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<jats:p>LTR-retrotransposons (LTR-RTs) are a class of RNA-replicating transposon elements (TEs) that can alter genome structure and function by moving positions, repositioning genes, shifting exons, and causing chromosomal rearrangements. LTR-RTs are widespread in many plant genomes and constitute a significant portion of the genome. Their movement and activity in eukaryotic genomes can provide insight into genome evolution and gene function, especially when LTR-RTs are located near or within genes. Building the redundant and non-redundant LTR-RTs libraries and their annotations for species lacking this resource requires extensive bioinformatics pipelines and expensive computing power to analyze large amounts of genomic data. This increases the need for online services that provide computational resources with minimal overhead and maximum efficiency. Here, we present MegaLTR as a web server and standalone pipeline that detects intact LTR-RTs at the whole-genome level and integrates multiple tools for structure-based, homologybased, and <jats:italic>de novo</jats:italic> identification, classification, annotation, insertion time determination, and LTR-RT gene chimera analysis. MegaLTR also provides statistical analysis and visualization with multiple tools and can be used to accelerate plant species discovery and assist breeding programs in their efforts to improve genomic resources. We hope that the development of online services such as MegaLTR, which can analyze large amounts of genomic data, will become increasingly important for the automated detection and annotation of LTR-RT elements.</jats:p>

<jats:p>The basic helix-loop-helix (bHLH) family is one of the most well-known transcription factor families in plants, and it regulates growth, development, and abiotic stress responses. However, systematic analyses of the bHLH gene family in <jats:italic>Prunus sibirica</jats:italic> have not been reported to date. In this study, 104 <jats:italic>PsbHLHs</jats:italic> were identified and classified into 23 subfamilies that were unevenly distributed on eight chromosomes. Nineteen pairs of segmental replication genes and ten pairs of tandem replication genes were identified, and all duplicated gene pairs were under purifying selection. <jats:italic>PsbHLHs</jats:italic> of the same subfamily usually share similar motif compositions and exon-intron structures. <jats:italic>PsbHLHs</jats:italic> contain multiple stress-responsive elements. <jats:italic>PsbHLHs</jats:italic> exhibit functional diversity by interacting and coordinating with other members. Twenty <jats:italic>PsbHLHs</jats:italic> showed varying degrees of expression. Eleven genes up-regulated and nine genes down-regulated in −4°C. The majority of <jats:italic>PsbHLHs</jats:italic> were highly expressed in the roots and pistils. Transient transfection experiments demonstrated that transgenic plants with overexpressed <jats:italic>PsbHLH42</jats:italic> have better cold tolerance. In conclusion, the results of this study have significant implications for future research on the involvement of bHLH genes in the development and stress responses of <jats:italic>Prunus sibirica</jats:italic>.</jats:p>

<jats:p>Although selenium (Se) is an essential trace element in humans, the intake of Se from food is still generally inadequate throughout the world. Inoculation with arbuscular mycorrhizal fungi (AMF) improves the uptake of Se in rice (<jats:italic>Oryza sativa</jats:italic> L.). However, the mechanism by which AMF improves the uptake of Se in rice at the transcriptome level is unknown. Only a few studies have evaluated the effects of uptake of other elements in rice under the combined effects of Se and AMF. In this study, Se combined with the AMF <jats:italic>Funneliformis mosseae</jats:italic> (Fm) increased the biomass and Se concentration of rice plants, altered the pattern of ionomics of the rice roots and shoots, and reduced the antagonistic uptake of Se with nickel, molybdenum, phosphorus, and copper compared with the treatment of Se alone, indicating that Fm can enhance the effect of fertilizers rich in Se. Furthermore, a weighted gene co-expression network analysis (WGCNA) showed that the hub genes in modules significantly associated with the genes that contained Se and were related to protein phosphorylation, protein serine/threonine kinase activity, membrane translocation, and metal ion binding, suggesting that the uptake of Se by the rice roots may be associated with these genes when Fm and Se act in concert. This study provides a reference for the further exploration of genes related to Se uptake in rice under Fm treatment.</jats:p>

<jats:p>Dirigent (DIR) proteins play essential roles in regulating plant growth and development, as well as enhancing resistance to abiotic and biotic stresses. However, the whole-genome identification and expression profiling analysis of <jats:italic>DIR</jats:italic> gene family in millet <jats:italic>(Setaria italica (Si))</jats:italic> have not been systematically understood. In this study, we conducted genome-wide identification and expression analysis of the <jats:italic>S. italica DIR</jats:italic> gene family, including gene structures, conserved domains, evolutionary relationship, chromosomal locations, <jats:italic>cis</jats:italic>-elements, duplication events, gene collinearity and expression patterns. A total of 38 <jats:italic>SiDIR</jats:italic> members distributed on nine chromosomes were screened and identified. SiDIR family members in the same group showed higher sequence similarity. The phylogenetic tree divided the <jats:italic>SiDIR</jats:italic> proteins into six subfamilies: DIR-a, DIR-b/d, DIR-c, DIR-e, DIR-f, and DIR-g. According to the tertiary structure prediction, DIR proteins (like SiDIR7/8/9) themselves may form a trimer to exert function. The result of the syntenic analysis showed that tandem duplication may play the major driving force during the evolution of <jats:italic>SiDIRs</jats:italic>. RNA-seq data displayed higher expression of 16 <jats:italic>SiDIR</jats:italic> genes in root tissues, and this implied their potential functions during root development. The results of quantitative real-time PCR (RT-qPCR) assays revealed that SiDIR genes could respond to the stress of CaCl<jats:sub>2</jats:sub>, CdCl, NaCl, and PEG6000. This research shed light on the functions of SiDIRs in responding to abiotic stress and demonstrated their modulational potential during root development. In addition, the membrane localization of SiDIR7/19/22 was confirmed to be consistent with the forecast. The results above will provide a foundation for further and deeper investigation of DIRs.</jats:p>

<jats:p>High temperatures have a significant impact on plant growth and metabolism. In recent years, the fruit industry has faced a serious threat due to high-temperature stress on fruit plants caused by global warming. In the present study, we explored the molecular regulatory mechanisms that contribute to high-temperature tolerance in kiwifruit. A total of 36 <jats:italic>Hsf</jats:italic> genes were identified in the <jats:italic>A. chinensis</jats:italic> (Ac) genome, while 41 <jats:italic>Hsf</jats:italic> genes were found in the <jats:italic>A. eriantha</jats:italic> (Ae) genome. Phylogenetic analysis revealed the clustering of kiwifruit <jats:italic>Hsfs</jats:italic> into three distinct groups (groups A, B, and C). Synteny analysis indicated that the expansion of the <jats:italic>Hsf</jats:italic> gene family in the Ac and Ae genomes was primarily driven by whole genome duplication (WGD). Analysis of the gene expression profiles revealed a close relationship between the expression levels of <jats:italic>Hsf</jats:italic> genes and various plant tissues and stress treatments throughout fruit ripening. Subcellular localization analysis demonstrated that GFP-AcHsfA2a/AcHsfA7b and AcHsfA2a/AcHsfA7b -GFP were localized in the nucleus, while GFP-AcHsfA2a was also observed in the cytoplasm of <jats:italic>Arabidopsis</jats:italic> protoplasts. The results of real-time quantitative polymerase chain reaction (RT-qPCR) and dual-luciferase reporter assay revealed that the majority of <jats:italic>Hsf</jats:italic> genes, especially <jats:italic>AcHsfA2a</jats:italic>, were expressed under high-temperature conditions. In conclusion, our findings establish a theoretical foundation for analyzing the potential role of <jats:italic>Hsfs</jats:italic> in high-temperature stress tolerance in kiwifruit. This study also offers valuable information to aid plant breeders in the development of heat-stress-resistant plant materials.</jats:p>

<jats:p>Biochar has been used to remediate contaminated-soil with heavy metals, however, less is known on how biochar interacts with planting density and nutrient fluctuation to affect the remediation. A pot experiment was conducted in the greenhouse to investigate the effects of biochar application (without vs. with 1% biochar, g/g substrate), nutrient fluctuation (constant vs. pulsed) and planting density (1-, 3- and 6-individuals per pot) on the growth, and cadmium (Cd) and nutrient uptake of <jats:italic>Trifolium repens</jats:italic> population. Our results found that the growth of <jats:italic>T. repens</jats:italic> population increased significantly with increasing planting density, and the increment decreased with increasing planting density. Both the Cd and nutrient uptake were higher at higher planting density (e.g., 3- and 6-individuals) than at lower planting density (e.g., 1-individual). Biochar application increased the biomass and shoot Cd uptake, but decreased the ratio of root to shoot and root Cd uptake of <jats:italic>T. repens</jats:italic> population, the effects of which were significantly influenced by planting density. Although nutrient fluctuation had no effect on the growth of <jats:italic>T. repens</jats:italic> population, but its interaction with planting density had significant effects on Cd uptake in tissues. Overall, the effects of biochar application and nutrient fluctuation on the growth and Cd uptake were both influenced by planting density in the present study. Our findings highlight that biochar application and constant nutrient supply at an appropriate planting density, such as planting density of 3-individuals per pot in the present study, could promote the growth, and Cd and nutrient uptake of <jats:italic>T. repens</jats:italic> population.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Seasonal droughts will become more severe and frequent under the context of global climate change, this would result in significant variations in the root distribution and water utilization patterns of plants. However, research on the determining factors of deep fine root and water utilization is limited.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We measured the fine root biomass and water utilization of trees, shrubs and herbs, and soil properties, light transmission, and community structure parameters in subtropical pine plantations with seasonal droughts.</jats:p></jats:sec><jats:sec><jats:title>Results and Discussion</jats:title><jats:p>We found that the proportion of deep fine roots (below 1 m depth) is only 0.2-5.1%, but that of deep soil water utilization can reach 20.9-38.6% during the dry season. Trees improve deep soil water capture capacity by enhancing their dominance in occupying deep soil volume, and enhance their deep resource foraging by increasing their branching capacity of absorptive roots. Shrubs and herbs showed different strategies for deep water competition: shrubs tend to exhibit a “conservative” strategy and tend to increase individual competitiveness, while herbs exhibited an “opportunistic” strategy and tend to increase variety and quantity to adapt to competitions.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>Our results improve our understanding of different deep fine root distribution and water use strategies between overstory trees and understory vegetations, and emphasize the importance of deep fine root in drought resistance as well as the roles of deep soil water utilization in shaping community assembly.</jats:p></jats:sec>

<jats:p>Agronomic biofortification of crops is a promising approach that can improve the nutritional value of staple foods by alleviating dietary micronutrient deficiencies. Iodine deficiency is prevalent in many countries, including Australia, but it is not clear what foliar application strategies will be effective for iodine fortification of grain. This study hypothesised that combining adjuvants with iodine in foliar sprays would improve iodine penetration in wheat, leading to more efficient biofortification of grains. The glasshouse experiment included a total of nine treatments, including three reference controls: 1) Water; 2) potassium iodate (KIO<jats:sub>3</jats:sub>) and 3) potassium chloride (KCl); and a series of six different non-ionic surfactant or oil-based adjuvants: 4) KIO<jats:sub>3</jats:sub> + BS1000; 5) KIO<jats:sub>3</jats:sub> + Pulse<jats:sup>®</jats:sup> Penetrant; 6) KIO<jats:sub>3</jats:sub> + Uptake<jats:sup>®</jats:sup>; 7) KIO<jats:sub>3</jats:sub> + Hot-Up<jats:sup>®</jats:sup>; 8) KIO<jats:sub>3</jats:sub> + Hasten<jats:sup>®</jats:sup> and 9) KIO<jats:sub>3</jats:sub> + Synerterol<jats:sup>®</jats:sup> Horti Oil. Wheat was treated at heading, and again during the early milk growth stage. Adding the organosilicon-based adjuvant (Pulse<jats:sup>®</jats:sup>) to the spray formulation resulted in a significant increase in grain loading of iodine to 1269 µg/kg compared to the non-adjuvant KIO<jats:sub>3</jats:sub> control at 231µg/kg, and the water and KCl controls (both 51µg/kg). The second most effective adjuvant was Synerterol<jats:sup>®</jats:sup> Horti Oil, which increased grain iodine significantly to 450µg/kg. The Uptake<jats:sup>®</jats:sup>, BS1000, Hasten<jats:sup>®</jats:sup>, and Hot-Up<jats:sup>®</jats:sup> adjuvants did not affect grain iodine concentrations relative to the KIO<jats:sub>3</jats:sub> control. Importantly, iodine application and the subsequent increase in grain iodine had no significant effects on biomass production and grain yield relative to the controls. These results indicate that adjuvants can play an important role in agronomic biofortification practices, and organosilicon-based products have a great potential to enhance foliar penetration resulting in a higher translocation rate of foliar-applied iodine to grains, which is required to increase the iodine density of staple grains effectively.</jats:p>

<jats:p>A clearer understanding of the stability of water use efficiency (WUE) and its driving factors contributes to improving water use efficiency and strengthening water resource management. However, the stability of WUE is unclear. Based on the EEMD method, this study analyses the spatial variations and mechanisms for the stability of WUE in China, especially in the National Forest Protection Project (NFPP) areas. It is found that the stable WUE was dominated by non-significant trends and increasing trends in China, accounting for 33.59% and 34.19%, respectively. The non-significant trend of stable WUE was mainly located in the Three-North shelterbelt program area, and the increasing trend of stable WUE was in Huaihe and Taihu, Taihang Mountains, and Pearl River shelterbelt program areas. Precipitation and soil moisture promoted the stable WUE in these project areas. The unstable WUE was dominated by positive reversals or negative reversals of WUE trends. The positive reversals of unstable WUE were mainly located in the Yellow River shelterbelt program areas, which was promoted by temperature and radiation, while the negative reversals of unstable WUE were mainly distributed in the Yangtze River and Liaohe shelterbelt program areas, which were mainly induced by saturation water vapor pressure difference (VPD). Our results highlight that some ecological restoration programs need to be improved to cope with the negative climate impact on the stability of WUE.</jats:p>

<jats:p>Rising temperatures impact different developmental stages of summer crops like mung bean, particularly during the crucial seed-filling stage. This study focused on two mung bean genotypes, categorized as heat-tolerant [HT] or heat-sensitive [HS]. These genotypes were grown in pots in an outdoor natural environment (average day/night temperature 36°C/24.3°C) until the onset of podding (40 days after sowing) and subsequently relocated to controlled-environment walk-in growth chambers for exposure to heat stress (42°C/30°C) or control conditions (35°C/25°C) until maturity. For all measured attributes, heat stress had a more pronounced effect on the HS genotype than on the HT genotype. Heat-stressed plants exhibited severe leaf damage, including membrane damage, reduced chlorophyll content, diminished chlorophyll fluorescence, and decreased leaf water content. Heat stress impeded the seed-filling rate and duration, decreasing starch, protein, fat, and mineral contents, with a notable decline in storage proteins. Heat stress disrupted the activities of several seed enzymes, inhibiting starch and sucrose accumulation and consequently decreasing individual seed weights and seed weight plant<jats:sup>−1</jats:sup>. This study revealed that heat stress during seed filling severely impaired mung bean seed yield and nutritional quality due to its impact on various stress-related traits in leaves and enzyme activities in seeds. Moreover, this research identified potential mechanisms related to heat tolerance in genotypes with contrasting heat sensitivity.</jats:p>