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Frontiers in Genetics 2024Small RNAs (sRNAs) are important non-coding RNA regulators that play key roles in the development and pathogenesis of plant pathogens, as well as in other biological...
Small RNAs (sRNAs) are important non-coding RNA regulators that play key roles in the development and pathogenesis of plant pathogens, as well as in other biological processes. However, whether these abundant and varying sRNAs are involved in development or infection remains enigmatic. In this study, sRNA sequencing of 4 asexual stages of (), namely, as mycelia (HY), sporangia (SP), zoospores (ZO), cysts (CY), and pepper infected with (IN), were performed, followed by sRNA analysis, microRNA (miRNA) identification, and miRNA target prediction. sRNAs were mainly distributed at 25-26 nt in HY, SP, and ZO but distributed at 18-34 nt in CY and IN. 92, 42, 176, 39, and 148 known miRNAs and 15, 19, 54, 13, and 1 novel miRNA were identified in HY, SP, ZO, CY, and IN, respectively. It was found that the expression profiles of known miRNAs vary greatly at different stages and could be divided into 4 categories. Novel miRNAs mostly belong to part I. Gene ontology (GO) analysis of known miRNA-targeting genes showed that they are involved in the catalytic activity pathway, binding function, and other biological processes. Kyoto Encyclopedia of Gene and Genome (KEGG) analysis of novel miRNA-targeting genes showed that they are involved in the lysine degradation pathway. The expression of candidate miRNAs was validated using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), and miRNAs were downregulated in or mutants. To further explore the function of the detected miRNAs, the precursor of a novel miRNA, miR91, was knockout by CRISPR-Cas9, the mutants displayed decreased mycelial growth, sporangia production, and zoospore production. It was found that 503142 (Inositol polyphosphate 5-phosphatase and related proteins) can be predicted as a target of miR91, and the interaction between miR91 and 503142 was verified using the tobacco transient expression system. Overall, our results indicate that the diverse and differentially expressed sRNAs are involved in the development and pathogenesis of
PubMed: 38919951
DOI: 10.3389/fgene.2024.1296533 -
AIMS Microbiology 2024In this study, we used 16S rRNA gene sequence analysis to describe the diversity of cultivable endophytic bacteria associated with fennel ( Mill.) and determined their...
In this study, we used 16S rRNA gene sequence analysis to describe the diversity of cultivable endophytic bacteria associated with fennel ( Mill.) and determined their plant-beneficial traits. The bacterial isolates from the roots of fennel belonged to four phyla: (BRN1 and BRN3), (BRN5, BRN6, and BRN7), (BRN2), and (BRN4). The bacterial isolates from the shoot of fennel represented the phyla (BSN1, BSN2, BSN3, BSN5, BSN6, BSN7, and BSN8), (BSN4, BRN1, and BRN3), and (BRN4). The bacterial species , , and were found both in the roots and shoots of fennel. The bacterial isolates were found to produce siderophores, HCN, and indole-3-acetic acid (IAA), as well as hydrolytic enzymes such as chitinase, protease, glucanase, and lipase. Seven bacterial isolates showed antagonistic activity against , , and . Our findings show that medicinal plants with antibacterial activity may serve as a source for the selection of microorganisms that exhibit antagonistic activity against plant fungal infections and may be considered as a viable option for the management of fungal diseases. They can also serve as an active part of biopreparation, improving plant growth.
PubMed: 38919721
DOI: 10.3934/microbiol.2024022 -
Plant Communications Jun 2024Genome-wide association study (GWAS) identifies trait-associated loci, but due in part to slow decay of linkage disequilibrium (LD), identifying the causal genes can be...
Genome-wide association study (GWAS) identifies trait-associated loci, but due in part to slow decay of linkage disequilibrium (LD), identifying the causal genes can be a bottleneck. Transcriptome-wide association study (TWAS) addresses this by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci (eQTLs) with GWAS results. Here, we used self-pollinated soybean (Glycine max [L.] Merr.) as a model to evaluate the application of TWAS in the genetic dissection of traits in plant species with slow LD decay. We generated RNA-Seq data of a soybean diversity panel, and identified the genetic expression regulation of 29,286 genes in soybean. Different TWAS solutions were less affected by LD and robust with source of expression that identified known genes related to traits from different development stages and tissues. A novel gene named pod color L2 was identified via TWAS and functionally validated by genome editing. By introducing the new exon proportion feature, we significantly improved the detection of expression variations resulting from structural variations and alternative splicing. As a result, the genes identified by our TWAS approach exhibited a diverse range of causal variations, including SNP, insertion/deletion, gene fusion, copy number variation, and alternative splicing. Using our TWAS approach, we identified genes associated with flowering time, including both previously known genes and novel genes that had not previously linked to this trait before, providing complementary insights with GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.
PubMed: 38918950
DOI: 10.1016/j.xplc.2024.101010 -
Scientific Reports Jun 2024Sphaeropsidins are iso-pimarane diterpenes produced by phytopathogenic fungi that display promising anticancer activities. Sphaeropsidin A, in particular, has been shown...
Sphaeropsidins are iso-pimarane diterpenes produced by phytopathogenic fungi that display promising anticancer activities. Sphaeropsidin A, in particular, has been shown to counteract regulatory volume increase, a process used by cancer cells to avoid apoptosis. This study reports the hemi-synthesis of new lipophilic derivatives obtained by modifications of the C15,C16-alkene moiety. Several of these compounds triggered severe ER swelling associated with strong proteasomal inhibition and consequently cell death, a feature that was not observed with respect to mode of action of the natural product. Significantly, an analysis from the National Cancer Institute sixty cell line testing did not reveal any correlations between the most potent derivative and any other compound in the database, except at high concentrations (LC). This study led to the discovery of a new set of sphaeropsidin derivatives that may be exploited as potential anti-cancer agents, notably due to their maintained activity towards multidrug resistant models.
Topics: Humans; Endoplasmic Reticulum; Cell Line, Tumor; Apoptosis; Antineoplastic Agents; Diterpenes; Abietanes
PubMed: 38918539
DOI: 10.1038/s41598-024-65335-3 -
Integrative and Comparative Biology Jun 2024Since the late 1800s, anthropogenic activities such as fossil fuel consumption and deforestation have driven up the concentration of atmospheric CO2 around the globe by...
Since the late 1800s, anthropogenic activities such as fossil fuel consumption and deforestation have driven up the concentration of atmospheric CO2 around the globe by more than 45%. Such heightened concentrations of carbon dioxide in the atmosphere are a leading contributor to global climate change with estimates of a 2-5 degree increase in global air temperature by the end of the century. While such climatic changes are mostly considered detrimental, a great deal of experimental work has shown that increased atmospheric CO2 will actually increase growth in various plants, which may lead to increased biomass for potential harvesting or CO2 sequestration. However, it is not clear whether this increase in growth or biomass will be beneficial to the plants, as such increases may lead to weaker plant materials. In this review, I examine our current understanding of how elevated atmospheric CO2 caused by anthropogenic effects may influence plant material properties focusing on potential effects on wood. For the first part of the review, I explore how aspects of wood anatomy and structure influence resistance to bending and breakage. This information is then used to review how changes in CO2 levels may later these aspects of wood anatomy and structure in ways that have mechanical consequences. The major pattern that emerges is that the consequences of elevated CO2 on wood properties is highly dependent on species, and environment, with different tree species showing contradictory responses to atmospheric changes. In the end, I describe a couple avenues for future research into better understanding the influence of atmospheric CO2 levels on plant biomaterial mechanics.
PubMed: 38918057
DOI: 10.1093/icb/icae081 -
International Journal of Food... May 2024Alternaria alternata is part of a genus comprised of over 600 different species that occur all over the world and cause damage to humans, plants and thereby to the...
Alternaria alternata is part of a genus comprised of over 600 different species that occur all over the world and cause damage to humans, plants and thereby to the economy. Yet, even though some species are causing tremendous issues, the past years have shown that assigning newly found isolates to known species was rather inconsistent. Most identifications are usually done on the basis of spore morphology, chemotype and molecular markers. In this work we used strains isolated from the wild as well as commercial strains of the DSMZ (German collection of microorganisms and cell cultures) as a reference, to show, that the variation within the Alternaria alternata species is comparable to the variation between different species of the genus Alternaria in regards to spore morphology and chemotype. We compared the different methods of identification and discerned the concatenation of multiple molecular markers as the deciding factor for better identification. Up until this point, usually a concatenation of two or three traditional molecular markers was used. Some of those markers being stronger some weaker. We show that the concatenation of five molecular markers improves the likeliness of a correct assignment, thus a better distinction between the different Alternaria species.
PubMed: 38917488
DOI: 10.1016/j.ijfoodmicro.2024.110746 -
The Plant Cell Jun 2024Although the strigolactone (SL) signaling pathway and SL-mediated anthocyanin biosynthesis have been reported, the molecular association between SL signaling and...
Although the strigolactone (SL) signaling pathway and SL-mediated anthocyanin biosynthesis have been reported, the molecular association between SL signaling and anthocyanin biosynthesis remains unclear. In this study, we identified the SL signal transduction pathway associated with anthocyanin biosynthesis and the crosstalk between gibberellin (GA) and SL signaling in apple (Malus × domestica). ELONGATED HYPOCOTYL5 (HY5) acts as a key node integrating SL signaling and anthocyanin biosynthesis, and the SL response factor AGAMOUS-LIKE MADS-BOX9 (AGL9) promotes anthocyanin biosynthesis by activating HY5 transcription. The SL signaling repressor SUPPRESSOR OF MAX2 1-LIKE8 (SMXL8) interacts with AGL9 to form a complex that inhibits anthocyanin biosynthesis by downregulating HY5 expression. Moreover, the E3 ubiquitin ligase PROTEOLYSIS1 (PRT1) mediates the ubiquitination-mediated degradation of SMXL8, which is a key part of the SL signal transduction pathway associated with anthocyanin biosynthesis. In addition, the GA signaling repressor REPRESSOR-of-ga1-3-LIKE2a (RGL2a) mediates the crosstalk between GA and SL by disrupting the SMXL8-AGL9 interaction that represses HY5 transcription. Taken together, our study reveals the regulatory mechanism of SL-mediated anthocyanin biosynthesis and uncovers the role of SL-GA crosstalk in regulating anthocyanin biosynthesis in apple.
PubMed: 38917246
DOI: 10.1093/plcell/koae191 -
Plant Disease Jun 2024Tobacco (Nicotiana tabacum L.) is one of the most widely cultivated industrial crops worldwide. From April to July 2023, about 40% of tobacco seedlings in the greenhouse...
Tobacco (Nicotiana tabacum L.) is one of the most widely cultivated industrial crops worldwide. From April to July 2023, about 40% of tobacco seedlings in the greenhouse exhibited irregular taupe lesions in Zhengzhou, Henan Province, China. At an early stage of the lesion development, light grey spots with the diameter of 1-2 mm were observed, these spots gradually expanded and connected into large irregular lesions causing leaf wrinkling or withered. A total of 12 infected leaf tissues were sterilized with 75% ethanol for 45 s, rinsed three times in sterilized water and then plated on potato dextrose agar (PDA) medium for 10 days at 28°C in darkness. Seven fungal colonies that show the similar appearance were isolated and three of them (MB-1, MB-2 and MB-3) were used for subsequent identification. Colonies of these strains on PDA with loose mycelium and orange-red pigment on the underside, white aerial in the center and light yellow hyphae near the periphery, formed in the shape of a concentric ring pattern. Ascomata appeared from the 14th day, were black, spherical or ellipsoid with walls of textura angularis, and size was 53.8-101.1 μm × 50.3-104.3 μm (n=30). Terminal hairs were brown and straight, gradually tapering toward the tips. Asci clavate or fusiform, spore bearing part 16.2-29.2 × 7.3-11.4 μm (n=21), with 8 irregularly arranged ascospores, evanescent. Ascospores are brown at maturity, biapiculate, navicular or fusiform shapes with size of 8.7-12.8 μm × 4.8-6.9 μm (n=100), and more or less inaequilateral. Single spore strains derived from these strains exhibited the morphological features consistent with the original strains. The morphological characteristics of the fungus were consistent with the description of Arcopilus aureus (Chivers) X.W. Wang & Samson (= Chaetomium aureum Chivers) (Lee et al. 2019). Furthermore, the sequences of RPB2 region were amplified from these strains and the result sequences (GenBank accession no. OR513105-OR513108) all showed a 100.00% identity with A. aureus strain CBS 538.73 (GenBank accession no. KX976807.1). It was reported that the RPB2 gene was efficient in discriminating Arcopilus species (Tavares et al. 2022), thus a maximum likelihood (ML) phylogenetic tree based on the RPB2 gene sequences were constructed using MEGA 7.0 with 1000 replications of bootstrapping (Kumar et al. 2016), which revealed that these strains formed a well-supported clade with A. aureus strains of (CBS 153.52 and CBS538.73) (Wang et al. 2022). Pathogenicity analysis were performed on healthy flue-cured tobacco seedlings leaves (cv Y85) by using mycelial agar plugs (5 mm in diameter) and spore suspension (1×106 spores/mL), and the PDA plugs and sterile water were used for control group, respectively. Tobacco seedlings were incubated in a 25°C and 70% RH growth chamber. After seven days, the leaves showed obvious symptoms, with taupe lesions and yellow halos on the periphery, whereas no symptoms were found on the control leaves. The A. aureu was then reisolated from inoculated diseased leaves. Previously, A. aureus has been only reported to cause leaf black disease on Pseudostellaria heterophylla in China (Yuan et al. 2021). To our knowledge, this is the first reported of A. aureus causing tobacco leaf grey spot worldwide. Arcopilus aureus has been reported as a plant biocontrol fungus (Wang et al. 2013). However, due to the potential serious damage in tobacco seedlings caused by this fungus, the use of A. aureus as a plant biocontrol agent needs to be given more attention, and disease control measures of this pathogen should be developed.
PubMed: 38916906
DOI: 10.1094/PDIS-04-24-0840-PDN -
Philosophical Transactions of the Royal... Jul 2024Negative density dependence (NDD) in biotic interactions of interference such as plant-plant competition, granivory and herbivory are well-documented mechanisms that...
Negative density dependence (NDD) in biotic interactions of interference such as plant-plant competition, granivory and herbivory are well-documented mechanisms that promote species' coexistence in diverse plant communities worldwide. Here, we investigated the generality of a novel type of NDD mechanism that operates through the mutualistic interactions of frugivory and seed dispersal among fruit-eating birds and plants. By sampling community-wide frugivory interactions at high spatial and temporal resolution in Pennsylvania, Puerto Rico, Peru, Brazil and Argentina, we evaluated whether interaction frequencies between birds and fruit resources occurred more often (selection), as expected, or below expectations (under-utilization) set by the relative fruit abundance of the fruit resources of each plant species. Our models considered the influence of temporal scales of fruit availability and bird phylogeny and diets, revealing that NDD characterizes frugivory across communities. Irrespective of taxa or dietary guild, birds tended to select fruits of plant species that were proportionally rare in their communities, or that became rare following phenological fluctuations, while they mostly under-utilized abundant fruit resources. Our results demonstrate that negative density-dependence in frugivore-plant interactions provides a strong equalizing mechanism for the dispersal processes of fleshy-fruited plant species in temperate and tropical communities, likely contributing to building and sustaining plant diversity. This article is part of the theme issue 'Diversitydependence of dispersal: interspecific interactions determine spatial dynamics'.
Topics: Animals; Birds; Fruit; Symbiosis; Seed Dispersal; Feeding Behavior; Population Density; Herbivory; Argentina; Pennsylvania; Brazil; Puerto Rico
PubMed: 38913067
DOI: 10.1098/rstb.2023.0128 -
Heliyon Jun 2024Chickpea is an important cash crop for Ada'a farmers as it does for farmers in Ethiopia and elsewhere in the world. Its production, however, has been dwindling due to...
Chickpea is an important cash crop for Ada'a farmers as it does for farmers in Ethiopia and elsewhere in the world. Its production, however, has been dwindling due to biotic and abiotic stresses. According to participant farmers from Ada'a district, the production of chickpea in some Kebeles of Ada'a such as has been abandoned because of root rot and foliar diseases such as fusarium wilt. This paper presents the evaluation of upscaled varieties' performance assessed by metric data as well as through beneficiary farmers' self-assessment data. Recognizant to the problem, five varieties of chickpea tested in the Goro district of the Southwest Shoa zone, were introduced as part of the upscaling of crowdsourcing winner crop varieties in Ethiopia. Crowdsourcing is an approach of outsourcing variety evaluation, selection, and dissemination to volunteer crowds of farmers. The introduction of the winner varieties and adjustment of the planting time was found effective in the Ada'a district. Higher grain yield was obtained from the upscaled winner varieties in the range of 2.4-2.53 t/ha, with slight variations over varieties. variety showed slightly higher performance than the others. Survey participant farmers have reported an increase in GY due to growing the winner varieties compared with varieties they used to grow before and gained higher annual income due to higher productivity, market demand of the upscaled varieties, and premium market price with 6-25 Ethiopian birr (ETB) per kilogram of sold grain of these varieties. High productivity is attributed to the genetic potential of the varieties, their response to farm management, and better adaptation to the local growing conditions. Participant farmers perceived that their livelihood has been improving because of the adoption of the upscaled varieties' productivity and market demand. The annual income of participant farmers is estimated to be 2500 to 181,000 ETB for growing the winner varieties. The results indicate that upscaling pre-tested chickpea varieties and delaying their planting time to early September are effective mechanisms for reducing yield loss to fusarium wilt and root rot diseases. It can be inferred that using the crowdsourcing approach for variety evaluation and selection for upscaling is a robust approach to improve the adoption and dissemination of improved agricultural technologies.
PubMed: 38912462
DOI: 10.1016/j.heliyon.2024.e32269