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<jats:p>Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla <jats:italic>Chlorophyta</jats:italic> and <jats:italic>Streptophyta</jats:italic> that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na<jats:sup>+</jats:sup>/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.</jats:p>

<jats:p>The MIKC<jats:sup>C</jats:sup>-type gene family plays important roles in plant growth, development, and tolerance of biotic and abiotic stress, especially during floral organ differentiation. However, there have been no studies of MIKC<jats:sup>C</jats:sup>-type genes in rose, and functional differentiation of family members has not been explored. In this study, we identified 42 MIKC<jats:sup>C</jats:sup>-type genes in rose, classified the genes into 12 subfamilies, and constructed a phylogenetic tree. We performed expression analysis of these genes, and found that expression patterns correlated with the predicted subfamily, indicating that the features of MIKC<jats:sup>C</jats:sup>-type genes were broadly conserved during evolution. Collinear analysis of MIKC<jats:sup>C</jats:sup> genes among Rosaceae species confirmed the occurrence of whole genome duplications (WGD) and revealed some species-specific MIKC<jats:sup>C</jats:sup> genes. Transcriptome analysis showed that the expression of some MIKC<jats:sup>C</jats:sup>-type genes responded to low temperatures (4°C, 24 h) during flower organ differentiation. These conserved, duplicated, and novel expression patterns of MIKC<jats:sup>C</jats:sup>-type genes may have facilitated the adaptation of rose to various internal and external environmental changes. The results of this study provide a theoretical basis for future functional analysis of the MIKC<jats:sup>C</jats:sup> genes in rose and investigation of the evolutionary pattern of the MIKC<jats:sup>C</jats:sup> gene family in the Rosaceae genome.</jats:p>

<jats:p>Food production in sustainable agricultural systems is one of the main challenges of modern agriculture. Vegetable intercropping may be a strategy to mitigate greenhouse gas (GHG) emissions, replacing monoculture systems. The objective is to identify the main emissions sources and to estimate GHG emissions of intercropping and monoculture production of collard greens, New Zealand spinach and chicory. Four scenarios were evaluated: ICS – intercropping collard greens and spinach; MCS – monoculture collard greens and spinach; ICC – intercropping collard greens and chicory; MCC - monoculture collard greens and chicory. The boundaries’ reach from “cradle-to-gate” and the calculation of GHG emissions were performed using IPCC methodology and specific factors (Tier 2). The total GHG emitted was standardized as CO<jats:sub>2</jats:sub> equivalent (CO<jats:sub>2</jats:sub>eq). The GHG emissions in ICS and ICC scenarios were approximately 31% lower than in MCS and MCC scenarios. Carbon footprint in ICS (0.030 kg CO<jats:sub>2</jats:sub>eq kg<jats:sup>-1</jats:sup> vegetables year<jats:sup>-1</jats:sup>) and ICC (0.033 kg CO<jats:sub>2</jats:sub>eq kg<jats:sup>-1</jats:sup> vegetables year<jats:sup>-1</jats:sup>) scenarios were also lower than in MCS (0.082 kg CO<jats:sub>2</jats:sub>eq kg<jats:sup>-1</jats:sup> vegetables year<jats:sup>-1</jats:sup>) and MCC (0.071 kg CO<jats:sub>2</jats:sub>eq kg<jats:sup>-1</jats:sup> vegetables year<jats:sup>-1</jats:sup>) scenarios. Fertilizers, fuel (diesel) and irrigation were the main contributing sources for total GHG emitted and carbon footprint in all evaluated scenarios. The results suggest that intercropping systems may reduce GHG emissions associated with the production of vegetables evaluated as compared with monoculture.</jats:p>

<jats:p>Sclerotinia disease and weeds of <jats:italic>Brassica napus</jats:italic> greatly reduce crop yields. However, brassinolides can improve the resistance of plants to sclerotinia diseases and herbicides. In this study, we investigated the effects of brassinolide on the occurrence, physiological indices, yield, and gene expression of Fanming No. 1 seeds under sclerotinia and glufosinate stress. The results showed that soaking of the seeds in 0.015% brassinolide for 6 h reduced the incidence of sclerotinia by 10%. Additionally, in response to glufosinate stress at the seedling stage, the enzyme activities of catalase and superoxide dismutase increased by 9.6 and 19.0 U/gFW/min, respectively, and the soluble sugar content increased by 9.4 mg/g, increasing the stress resistance of plants and yield by 2.4%. <jats:italic>LHCB1</jats:italic>, <jats:italic>fabF</jats:italic>, <jats:italic>psbW</jats:italic>, <jats:italic>CYP90A1</jats:italic>, <jats:italic>ALDH3F1</jats:italic>, <jats:italic>ACOX1</jats:italic>, <jats:italic>petF</jats:italic>, and <jats:italic>ACSL</jats:italic> were screened by transcriptome analysis. <jats:italic>ALDH3F1</jats:italic> and <jats:italic>CYP90A1</jats:italic> were identified as key genes. Following glufosinate treatment, transgenic plants overexpressing ALDH3F1 and CYP90A1 were found to be resistant to glufosinate, and the expression levels of the <jats:italic>ALDH3F1</jats:italic> and <jats:italic>CYP90A1</jats:italic> were 1.03–2.37-fold as high as those in the control. The expression level of <jats:italic>ATG3</jats:italic>, which is an antibacterial gene related to sclerotinia disease, in transgenic plants was 2.40–2.37-fold as high as that in the control. Our results indicate that these two key genes promote plant resistance to sclerotinia and glufosinate. Our study provides a foundation for further studies on the molecular mechanisms of rapeseed resistance breeding and selection of new resistant varieties.</jats:p>

<jats:p><jats:italic>Paeonia ostii</jats:italic>, a widely cultivated tree peony species in China, is a resourceful plant with medicinal, ornamental and oil value. However, fleshy roots lead to a low tolerance to waterlogging in <jats:italic>P. ostii</jats:italic>. In this study, <jats:italic>P. ostii</jats:italic> roots were sequenced using a hybrid approach combining single-molecule real-time and next-generation sequencing platforms to understand the molecular mechanism underlying the response to this sequentially waterlogging stress, the normal growth, waterlogging treatment (WT), and waterlogging recovery treatment (WRT). Our results indicated that the strategy of <jats:italic>P. ostii</jats:italic>, in response to WT, was a hypoxic resting syndrome, wherein the glycolysis and fermentation processes were accelerated to maintain energy levels and the tricarboxylic acid cycle was inhibited. <jats:italic>P. ostii</jats:italic> enhanced waterlogging tolerance by reducing the uptake of nitrate and water from the soil. Moreover, transcription factors, such as AP2/EREBP, WRKY, MYB, and NAC, played essential roles in response to WT and WRT. They were all induced in response to the WT condition, while the decreasing expression levels were observed under the WRT condition. Our results contribute to understanding the defense mechanisms against waterlogging stress in <jats:italic>P. ostii</jats:italic>.</jats:p>

<jats:p>Crop Wild Relatives (CWR) are a valuable source of genetic diversity that can be transferred to commercial crops, so their conservation will become a priority in the face of climate change. Bizarrely, <jats:italic>in situ</jats:italic> conserved CWR populations and the traits one might wish to preserve in them are themselves vulnerable to climate change. In this study, we used a quantitative machine learning predictive approach to project the resistance of CWR populations of lentils to a common disease, lentil rust, caused by fungus <jats:italic>Uromyces viciae-fabae</jats:italic>. Resistance is measured through a proxy quantitative value, DSr (Disease Severity relative), quite complex and expensive to get. Therefore, machine learning is a convenient tool to predict this magnitude using a well-curated georeferenced calibration set. Previous works have provided a binary outcome (resistant <jats:italic>vs.</jats:italic> non-resistant), but that approach is not fine enough to answer three practical questions: which variables are key to predict rust resistance, which CWR populations are resistant to rust under current environmental conditions, and which of them are likely to keep this trait under different climate change scenarios. We first predict rust resistance in present time for crop wild relatives that grow up inside protected areas. Then, we use the same models under future climate IPCC (Intergovernmental Panel on Climate Change) scenarios to predict future DSr values. Populations that are rust-resistant by now and under future conditions are optimal candidates for further evaluation and <jats:italic>in situ</jats:italic> conservation of this valuable trait. We have found that rust-resistance variation as a result of climate change is not uniform across the geographic scope of the study (the Mediterranean basin), and that candidate populations share some interesting common environmental conditions.</jats:p>

<jats:p>The carbamoyltransferase or aspartate carbamoyltransferase (ATCase)/ornithine carbamoyltransferase (OTCase) is an evolutionary conserved protein family, which contains two genes, ATCase and OTCase. The ATCase catalyzes the committed step in the synthesis of UMP from which all pyrimidine molecules are synthesized. The second member, OTCase, catalytically regulates the conversion of ornithine to citrulline. This study traces the evolution of the carbomoyltransferase genes in the plant kingdom and their role during fruit ripening in fleshy fruits. These genes are highly conserved throughout the plant kingdom and, except for melon and watermelon, do not show gene expansion in major fleshy fruits. In this study, 393 carbamoyltransferase genes were identified in the plant kingdom, including 30 fleshy fruit representatives. Their detailed phylogeny, evolutionary patterns with their expression during the process of fruit ripening, was analyzed. The ATcase and OTcase genes were conserved throughout the plant kingdom and exhibited lineage-specific signatures. The expression analysis of the ATcase and OTcase genes during fruit development and ripening in climacteric and non-climacteric fruits showed their involvement in fruit ripening irrespective of the type of fruits. No direct role in relation to ethylene-dependent or -independent ripening was identified; however, the co-expression network suggests their involvement in the various ripening processes.</jats:p>

<jats:p><jats:italic>AINTEGUMENTA-LIKE</jats:italic> (AIL) transcription factors are widely studied and play crucial roles in plant growth and development. However, the functions of the <jats:italic>AIL</jats:italic> family in legume species are largely unknown. In this study, 11 <jats:italic>MtAIL</jats:italic> genes were identified in the model legume <jats:italic>Medicago truncatula</jats:italic>, of which four of them are <jats:italic>MtANTs</jats:italic>. <jats:italic>In situ</jats:italic> analysis showed that <jats:italic>MtANT1</jats:italic> was highly expressed in the shoot apical meristem (SAM) and leaf primordium. Characterization of <jats:italic>mtant1 mtant2 mtant3 mtant4</jats:italic> quadruple mutants and <jats:italic>MtANT1</jats:italic>-overexpressing plants revealed that <jats:italic>MtANTs</jats:italic> were not only necessary but also sufficient for the regulation of leaf size, and indicated that they mainly function in the regulation of cell proliferation during secondary morphogenesis of leaves in <jats:italic>M. truncatula</jats:italic>. This study systematically analyzed the <jats:italic>MtAIL</jats:italic> family at the genome-wide level and revealed the functions of <jats:italic>MtANTs</jats:italic> in leaf growth. Thus, these genes may provide a potential application for promoting the biomass of legume forages.</jats:p>