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<jats:p>Anthracnose is responsible for large yield losses in common bean crops. RNA-sequencing was used to investigate the differentially expressed genes (DEGs) in response to race 38 of <jats:italic>Colletotrichum lindemuthianum</jats:italic> in two near-isogenic lines (A25 and A4804) that differ in the presence of a resistance gene located in the cluster Co-2. Their responses were analyzed at different hours after inoculation (0, 24, and 48) and within and between genotypes. In all, 2,850 DEGs were detected, with 2,373 assigned to at least one functional GO term. Enriched GO terms in the resistant genotype were mainly related to functions as a response to stimulus, hormone signaling, cellular component organization, phosphorylation activities, and transcriptional regulation. The region containing the <jats:italic>Co-2</jats:italic> cluster was delimited at the end of chromosome Pv11 (46.65–48.65 Mb) through a comparison with the SNP genotypes, obtained using ‘Genotyping by Sequencing,’ among seven resistant lines harboring the Co-2 gene and the susceptible line A25. The delimited region contained 23 DEGs, including 8 typical R genes, that showed higher expression levels in the resistant genotype and non-changes in the susceptible genotype after inoculation. Six R genes encoding protein kinases and an LRR domain formed a cluster in a core region between 46.98 and 47.04 Mb. The alignment of the raw transcriptome reads in the core region revealed structural changes that were used to design four potential breeder-friendly DNA markers, and it revealed some alignments with the intergenic regions, suggesting the presence of genes in addition to those annotated in the reference genome.</jats:p>

<jats:p>As the largest genus in Moraceae, <jats:italic>Ficus</jats:italic> is widely distributed across tropical and subtropical regions and exhibits a high degree of adaptability to different environments. At present, however, the phylogenetic relationships of this genus are not well resolved, and chloroplast evolution in <jats:italic>Ficus</jats:italic> remains poorly understood. Here, we sequenced, assembled, and annotated the chloroplast genomes of 10 species of <jats:italic>Ficus</jats:italic>, downloaded and assembled 13 additional species based on next-generation sequencing data, and compared them to 46 previously published chloroplast genomes. We found a highly conserved genomic structure across the genus, with plastid genome sizes ranging from 159,929 bp (<jats:italic>Ficus langkokensis</jats:italic>) to 160,657 bp (<jats:italic>Ficus religiosa</jats:italic>). Most chloroplasts encoded 113 unique genes, including a set of 78 protein-coding genes, 30 transfer RNA (tRNA) genes, four ribosomal RNA (rRNA) genes, and one pseudogene (<jats:italic>infA</jats:italic>). The number of simple sequence repeats (SSRs) ranged from 67 (<jats:italic>Ficus sagittata</jats:italic>) to 89 (<jats:italic>Ficus microdictya</jats:italic>) and generally increased linearly with plastid size. Among the plastomes, comparative analysis revealed eight intergenic spacers that were hotspot regions for divergence. Additionally, the <jats:italic>clpP</jats:italic>, <jats:italic>rbcL</jats:italic>, and <jats:italic>ccsA</jats:italic> genes showed evidence of positive selection. Phylogenetic analysis indicated that none of the six traditionally recognized subgenera of <jats:italic>Ficus</jats:italic> were monophyletic. Divergence time analysis based on the complete chloroplast genome sequences showed that <jats:italic>Ficus</jats:italic> species diverged rapidly during the early to middle Miocene. This research provides basic resources for further evolutionary studies of <jats:italic>Ficus</jats:italic>.</jats:p>

<jats:p>Storage at the putative chilling threshold temperature (CTT) to avoid chilling injury still limits postharvest handling of tropical fruit like banana in that ripening may occur at the CTT. To determine whether chilling injury (CI) symptoms would develop in mature green (MG) banana fruit if the CTT exposure was extended by inhibiting ethylene action and thus ripening, 1-methylcyclopropene (1-MCP) was applied. Individual ‘fingers’ from multiple ‘clusters’ of MG bananas were either immersed in water or 50 μg L<jats:sup>−1</jats:sup> 1-MCP (a.i.) solution and each treatment was divided into three subgroups for storage at 5.0°C (severe CI), 13.0°C (mild CI), or 14.0°C (CTT) ± 0.1°C. 1-MCP delayed ripening in terms of color change for 10 days for fruit stored at the CTT. Ethylene production by fruit at 5.0°C remained around 0.04 ng kg<jats:sup>−1</jats:sup> s<jats:sup>−1</jats:sup> with no obvious increase during 31-day storage. Ethylene production at 14.0°C (−1-MCP/+1-MCP) increased on Day 33 while increasing on Day 38 for 13.0°C fruit without 1-MCP and on Day 39 for fruit with 1-MCP. Peak climacteric ethylene occurred on Days 44 and 39 for 13.0 and 14.0°C fruit without 1-MCP, respectively, and on Days 59 and 51 for 13.0°C and 14.0°C 1-MCP-treated fruit, respectively. As hypothesized, longer exposure of MG banana fruit to the CTT of 14.0°C without onset of ripening as was allowed by prior 1-MCP treatment allowed CI to develop at that normally non-chilling temperature. Vascular browning was the first visual and most sensitive CI symptom in the experiment and was observed on Day 4 at 5.0°C, Day 10 at 13.0°C, Day 19 at 14.0°C without 1-MCP, and on Day 28 at 14.0°C with 1-MCP. Using a 1-MCP pre-treatment to remove the influence of ethylene from bananas stored at 13°C or 14°C also resulted in slight reduction in vascular browning severity. In conclusion, a putative safe temperature may become a CI temperature if the shelf-life-limiting factor is removed, allowing longer exposure. Chilling at the CTT caused relatively mild injury on fruit, and vascular browning is a sensitive indicator of CI status, while the light-adapted quantum yield of photosystem II [Y(II)] could be a non-destructive indicator of early CI stress in MG banana. Fruit at 13.0/14.0°C developed CI symptoms slightly later with 1-MCP than without 1-MCP. This suggests that ethylene might be involved in early CI symptom development.</jats:p>

<jats:p>A pot experiment was performed under rain–shelter conditions to explore the effects of drought stress and post-drought rewatering on the abundance of an ammonia-oxidizing bacteria (AOB) strain in corn (<jats:italic>Zea mays</jats:italic> L.) rhizosphere soils and the relationship between the AOB strain and corn (<jats:italic>Zea mays</jats:italic> L.) compensatory growth after drought stress rewatering. Corn seedlings were used as test materials, and one AOB strain was isolated and screened from the soil. The experimental design included six treatments: (1) wet (WT), (2) wet with AOB strain inoculation during wetness (WI), (3) wet with AOB strain inoculation during rewatering (WR), (4) post-drought rewatering (DT), (5) post-drought rewatering with AOB strain inoculation during wetness (DI), and (6) post-drought rewatering with AOB strain inoculation during rewatering (DR). Wetness and drought stress were obtained by keeping the soil water content at 75–80% and 50–55% of the field capacities, respectively. The results showed that the isolated and screened AOB strain (S2_8_1) had 100% similarity to <jats:italic>Ensifer sesbaniae</jats:italic>. The inoculation of S2_8_1 during the wet period in the DI treatment caused it to colonize the rhizosphere soil. Drought stress decreased its abundance, but rewatering resulted in a great increase. The S2_8_1 in the DI treatment increased the total biomass, water use efficiencies, net photosynthetic rates, rhizosphere soil nitrification rates, leaf cytokinin concentrations, xylem sap cytokinin concentrations, copy number of S2_8_1 in rhizosphere soils, and organic carbon contents in rhizosphere soils by 23, 104, 35, 30, 18, 29, 104, and 23% on day 10 after rewatering compared with WT treatment. In the DI treatment, the increase in rhizosphere soil nitrification rates caused by S2_8_1 during wetness was closely related to the cytokinin delivery from roots to leaves and increased leaf cytokinin concentrations. The increase in leaf cytokinin concentrations improved rewatering corn growth, which caused compensatory growth and increased water use. Compensatory and over-compensatory growths occurred in DT and DR treatments, respectively. Therefore, the coexistence of the strain of AOB with corn in rhizosphere soil increased the corn compensatory growth by regulating soil nitrification and root-induced leaf cytokinin.</jats:p>

<jats:p>For continual learning in the process of plant disease recognition it is necessary to first distinguish between unknown diseases from those of known diseases. This paper deals with two different but related deep learning techniques for the detection of unknown plant diseases; Open Set Recognition (OSR) and Out-of-Distribution (OoD) detection. Despite the significant progress in OSR, it is still premature to apply it to fine-grained recognition tasks without outlier exposure that a certain part of OoD data (also called known unknowns) are prepared for training. On the other hand, OoD detection requires intentionally prepared outlier data during training. This paper analyzes two-head network included in OoD detection models, and semi-supervised OpenMatch associated with OSR technology, which explicitly and implicitly assume outlier exposure, respectively. For the experiment, we built an image dataset of eight strawberry diseases. In general, a two-head network and OpenMatch cannot be compared due to different training settings. In our experiment, we changed their training procedures to make them similar for comparison and show that modified training procedures resulted in reasonable performance, including more than 90% accuracy for strawberry disease classification as well as detection of unknown diseases. Accurate detection of unknown diseases is an important prerequisite for continued learning.</jats:p>

<jats:p>Carbon and nitrogen metabolism are basic, but pivotal metabolic pathways in plants and are tightly coupled. Maintaining the balance of carbon and nitrogen metabolism is critical for plant survival. Comprehensively revealing the metabolic balance of carbon–nitrogen interactions is important and helpful for understanding the adaptation of freshwater plants to CO<jats:sub>2</jats:sub> limited aqueous environment. A comprehensive metabolomics analysis combined with physiological measurement was performed in the freshwater plant <jats:italic>Ottelia alismoides</jats:italic> acclimated to high and low CO<jats:sub>2</jats:sub>, respectively, for a better understanding of how the carbon and nitrogen metabolic adjustment in freshwater plants respond to carbon limitation. The present results showed that low CO<jats:sub>2</jats:sub> acclimated <jats:italic>O. alismoides</jats:italic> exhibited significant diurnal titratable acidity and malate fluctuations, as well as an opposite diel pattern of starch change and high enzymatic activities required for crassulacean acid metabolism (CAM) photosynthesis, which indicates that CAM was induced under low CO<jats:sub>2</jats:sub>. Moreover, the metabolomic analysis showed that most intermediates of glycolysis, pentose phosphate pathway (PPP) and tricarboxylic acid (TCA) cycle, were increased under low CO<jats:sub>2</jats:sub>, indicative of active respiration in low-CO<jats:sub>2</jats:sub>-treated <jats:italic>O. alismoides</jats:italic>. Meanwhile, the majority of amino acids involved in pathways of glutamate and arginine metabolism, aspartate metabolism, and the branched-chain amino acids (BCAAs) metabolism were significantly increased under low CO<jats:sub>2</jats:sub>. Notably, γ-aminobutyric acid (GABA) level was significantly higher in low CO<jats:sub>2</jats:sub> conditions, indicating a typical response with GABA shunt compensated for energy deprivation at low CO<jats:sub>2</jats:sub>. Taken together, we conclude that in low-CO<jats:sub>2</jats:sub>-stressed <jats:italic>O. alismoides</jats:italic>, CAM photosynthesis was induced, leading to higher carbon and nitrogen as well as energy requirements. Correspondingly, the respiration was greatly fueled <jats:italic>via</jats:italic> numerous starch degradation to ensure CO<jats:sub>2</jats:sub> fixation in dark, while accompanied by linked promoted N metabolism, presumably to produce energy and alternative carbon sources and nitrogenous substances for supporting the operation of CAM and enhancing tolerance for carbon limitation. This study not only helps to elucidate the regulating interaction between C and N metabolism to adapt to different CO<jats:sub>2</jats:sub> but also provides novel insights into the effects of CO<jats:sub>2</jats:sub> variation on the metabolic profiling of <jats:italic>O. alismoides</jats:italic>.</jats:p>

<jats:p>Plant growth-promoting rhizobacteria are important for improving plant iron nutrition, but the interactions among inoculants, host plants and soil microorganisms have not been greatly explored. <jats:italic>Rahnella aquatilis</jats:italic> JZ-GX1 was applied to treat the increasingly serious iron deficiency chlorosis in <jats:italic>Cinnamomum camphora</jats:italic>, and the resulting improvement in chlorosis was determined by assessing the contents of chlorophyll, active iron, Fe<jats:sup>2+</jats:sup> and antioxidant enzymes in leaves, the effects on the soil microbial community and the metabolism in the rhizosphere by high-throughput sequencing techniques and liquid chromatography–mass spectrometry (LC–MS). The results showed that inoculation with JZ-GX1 significantly increased the chlorophyll content of <jats:italic>C. camphora</jats:italic>, which promoted the redistribution of active iron in roots and leaves, increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX), and thus reduced membrane damage in iron-deficient <jats:italic>C. camphora</jats:italic> caused by reactive oxygen species. According to genome prediction and ultra-performance liquid chromatography–mass spectrometry (UPLC–MS) analysis, the JZ-GX1 strain could secrete desferrioxamine (DFO), and the concentration of DFO in <jats:italic>C. camphora</jats:italic> rhizosphere was 21-fold higher than that in uninoculated soil. The exogenous application of DFO increased the SPAD and Fe<jats:sup>2+</jats:sup> contents in leaves. In addition, the inoculant affected the fungal community structure and composition in the <jats:italic>C. camphora</jats:italic> rhizosphere soil and increased the abundances of specific taxa, such as <jats:italic>Glomus</jats:italic>, <jats:italic>Mortierella</jats:italic>, <jats:italic>Trichoderma,</jats:italic> and <jats:italic>Penicillium</jats:italic>. Therefore, <jats:italic>R. aquatilis</jats:italic> JZ-GX1 application promoted iron absorption in <jats:italic>C. camphora</jats:italic> trees by secreting DFO and alleviated iron deficiency chlorosis through interactions with the local fungal community.</jats:p>

<jats:p><jats:italic>Tetrastigma hemsleyanum</jats:italic> Diels et Gilg is a folk herb in Zhejiang Province with anti-inflammatory, antineoplastic, and anti-oxidation effects. Given its pharmacological activity, <jats:italic>T. hemsleyanum</jats:italic> is known as New “Zhebawei” and included in the medical insurance system of Zhejiang and other provinces. Flavonoids are the most important components of <jats:italic>T. hemsleyanum</jats:italic>, and their contents are mainly regulated by ultraviolet (UV) radiation. In this study, the total flavonoid contents, flavonoid monomer contents, and flavonoid synthesis related enzyme activities (phenylalanine ammonia–lyase, chalcone synthase, and chalcone isomerase), anti-oxidant enzyme activities (catalase, peroxidase, and superoxide dismutase), and biochemical indicators (malondialdehyde, free amino acid, soluble protein, and soluble sugar) in the leaves (L) and root tubers (R) of <jats:italic>T. hemsleyanum</jats:italic> with UV treatments were determined. Three kinds of UV radiation (UV-A, UV-B, and UV-C) and six kinds of radiation durations (15 and 30 min, 1, 2, 3, and 5 h) were used. Appropriate doses of UV-B and UV-C radiation (30 min to 3 h) induced eustress, which contributed to the accumulation of flavonoids and improve protective enzyme system activities and bioactive compound contents. Especially, certain results were observed in several special structures of the flavonoid monomer: quercetin contents in L increased by nearly 20 times, isoquercitrin contents in R increased by nearly 34 times; most of flavonoids with glycoside content, such as quercitrin (19 times), baicalin (16 times), and apigenin-7G (13 times), increased multiple times. Compared with the CK group, the flavonoid synthase activities, anti-oxidant enzyme activities, and biochemical substance contents in L and R all increased with UV treatments. This study provides a theoretical foundation for regulating flavonoids by light factors and improving the quality of <jats:italic>T. hemsleyanum</jats:italic> in production and medical industries.</jats:p>

<jats:p>Slight crack of cottonseed is a critical factor influencing the germination rate of cotton due to foamed acid or water entering cottonseed through testa. However, it is very difficult to detect cottonseed with slight crack using common non-destructive detection methods, such as machine vision, optical spectroscopy, and thermal imaging, because slight crack has little effect on morphology, chemical substances or temperature. By contrast, the acoustic method shows a sensitivity to fine structure defects and demonstrates potential application in seed detection. This paper presents a novel method to detect slightly cracked cottonseed using air-coupled ultrasound with a light-weight vision transformer (ViT) and a sound-to-image encoding method. The echo signal of air-coupled ultrasound from cottonseed is obtained by non-contact and non-destructive methods. The intrinsic mode functions (IMFs) of ultrasound signal are obtained as the sound features using variational mode decomposition (VMD) approach. Then the sound features are converted into colorful images by a color encoding method. This method uses different colored lines to represent the changes of different values of IMFs according to the specified encoding period. A light-weight MobileViT method is utilized to identify the slightly cracked cottonseeds using encoding colorful images corresponding to cottonseeds. The experimental results show an average overall recognition accuracy of 90.7% for slightly cracked cottonseed from normal cottonseed, which indicates that the proposed method is reliable to applications in detection task of cottonseed with slight crack.</jats:p>