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<jats:p>Tree species establish mycorrhizal associations with both ectomycorrhizal (EM) and arbuscular mycorrhizal fungi (AM), which play crucial roles in facilitating plant phosphorus (P) acquisition. However, little attention has been given to the effects of EM and AM species on soil P dynamics and the underlying mechanisms in subtropical forests, where P availability is typically low. To address this knowledge gap, we selected two EM species (<jats:italic>Pinus massoniana</jats:italic> - PM and <jats:italic>Castanopsis carlesii</jats:italic> - CC) and two AM species (<jats:italic>Cunninghamia lanceolata</jats:italic> - Chinese fir, CF and <jats:italic>Michelia macclurei</jats:italic> - MM) in a common garden established in 2012 in subtropical China. We investigated soil properties (e.g., pH, soil organic carbon, total nitrogen, and dissolved organic nitrogen), soil P fractions, phospholipid fatty acids (PLFAs), enzyme activities, foliar manganese (Mn) concentration, and foliar nutrients and stoichiometry. Our findings revealed that soils hosting EM species had higher levels of resin P, NaHCO<jats:sub>3</jats:sub>-Pi, extractable Po, total P, and a greater percentage of extractable Po to total P compared to soils with AM species. These results indicate that EM species enhance soil P availability and organic P accumulation in contrast to AM species. Moreover, EM species exhibited higher P return to soil (indicated by higher foliar P concentrations) when compared to AM species, which partly explains higher P accumulation in soils with EM species. Additionally, resin P showed a positive correlation with acid phosphatase (ACP) activity, whereas no correlation was found with foliar Mn concentration, which serves as a proxy for the mobilization of sorbed soil P. Such findings indicate that organic P mineralization has a more substantial impact than inorganic P desorption in influencing P availability in soils hosting both EM and AM species. In summary, our study contributes to a more comprehensive understanding of the effects of mycorrhizal associations on soil P accumulation in subtropical forests and provide valuable insights into plant-soil interactions and their role in P cycling in regions with limited P availability.</jats:p>

<jats:p>Duckweed is an aquatic model plant with tremendous potential in industrial and agricultural applications. Duckweed rarely flowers which significantly hinders the resource collection and heterosis utilization. Salicylic acid (SA) can significantly induce duckweed to flower; however, the underlying regulatory mechanisms remain largely unknown. In this work, transcriptome and proteome were conducted in parallel to examine the expression change of genes and proteins in <jats:italic>Lemna gibba</jats:italic> under SA treatment. A high-quality reference transcriptome was generated using Iso-Seq strategy, yielding 42,281 full-length transcripts. A total of 422, 423, and 417 differentially expressed genes (DEGs), as well as 213, 51, and 92 differentially expressed proteins (DEPs), were identified at flower induction, flower initiation, and flowering stages by ssRNA-seq and iTRAQ methods. Most DEGs and DEPs were only regulated at either the transcriptomic or proteomic level. Additionally, DEPs exhibited low expression correlations with the corresponding mRNAs, suggesting that post-transcriptional regulation plays a pivotal role in SA-induced flowering in <jats:italic>L. gibba</jats:italic>. Specifically, the genes related to photosynthesis, stress, and hormone metabolism were mainly regulated at the mRNA level, those associated with mitochondrial electron transport / ATP synthesis, nucleotide synthesis, and secondary metabolism were regulated at the protein level, while those related to redox metabolism were regulated at the mRNA and/or protein levels. The post-transcriptional regulation of genes relevant to hormone synthesis, transcription factors, and flowering was also extensively analyzed and discussed. This is the first study of integrative transcriptomic and proteomic analyses in duckweed, providing novel insights of post-transcriptional regulation in SA-induced flowering of <jats:italic>L. gibba</jats:italic>.</jats:p>

<jats:p>The European Green Deal aims to reduce the pesticide use, notably by developing biocontrol products to protect crops from diseases. Indeed, the use of significant amounts of chemicals negatively impact the environment such as soil microbial biodiversity or groundwater quality, and human health. Grapevine (<jats:italic>Vitis vinifera</jats:italic>) was selected as one of the first targeted crop due to its economic importance and its dependence on fungicides to control the main damaging diseases worldwide: grey mold, downy and powdery mildews. Chitosan, a biopolymer extracted from crustacean exoskeletons, has been used as a biocontrol agent in many plant species, including grapevine, against a variety of cryptogamic diseases such as downy mildew (<jats:italic>Plasmopara viticola</jats:italic>), powdery mildew (<jats:italic>Erysiphe necator</jats:italic>) and grey mold (<jats:italic>Botrytis cinerea</jats:italic>). However, the precise molecular mechanisms underlying its mode of action remain unclear: is it a direct biopesticide effect or an indirect elicitation activity, or both? In this study, we investigated six chitosans with diverse degrees of polymerization (DP) ranging from low to high DP (12, 25, 33, 44, 100, and 470). We scrutinized their biological activities by evaluating both their antifungal properties and their abilities to induce grapevine immune responses. To investigate their elicitor activity, we analyzed their ability to induce MAPKs phosphorylation, the activation of defense genes and metabolite changes in grapevine. Our results indicate that the chitosans with a low DP are more effective in inducing grapevine defenses and possess the strongest biopesticide effect against <jats:italic>B. cinerea</jats:italic> and <jats:italic>P. viticola</jats:italic>. We identified chitosan with DP12 as the most efficient resistance inducer. Then, chitosan DP12 has been tested against downy and powdery mildews in the vineyard trials performed during the last three years. Results obtained indicated that a chitosan-based biocontrol product could be sufficiently efficient when the amount of pathogen inoculum is quite low and could be combined with only two fungicide treatments during whole season programs to obtain a good protection efficiency. On the whole, a chitosan-based biocontrol product could become an interesting alternative to meet the chemicals reduction targeted in sustainable viticulture.</jats:p>

<jats:p>Holocentric karyotypes are assumed to rapidly evolve through chromosome fusions and fissions due to the diffuse nature of their centromeres. Here, we took advantage of the recent availability of a chromosome-scale reference genome for <jats:italic>Rhynchospora breviuscula</jats:italic>, a model species of this holocentric genus, and developed the first set of oligo-based barcode probes for a holocentric plant. These probes were applied to 13 additional species of the genus, aiming to investigate the evolutionary dynamics driving the karyotype evolution in <jats:italic>Rhynchospora</jats:italic>. The two sets of probes were composed of 27,392 (green) and 23,968 (magenta) oligonucleotides (45-nt long), and generated 15 distinct FISH signals as a unique barcode pattern for the identification of all five chromosome pairs of the <jats:italic>R. breviuscula</jats:italic> karyotype. Oligo-FISH comparative analyzes revealed different types of rearrangements, such as fusions, fissions, putative inversions and translocations, as well as genomic duplications among the analyzed species. Two rounds of whole genome duplication (WGD) were demonstrated in <jats:italic>R. pubera</jats:italic>, but both analyzed accessions differed in the complex chain of events that gave rise to its large, structurally diploidized karyotypes with 2<jats:italic>n</jats:italic> = 10 or 12. Considering the phylogenetic relationships and divergence time of the species, the specificity and synteny of the probes were maintained up to species with a divergence time of ~25 My. However, karyotype divergence in more distant species hindered chromosome mapping and the inference of specific events. This barcoding system is a powerful tool to study chromosomal variations and genomic evolution in holocentric chromosomes of <jats:italic>Rhynchospora</jats:italic> species.</jats:p>

<jats:p><jats:italic>Astragalus membranaceus</jats:italic> is a medicinal plant mainly used in East Asia and contains abundant secondary metabolites. Despite the importance of this plant, the available genomic and genetic information is still limited. <jats:italic>De novo</jats:italic> transcriptome construction is recognized as an essential method for transcriptome research when reference genome information is incomplete. In this study, we constructed three individual transcriptome sets (unigene sets) for detailed analysis of the phenylpropanoid biosynthesis pathway, a major metabolite of <jats:italic>A. membranaceus</jats:italic>. Set-1 was a circular consensus sequence (CCS) generated using PacBio sequencing (PacBio-seq). Set-2 consisted of hybridized assembled unigenes with Illumina sequencing (Illumina-seq) reads and PacBio CCS using rnaSPAdes. Set-3 unigenes were assembled from Illumina-seq reads using the Trinity software. Construction of multiple unigene sets provides several advantages for transcriptome analysis. First, it provides an appropriate expression filtering threshold for assembly-based unigenes: a threshold transcripts per million (TPM) ≥ 5 removed more than 88% of assembly-based unigenes, which were mostly short and low-expressing unigenes. Second, assembly-based unigenes compensated for the incomplete length of PacBio CCSs: the ends of the 5`/3` untranslated regions of phenylpropanoid-related unigenes derived from set-1 were incomplete, which suggests that PacBio CCSs are unlikely to be full-length transcripts. Third, more isoform unigenes could be obtained from multiple unigene sets; isoform unigenes missing in Set-1 were detected in set-2 and set-3. Finally, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that phenylpropanoid biosynthesis and carbohydrate metabolism were highly activated in <jats:italic>A. membranaceus</jats:italic> roots. Various sequencing technologies and assemblers have been developed for <jats:italic>de novo</jats:italic> transcriptome analysis. However, no technique is perfect for <jats:italic>de novo</jats:italic> transcriptome analysis, suggesting the need to construct multiple unigene sets. This method enables efficient transcript filtering and detection of longer and more diverse transcripts.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Eelgrass is a typical marine angiosperm that exhibits strong adaptability to high-salt environments. Previous studies have shown that various growth and physiological indicators were significantly affected after the nitrate reductase (NR) pathway for nitric oxide (NO) synthesis in eelgrass was blocked.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>To analyze the molecular mechanism of NO on the adaptability to high-salt environment in eelgrass, we treated eelgrass with artificial seawater (control group) and artificial seawater with 1 mM/L Na<jats:sub>2</jats:sub>WO<jats:sub>4</jats:sub> (experimental group). Based on transcriptomics and metabolomics, we explored the molecular mechanism of NO affecting the salt tolerance of eelgrass.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We obtained 326, 368, and 859 differentially expressed genes (DEGs) by transcriptome sequencing in eelgrass roots, stems, and leaves, respectively. Meanwhile, we obtained 63, 52, and 36 differentially accumulated metabolites (DAMs) by metabolomics in roots, stems, and leaves, respectively. Finally, through the combined analysis of transcriptome and metabolome, we found that the NO regulatory mechanism of roots and leaves of eelgrass is similar to that of terrestrial plants, while the regulatory mechanism of stems has similar and unique features.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>NO in eelgrass roots regulates osmotic balance and antioxidant defense by affecting genes in transmembrane transport and jasmonic acid-related pathways to improve the adaptability of eelgrass to high-salt environments. NO in eelgrass leaves regulates the downstream antioxidant defense system by affecting the signal transduction of plant hormones. NO in the stems of eelgrass regulates ion homeostasis by affecting genes related to ion homeostasis to enhance the adaptability of eelgrass to high-salt environments. Differently, after the NO synthesis was inhibited, the glyoxylate and dicarboxylate metabolism, as well as the tricarboxylic acid (TCA) cycle, was regulated by glucose metabolism as a complementary effect to cope with the high-salt environment in the stems of eelgrass. These are studies on the regulatory mechanism of NO in eelgrass, providing a theoretical basis for the study of the salt tolerance mechanism of marine plants and the improvement of terrestrial crop traits. The key genes discovered in this study can be applied to increase salt tolerance in terrestrial crops through cloning and molecular breeding methods in the future.</jats:p></jats:sec>

<jats:p>Soybean [<jats:italic>Glycine max</jats:italic> (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the <jats:italic>E8</jats:italic> locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524<jats:sub>F2:F3</jats:sub> and QS15544<jats:sub>RIL</jats:sub>) having fixed <jats:italic>E1</jats:italic>, <jats:italic>E2</jats:italic>, <jats:italic>E3</jats:italic>, and <jats:italic>E4</jats:italic> alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the <jats:italic>E8</jats:italic> region: GM04:16,974,874-17,152,230 (<jats:italic>E8-r1</jats:italic>); GM04:35,168,111-37,664,017 (<jats:italic>E8-r2</jats:italic>); and GM04:41,808,599-42,376,237 (<jats:italic>E8-r3</jats:italic>). Using a five-step variant analysis pipeline, we identified <jats:italic>Protein far-red elongated hypocotyl 3</jats:italic> (<jats:italic>Glyma.04G124300</jats:italic>; <jats:italic>E8-r1</jats:italic>), <jats:italic>E1-like-a</jats:italic> (<jats:italic>Glyma.04G156400</jats:italic>; <jats:italic>E8-r2</jats:italic>), <jats:italic>Light-harvesting chlorophyll-protein complex I subunit A4</jats:italic> (<jats:italic>Glyma.04G167900</jats:italic>; <jats:italic>E8-r3</jats:italic>), and <jats:italic>Cycling dof factor 3</jats:italic> (<jats:italic>Glyma.04G168300</jats:italic>; <jats:italic>E8-r3</jats:italic>) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including <jats:italic>Glyma.04G050200</jats:italic> (<jats:italic>Early flowering 3/E6</jats:italic> locus), with the <jats:italic>E8-r3</jats:italic> region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene <jats:italic>Glyma.07G058200</jats:italic> (<jats:italic>Protein suppressor of PHYA-105</jats:italic>). These findings demonstrate that the locus known as <jats:italic>E8</jats:italic> is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.</jats:p>

<jats:p>Soil salinization represents an increasingly serious threat to agronomic productivity throughout the world, as rising ion concentrations can interfere with the growth and development of plants, ultimately reducing crop yields and quality. A combination of factors is driving this progressive soil salinization, including natural causes, global climate change, and irrigation practices that are increasing the global saline-alkali land footprint. Salt stress damages plants both by imposing osmotic stress that reduces water availability while also inducing direct sodium- and chlorine-mediated toxicity that harms plant cells. <jats:italic>Vitis vinifera</jats:italic> L. exhibits relatively high levels of resistance to soil salinization. However, as with other crops, grapevine growth, development, fruit yields, and fruit quality can all be adversely affected by salt stress. Many salt-tolerant grape germplasm resources have been screened in recent years, leading to the identification of many genes associated to salt stress and the characterization of the mechanistic basis for grapevine salt tolerance. These results have also been leveraged to improve grape yields through the growth of more tolerant cultivars and other appropriate cultivation measures. The present review was formulated to provide an overview of recent achievements in the field of research focused on grapevine salt tolerance from the perspectives of germplasm resource identification, the mining of functional genes, the cultivation of salt-tolerant grape varieties, and the selection of appropriate cultivation measures. Together, we hope that this systematic review will offer insight into promising approaches to enhancing grape salt tolerance in the future.</jats:p>

<jats:p>New transposon insertions are deleterious to genome stability. The RNA-directed DNA methylation (RdDM) pathway evolved to regulate transposon activity via DNA methylation. However, current studies have not yet clearly described the transposition regulation. <jats:italic>ONSEN</jats:italic> is a heat-activated retrotransposon that is activated at 37°C. The plant-specific SUPPRESSOR OF VARIEGATION 3–9 HOMOLOG (SUVH) family proteins function downstream of the RdDM pathway. The SUVH protein families are linked to TE silencing by two pathways, one through DNA methylation and the other through chromatin remodeling. In this study, we analyzed the regulation of <jats:italic>ONSEN</jats:italic> activity by SUVH2. We observed that <jats:italic>ONSEN</jats:italic> transcripts were increased; however, there was no transpositional activity in Arabidopsis <jats:italic>suvh2</jats:italic> mutant. The <jats:italic>suvh2</jats:italic> mutant produced siRNAs from the <jats:italic>ONSEN</jats:italic> locus under heat stress, suggesting that siRNAs are involved in suppressing transposition. These results provide new insights into the regulatory mechanisms of retrotransposons that involve siRNA in the RdDM pathway.</jats:p>