (MrBayes and RAxML under site-homogeneous models and PhyloBayes under a site-heterogeneous CAT + GTR model) and two mitogenomic datasets (nucleotides and amino acids). The tree topology test using seven methods statistically supported a phylogeny of (Aradoidea + (Pentatomoidea + (Lygaeoidea + (Pyrrhocoroidea + Coreoidea)))) as the best topology, as recognized by both RAxML and MrBayes based on the two datasets.

Genome-wide identification of LRR-containing sequences and the response of these sequences to nematode infection in Arachis duranensis.

BACKGROUND: Leucine-rich repeat (LRR)-containing genes are involved in responses to various diseases. Recently, RNA-seq data from A. duranensis after nematode (Meloidogyne arenaria) infection were released. However, the number of LRR-containing genes present in A. duranensis and the response of LRR-containing genes to nematode infection are poorly understood. RESULTS: In this study, we found 509 amino acid sequences containing nine types of LRR domains in A. duranensis. The inferred phylogenetic relationships revealed that the nine types of LRR domains had two originations. The inferred selective pressure was mainly consistent with LRR domains undergoing purifying selection. Twenty-one LRR-containing genes were associated with possible resistance to nematode infection after 3, 6, and 9 days. Among them, Aradu.T5WNW, Aradu.JM17V, and Aradu.MKP1A were up-regulate at these three time points, while Aradu.QD5DS and Aradu.M0ENQ were up-regulated 6 and 9 days after nematode infection. The expression of the above mentioned five genes was significantly and negatively correlated with the number of LRR8 domain, indicating that fewer LRR8 domains are associated with the promotion of LRR-containing genes that resist nematode infection. Patterns of co-expression and cis-acting elements indicated that WRKY possibly regulate the responses of LRR-containing genes to nematode infection and that expansin genes may work together with LRR-containing genes in response to nematode infection. CONCLUSIONS: We identified the number and type of LRR-containing genes in A. duranensis. The LRR-containing genes that were found appear to be involved in responses to nematode infection. The number of LRR8 domains was negatively correlated with expression after nematode infection. The WRKY transcription factor may regulate resistance to nematode infection based on LRR-containing genes. Our results could improve the understanding of resistance to nematodes and molecular breeding in peanuts.