Plant Direct最新文献

This study presents three genome assemblies within the Capsicum genus, enabling comprehensive comparative analyses for the Annuum and Baccatum complexes within the genus. We produced highly continuous assemblies of the nuclear genomes and complete chloroplast assemblies. Subsequent genome annotation identified 34,580 genes in nonpungent C. annuum cv. ECW, and 32,704 and 33,994 genes in pungent C. chacoense and C. galapagoense, respectively. These assemblies, including the first complete genomes for C. chacoense and C. galapagoense, provide additional genomic resolution within the Capsicum genus. The novel genomes were analyzed within a pangenomic framework, integrating 16 Capsicum genomes across the Annuum, Baccatum, and Pubescens complexes. Homology grouping was used to identify core, accessory and unique genes and showed a wide spectrum of genetic diversity, particularly in homology groups exclusive to C. chacoense and C. galapagoense. Out of 79,267 homology groups identified, 13% were core groups, present in all accessions, corresponding to approximately 30% of core genes per genome. Comparative analyses revealed distinct species and genus-specific genomic characteristics. Additionally, we used the graph pangenome to illustrate locus-level exploration by examining the Pun1 locus associated with capsaicinoid biosynthesis, identifying multiple Pun1-like genes including their genomic position and homology information. The integration of these new resources into a dynamic Capsicum pangenome framework provides a versatile platform for extracting genetic information relevant to both fundamental research and breeding applications.

Drought stress, which is exacerbated by climate change, is a major contributor to crop production losses in rainfed agriculture. Two genotypes of cowpea (Vigna unguiculata, (L.) Walp.) with determinate (IT-16) and indeterminate (IT-96D-610) growth patterns were grown either well-watered or subjected to drought stress at vegetative and flowering stages in a pot experiment in a glasshouse. Stomatal conductance (g_s) and soil moisture were measured daily during the drought stress periods, while chlorophyll fluorescence data were collected every third day. Both genotypes maintained relatively high-water content (RWC > 80%), indicating dehydration avoidance; however, IT-96D-610 consistently maintained a higher RWC than IT-16. Under drought stress, IT-96D-610 exhibited lower g_s and less sensitive stomata, greater total root length, root surface area and a higher root-to-shoot ratio compared to IT-16. These traits were associated with higher seed yield and water productivity in IT-96D-610 than in IT-16. In contrast to IT-96D-610, genotype IT-16 showed higher photosynthetic efficiency, indicated by higher F_q'/F_m' and qP, and produced more biomass, but with reduced grain yield. This study underscores the importance of selecting traits for dehydration avoidance, such as RWC, deep-fine roots and moderated stomatal conductance, in cowpea breeding programs aimed at improving productivity under drought conditions.

Distyly is a reproductive system, characterized by the presence of two floral morphs, which promotes outcrossing via physical and biochemical means. In distylous Turnera, the mating type of the S-morph is determined by two genes: YUC6 (male) and BAHD (female). Despite the importance of these S-genes, it is likely that additional genes are involved in the distylous syndrome. Here, we use comparative mass spectrometry analysis to identify differentially expressed proteins in a series of self-compatible mutants and wildtype distylous members of Turnera. Our analysis identified a member of the Glutathione S-transferase family that overwhelmingly correlated with L-morph male mating type. Exploration of the large datasets and previously published work led to the proposal that differential ROS levels in the pistil may contribute towards the self-incompatibility response. To support this hypothesis, we generated a co-expression network for whole flower buds from self-compatible and WT Turnera joelii. This network led to the identification of a series of ROS and auxin-related genes that correlated with self-compatibility. We update previously proposed SI response models to reflect how ROS, jasmonic acid, and brassinosteroid signaling likely establish the S-morph female self-incompatibility response. Overall, this work has identified genes potentially related to self-compatibility and has provided a foundation for future empirical work investigating the basis of the SI response in Turnera.

Trichomes are found on almost all terrestrial plants and are derived from epidermal cells. Nonglandular trichomes (NGTs) protect plants from environmental stress, such as pest and pathogen invasion, reduce water loss, and increase resistance to abiotic stressors, including UV radiation, cold, and extreme temperatures. Trichomes provide an excellent model system for studying the growth and differentiation of plant cells. Although several such genes that govern the specification and patterning of trichomes have been molecularly characterized in a few model plants, including Arabidopsis thaliana, most aspects of trichome initiation remain unclear. In this review, we summarize the structural and morphological characteristics of NGTs in diverse crops as well as report recent investigations providing insights into the regulation of NGT formation in plants. We also discuss how NGTs help plants resist various abiotic factors that impose multiple stresses on plant life. This review provides a foundation for understanding the valuable role of NGTs in protecting plants from multiple stresses.

Crossover recombination is a pivotal event that takes place during meiosis of germinal cells, leading to the rearrangement of parental chromosomes and generating novel allele combinations, thereby enhancing genetic diversity. This process holds significant importance for plant breeders as it enables the transfer of gene variants from one variety to another. Recent studies have explored diverse strategies to predict recombination events along chromosomes in key plant species, employing various types of genome features. In this study, the relationship between genome structure, quantified using k-mers, and crossover recombination is investigated. To facilitate this analysis, the Python package kmerExtractor is introduced; it uses frequency chaos game representation (FCGR) to count k-mers from genome fasta files and adds them as column features for subsequent analysis. This package is used to explore the genomes of one model and five crop plant species, namely, Arabidopsis, bean, maize, rice, sorghum, and tomato. The investigation reveals both positive and negative trends between 3-mers, 2-mers, and recombination rates. Furthermore, the information derived from k-mers was used to train regression-based machine learning models for predicting recombination rates along chromosomes. The results demonstrate the efficacy of using k-mer for predicting purposes, particularly for sorghum and tomato datasets, highlighting linear relationships between several k-mers and recombination events. We hope that this predictive strategy based on genomic sequence information can be useful for the development of new plant crosses.

Seseli tomentosum Vis. is an endemic species distributed along the eastern coast of the Adriatic Sea. In this study, the leaf structure as observed by light and electron microscopy, the phytochemical composition of the volatile organic compounds, and the cytotoxic activity of S. tomentosum are presented. The secretory ducts located above and within the phloem and below the xylem part of the vascular bundle represent the first description of the leaf secretory structures of S. tomentosum. The essential oil and hydrosol were extracted from air-dried leaves by Clevenger distillation and analyzed by gas chromatography-mass spectrometry, combined with headspace solid-phase microextraction of volatiles from the hydrosol and fresh plant material. α-Amorphene, β-caryophyllene, germacrene D, β-cadinene, and α-copaene were the most abundant sesquiterpenes in the essential oil and fresh plant material. Among the monoterpenes, α-pinene was most abundant in the essential oil, limonene in fresh plant material, and α-terpineol in the hydrosol. Moderate cytotoxic activity of the methanolic extract of S. tomentosum, with higher inhibition of cell division observed in the human cervical cancer and osteosarcoma cell lines, and weaker activity in the healthy retinal pigmented epithelial and colon cancer cell lines, was detected using the MTS-based assay. With these results, we aim to highlight the potential of endemic plants, emphasizing the importance of studying species such as S. tomentosum and their contributions to biodiversity and human health as sources of bioactive compounds.

SnRK1 is an evolutionarily conserved protein kinase belonging to the SNF1/AMPK family of protein kinases that is central to adjusting growth in response to the energy status. Numerous studies have shown adaptive and developmental roles of SnRK1, but the understanding of the SnRK1 signaling network in monocots is limited. Using CRISPR/Cas9 mutagenesis to target the functional kinase subunits in rice, we carried out comprehensive phenotypic, transcriptomic, proteomic, and phosphoproteomic analyses of rice snrk1 mutants displaying growth defects under normal and starvation conditions. These analyses revealed the role of SnRK1 signaling in controlling growth and stress-related processes in both energy-sufficient and energy-limited conditions and pointed to the subfunctionalization of SnRK1 kinase subunit genes. In addition to the classical protein targets of SnRK1, phosphoproteomics revealed novel targets including the key components of intracellular membrane trafficking, ethylene signaling, and ion transport. The upregulation of stress-related processes and suppression of growth-related processes in snrk1 mutants correlated with their phenotypic defects. Overall, this study highlights a dual role of SnRK1 as a promoter of growth under favorable conditions and a critical regulator of adaptive response under stress conditions.

One class of enzymes that plant pathogens employ to manipulate innate immunity and physiology of the infected cells is host-targeted ADP-ribosyltransferases. The bacterial pathogen Pseudomonas syringae uses its Type III secretion system to inject several effector proteins with ADP-ribosyltransferase activity into plant cells. One of them, AvrRpm1, ADP-ribosylates the plasma membrane-associated RPM1-INTERACTING PROTEIN 4 (RIN4) in Glycine max and Arabidopsis thaliana to attenuate targeted secretion of defense-promoting compounds. Substrate identification of host-targeted ADP-ribosyltransferases is complicated by the biochemical lability of the protein modification during plant protein extraction and in several cases requires prior knowledge of plant immune signaling pathways that are impaired by the ADP-ribosylating Type III effector. Using the AvrRpm1-RIN4 pair as a proof of concept, we present an untargeted proteomics workflow for enrichment and detection of ADP-ribosylated proteins and peptides from plant cell extracts that in several cases provides site resolution for the modification.

The reproductive cycle of interior lodgepole pine spans approximately 26 months, with seed cones initiating in late summer, followed by pollen conelets emerging the next spring when pollination occurs. Fertilization and cone maturation occur in the subsequent spring and fall. Successful pollination, critical for seed conelet retention, requires an ~80% success rate. In June 2020, 30 pine clones (genotypes), with contrasting conelet abortion rates, were selected from a production seed orchard in Alberta, Canada. Sixty conelets per clone (30 aborted and 30 healthy) were collected for synchrotron radiation-based microcomputed tomography (SR-μCT) analysis. A subset of two contrasting clones (1401 and 596) was selected for detailed study. Conelets were transported to the Canadian Light Source in Saskatoon, Saskatchewan, for SR-μCT Phase Contrast Imaging (PCI), where samples were mounted and scanned using a PCO Edge 5.5 sCMOS camera and analyzed using Avizo software to visualize internal structures. Results showed that healthy conelets in clones 1401 and 596 had greater tissue volume (248.8 and 251.9 mm³, respectively) and more organized cavity spaces than aborted conelets (64.7 and 102.1 mm³, respectively), with differential internal air space volume (clone 1401: 8.7 mm³ in aborted vs. 17.5 mm³ in healthy; clone 596: 6.9 mm³ in aborted vs. 11.5 mm³ in healthy). Overall, SR-μCT imaging demonstrated significant advantages over traditional methods of visualization by providing a nondestructive, high-resolution analysis of internal structures. In addition, this technology enhances our understanding of pine reproductive processes, improving management practices in seed orchards-the delivery system for tree improvement programs.

This beginner's guide is intended for plant biologists new to network analysis. Here, we introduce key concepts and resources for researchers interested in incorporating network analysis into research, either as a stand-alone component for generating hypotheses or as a framework for examining and visualizing experimental results. Network analysis provides a powerful tool to predict gene functions. Advances in and reduced costs for systems biology techniques, such as genomics, transcriptomics, and proteomics, have generated abundant omics data for plants; however, the functional annotation of plant genes lags. Therefore, predictions from network analysis can be a starting point to annotate genes and ultimately elucidate genotype-phenotype relationships. In this paper, we introduce networks and compare network-building resources available for plant biologists, including databases and software for network analysis. We then compare four databases available for plant biologists in more detail: AraNet, GeneMANIA, ATTED-II, and STRING. AraNet and GeneMANIA are functional association networks, ATTED-II is a gene coexpression database, and STRING is a protein-protein interaction database. AraNet and ATTED-II are plant-specific databases that can analyze multiple plant species, whereas GeneMANIA builds networks for Arabidopsis thaliana and nonplant species and STRING for multiple species. Finally, we compare the performance of the four databases in predicting known and probable gene functions of the A. thaliana Nuclear Factor-Y (NF-Y) genes. We conclude that plant biologists have an invaluable resource in these databases and discuss how users can decide which type of database to use depending on their research question.