Transcriptome Analysis and Identification of Genes Associated with Starch Metabolism in Castanea henryi Seed (Fagaceae)

Transcriptome and metabolome analysis of senescent rice (Oryza sativa L.) seeds: insights into the mechanism of germination vigor and seedling morphogenesis

Seeds germination and seedlings growth are crucial factors in ensuring effective rice grain productivity. However, the mechanisms for maintaining seed vigor remains largely unknown. The seed aging phenomenon that occurs during storage poses a significant challenge to crop production, as it can lead to reduced germination rates and impaired seed vitality. The current study explored the underlying mechanisms that enable rice seeds to maintain high germination rates and seedling vigor after long - term storage. We employed transcriptomic and metabolomic techniques to identify metabolic changes and key genes associated with the aging of rice seeds during long - term storage. We utilized indicators such as imbibition rate (IR), germination rate (GR), mean germination time (MGT), germination coefficient (GC), germination index (GI), and germination potential (GP) to comprehensively assess germination activity. Traits including seedling emergence rate, seedling strength index, photosynthetic parameters, carbohydrate accumulation, and enzyme activity related to carbon metabolism were used to determine the impact of seed storage duration on seedling growth. Our research findings revealed significant differences in gene expression patterns and metabolic characteristics among seeds stored for different duration. Notably, IAA levels, the IAA/ABA ratio, and linoleic acid metabolism were identified as key factors affecting germination and seedling development. Results indicated that with the extension of storage duration, the germination potential and seedling development significantly declined. Current study provided a comprehensive understanding of the physiological and molecular mechanisms behind the germination and morphogenesis of rice seeds under different storage years. The insights gained from this study could be utilized to improve the storage and quality control of rice seeds, thereby ultimately enhancing agricultural productivity.

Enhancing sweet sorghum emergence and stress resilience in saline-alkaline soils through ABA seed priming: insights into hormonal and metabolic reprogramming

Sweet sorghum (Sorghum bicolor Moench) seedling emergence and growth are significantly impeded by physical soil crusts (PSCs) in saline-alkaline soils. Abscisic acid (ABA) is a potent seed priming agent known for modulating plant physiological and metabolic responses under salinity stress. However, the influence of ABA priming on seedling emergence in PSCs remains unclear. This study conducted both pot and field experiment to examine the effects of ABA priming on enhancing seedling emergence under PSC conditions. ABA priming altered the balance of at least 24 endogenous phytohormones, including abscisic acid, jasmonic acid, gibberellins, ethylene, auxins, and cytokinins. Additionally, it reprogrammed starch and sucrose metabolism, resulting in the differential expression of genes encoding key enzymes such as AMY, BAM, and INV, which are crucial for converting complex sugars into readily available energy sources, thereby supporting seedling growth. Furthermore, 52 differentially expressed metabolites (DEMs) of flavonoids were identified in germinating seedlings, including 15 anthocyanins, 3 flavones, 7 flavonols, 6 isoflavones, 7 flavanones, and 14 other flavonoids. Genetic and metabolic co-expression network analysis, along with flavonoid biosynthesis pathway exploration, revealed that the biosynthesis of 17 key DEMs-including liquiritigenin, apigenin, kaempferide, syringetin, phloretin, formononetin, dihydrokaempferol, and xanthohumol-was regulated by 10 differentially expressed genes (DEGs) associated with flavonoid biosynthesis. These DEGs encoded 7 enzymes critical for this pathway, including chalcone synthase, shikimate O-hydroxycinnamoyltransferase, bifunctional dihydroflavonol 4-reductase, naringenin 7-O-methyltransferase, and anthocyanidin reductase. This regulation, along with reduced levels of superoxide anion (O2-) and malondialdehyde and increased antioxidant enzyme activities, suggested that flavonoids played a vital role in mitigating oxidative stress. These findings demonstrate that ABA priming can effectively enhance sweet sorghum seedling emergence in PSCs by accelerating emergence and boosting stress resistance.

Harnessing de novo transcriptome sequencing to identify and characterize genes regulating carbohydrate biosynthesis pathways in Salvia guaranitica L

Introduction

Carbohydrate compounds serve multifaceted roles, from energy sources to stress protectants, found across diverse organisms including bacteria, fungi, and plants. Despite this broad importance, the molecular genetic framework underlying carbohydrate biosynthesis pathways, such as starch, sucrose, and glycolysis/gluconeogenesis in Salvia guaranitica, remains largely unexplored.

Methods

In this study, the Illumina-HiSeq 2500 platform was used to sequence the transcripts of S. guaranitica leaves, generating approximately 8.2 Gb of raw data. After filtering and removing adapter sequences, 38 million reads comprising 210 million high-quality nucleotide bases were obtained. De novo assembly resulted in 75,100 unigenes, which were annotated to establish a comprehensive database for investigating starch, sucrose, and glycolysis biosynthesis. Functional analyses of glucose-6-phosphate isomerase (SgGPI), trehalose-6-phosphate synthase/phosphatase (SgT6PS), and sucrose synthase (SgSUS) were performed using transgenic Arabidopsis thaliana.

Results

Among the unigenes, 410 were identified as putatively involved in these metabolic pathways, including 175 related to glycolysis/gluconeogenesis and 235 to starch and sucrose biosynthesis. Overexpression of SgGPI, SgT6PS, and SgSUS in transgenic A. thaliana enhanced leaf area, accelerated flower formation, and promoted overall growth compared to wild-type plants.

Discussion

These findings lay a foundation for understanding the roles of starch, sucrose, and glycolysis biosynthesis genes in S. guaranitica, offering insights into future metabolic engineering strategies for enhancing the production of valuable carbohydrate compounds in S. guaranitica or other plants.

Combined transcriptome and metabolome analysis of sugar and fatty acid of aromatic coconut and non-aromatic coconut in China

Sugar and fatty acid content are among the important factors that contribute to the intensity of flavor in aromatic coconut. Gaining a comprehensive understanding of the sugar and fatty acid metabolites in the flesh of aromatic coconuts, along with identifying the key synthetic genes, is of significant importance for improving the development of desirable character traits in these coconuts. However, the related conjoint analysis of metabolic targets and molecular synthesis mechanisms has not been carried out in aromatic coconut until now. UPLC-MS/MS combined with RNA-Seq were performed in aromatic coconut (AC) and non-aromatic coconut (NAC) meat at 7, 9 and 11 months. The results showed that D-fructose in AC coconut meat was 3.48, 2.56 and 3.45 fold higher than that in NAC coconut meat. Similarly, D-glucose in AC coconut meat was 2.48, 2.25 and 3.91 fold higher than that in NAC coconut meat. The NAC coconut meat showed a 1.22-fold rise in the content of lauric acid compared to the AC coconut meat when it reached 11 months of age. Myristic acid content in NAC coconut meat was 1.47, 1.44 and 1.13 fold higher than that in AC coconut meat. The palmitic acid content in NAC coconut meat was 1.62 and 1.34 fold higher than that in AC coconut meat. The genes SPS, GAE, GALE, GLCAK, UGE, UGDH, FBP, GMLS, PFK, GPI, RHM, ACC, FabF, FatA, FabG, and FabI exhibited a negative correlation with D-fructose (r = -0.81) and D-glucose (r = -0.99) contents, while showing a positive correlation (r = 0.85-0.96) with lauric acid and myristic acid. Furthermore, GALE, GLCAK, FBP, GMLS, and ACC displayed a positive correlation (r = 0.83-0.94) with palmitic acid content. The sugar/organic acid ratio exhibited a positive correlation with SPS, GAE, UGE, FabF, FabZ and FabI.

Comparative transcriptome analysis reveals the potential mechanism of GA3-induced dormancy release in Suaeda glauca black seeds

Suaeda glauca Bunge produces dimorphic seeds on the same plant, with brown seeds displaying non-dormant characteristics and black seeds exhibiting intermediate physiological dormancy traits. Previous studies have shown that black seeds have a very low germination rate under natural conditions, but exogenous GA3 effectively enhanced the germination rate of black seeds. However, the physiological and molecular mechanisms underlying the effects of GA3 on S. glauca black seeds are still unclear. In this study, transcriptomic profiles of seeds at different germination stages with and without GA3 treatment were analyzed and compared, and the TTF, H2O2, O2 -, starch, and soluble sugar contents of the corresponding seed samples were determined. The results indicated that exogenous GA3 treatment significantly increased seed vigor, H2O2, and O2 - contents but decreased starch and soluble sugar contents of S. glauca black seeds during seed dormancy release. RNA-seq results showed that a total of 1136 DEGs were identified in three comparison groups and were involved mainly in plant hormone signal transduction, diterpenoid biosynthesis, flavonoid biosynthesis, phenylpropanoid biosynthesis, and carbohydrate metabolism pathway. Among them, the DEGs related to diterpenoid biosynthesis (SgGA3ox1, SgKAO and SgGA2ox8) and ABA signal transduction (SgPP2Cs) could play important roles during seed dormancy release. Most genes involved in phenylpropanoid biosynthesis were activated under GA3 treatment conditions, especially many SgPER genes encoding peroxidase. In addition, exogenous GA3 treatment also significantly enhanced the expression of genes involved in flavonoid synthesis, which might be beneficial to seed dormancy release. In accordance with the decline in starch and soluble sugar contents, 15 genes involved in carbohydrate metabolism were significantly up-regulated during GA3-induced dormancy release, such as SgBAM, SgHXK2, and SgAGLU, etc. In a word, exogenous GA3 effectively increased the germination rate and seed vigor of S. glauca black seeds by mediating the metabolic process or signal transduction of plant hormones, phenylpropanoid and flavonoid biosynthesis, and carbohydrate metabolism processes. Our results provide novel insights into the transcriptional regulation mechanism of exogenous GA3 on the dormancy release of S. glauca black seeds. The candidate genes identified in this study may be further studied and used to enrich our knowledge of seed dormancy and germination.

Combined effects of micron-sized polyvinyl chloride particles and copper on seed germination of perilla

Microplastics (MPs) and copper (Cu) pollution coexist widely in cultivation environment. In this paper, polyvinyl chloride (PVC) were used to simulate the MPs exposure environment, and the combined effects of MPs + Cu on the germination of perilla seeds were analyzed. The results showed that low concentrations of Cu promoted seed germination, while medium to high concentrations exhibited inhibition and deteriorated the morphology of germinated seeds. The germination potential, germination index and vitality index of 8 mg • L-1 Cu treatment group with were 23.08%, 76.32% and 65.65%, respectively, of the control group. The addition of low concentration PVC increased the above indicators by 1.27, 1.15, and 1.35 times, respectively, while high concentration addition led to a decrease of 65.38%, 82.5%, and 66.44%, respectively. The addition of low concentration PVC reduced the amount of PVC attached to radicle. There was no significant change in germination rate. PVC treatment alone had no significant effect on germination. MPs + Cu inhibited seed germination, which was mainly reflected in the deterioration of seed morphology. Cu significantly enhanced antioxidant enzyme activity, increased reactive oxygen species (ROS) and MDA content. The addition of low concentration PVC enhanced SOD activity, reduced MDA and H2O2 content. The SOD activity of the Cu2+8 + PVC10 group was 4.05 and 1.35 times higher than that of the control group and Cu treatment group at their peak, respectively. At this time, the CAT activity of the Cu2+8 + PVC5000 group increased by 2.66 and 1.42 times, and the H2O2 content was 2.02 times higher than the control. Most of the above indicators reached their peak at 24 h. The activity of α-amylase was inhibited by different treatments, but β-amylase activity, starch and soluble sugar content did not change regularly. The research results can provide new ideas for evaluating the impact of MPs + Cu combined pollution on perilla and its potential ecological risk.

Transcriptome analysis reveals the mechanism of nitrogen fertilizers in starch synthesis and quality in waxy and non-waxy proso millet

Recent findings suggest that optimal application of nitrogen fertilizers can effectively improve the quality of proso millet (PM). Here, we aimed to investigate the pathways associated with starch synthesis and metabolism to elucidate the effect and molecular mechanisms of nitrogen fertilization in starch synthesis and properties in waxy and non-waxy PM varieties using transcriptomic techniques. Co-expression network analysis revealed that the regulation of starch synthesis and quality in PM by nitrogen fertilizer mainly occurred in the S2 and S3 stages during grain filling. Nitrogen fertilization inhibited glycolysis/gluconeogenesis and starch biosynthesis in grains, but increased starch degradation to maltose and dextrin and then to glucose. Moreover, nitrogen fertilization increased starch accumulation by upregulating the expression of SuS and malZ genes, thereby increasing the total starch content in grains. In contrast, nitrogen fertilization suppressed the expression of GBSS gene and decreased amylose content in PM grains, resulting in a relatively higher crystallinity, light transmittance, and breakdown viscosity in the two PM varieties. Overall, these results provided transcriptomics insights into the molecular mechanisms by which nitrogen fertilization regulates starch quality in PM, identified key genes that associated with the starch properties, and provided new insights into the quality cultivation of PM.

Cryopreservation of herbaceous Asteraceae seeds: Effects of seed reserves on seed germination and seedling regrowth

Carbohydrate, lipid and protein, the three main storage reserves of seeds, are the main sources of raw materials and energy for seed germination and early growth stage of seedlings. In this study, the seed of 16 Asteraceae herbaceous ornamentals were used to compare the changes in seed germination, seedling growth indexes and four major storage reserves of seeds before and after cryopreservation. After cryopreservation, seed germination and seedling growth were preserved in most species (11/16), while one species showed significantly improved post-thaw germination and four had decreased germination. In seeds with preserved germination, no clear variation was noted with regards to the four kinds of storage reserves, or only a slight change in one. However, significantly reduced soluble protein, soluble sugar and fat content and increased starch content were detected in seeds showing reduced germination after cryopreservation. The correlation study further showed that the changes in seed germination were positively correlated with soluble protein, soluble sugar and fat, and negatively correlated with starch. In seedling growth indexes, only cotyledon area was correlated to the content of soluble protein, starch, fat, and seed germination after cryopreservation. These results support the use of soluble protein, soluble sugar, starch and fat as indicators of seed germination after cryopreservation, but not for predicting the seedling growth indexes.

CRISPR/Cas9-mediated deletion of large chromosomal segments identifies a minichromosome modulating the Colletotrichum graminicola virulence on maize

Colletotrichum graminicola causes anthracnose on maize, an economically significant disease worldwide. To decipher how the pathogen controls its virulence/pathogenicity on maize at the minichromosomal level, we sequenced the genome and transcriptome of the C. graminicola strain T1-3-3. The 61.91 Mb genome contains three transcriptionally repressed, full-length strain-specific minichromosomes (<1 Mb; Chr11 through Chr13). A CRISPR/Cas9-based system was developed to knock out large chromosomal segments; it involved the generation of multiple simultaneous DNA double-strand breaks across a targeted genomic region, followed by homology-directed replacement thereof with a donor DNA template carrying the selectable marker hygromycin phosphotransferase gene flanked by homologous sequence arms of the targeted region. Using this system, we obtained distinct mutants functionally nullisomic for individual minichromosomes. Only the ΔChr12 mutant lacking the 498.44 Kb genomic region carrying all of the 31 genes of Chr12 exhibited attenuated virulence on maize and was indistinguishable from T1-3-3 in fungal growth and conidiation, indicating that Chr12 is a conditionally dispensable minichromosome and imparts full virulence to C. graminicola on maize. The CRISPR/Cas9-mediated genome editing system developed in this study will enable the determination of the biological functions of minichromosomes or large chromosomal segments in fungal plant pathogens.

Improvement of Seed Germination under Salt Stress via Overexpressing Caffeic Acid O-methyltransferase 1 (SlCOMT1) in Solanum lycopersicum L

Melatonin (MT) is a phytohormone-like substance and is profoundly involved in modulating nearly all aspects of plant development and acclimation to environmental stressors. However, there remain no studies about the effects of MT on tomato seed germination under salt stress. Here we reported that the overexpression of caffeic acid O-methyltransferase 1 (SlCOMT1) significantly increased both MT content and salt tolerance in the germinated seeds of a transgenic tomato relative to wild type (WT) samples. Physiological investigation showed higher amylase activity in the stressed overexpression seeds than WT, leading to the promoted starch decomposition and enhanced soluble sugar content. The stimulated production of osmolytes and enhanced activities of SOD, POD, and CAT, together with the significant reduction in H₂O₂ and O₂^·- accumulation, were revealed in the stressed overexpression seeds relative to WT, largely accounting for their lower membrane lipid peroxidation. qPCR assay showed that, upon salt stress, the transcript abundance of hub genes related to germination (SlCYP707A1, SlABA1, SlGA3ox2 and SlGA2ox4) and stress tolerance (SlCDPK1, SlWRKY33 and SlMAPK1) were distinctly altered in the overexpression samples when compared to WT, providing a molecular basis for MT-mediated improvement of seed salt tolerance. Altogether, our observations shed new insights into biological functions of SlCOMT1 and could expand its utilization in genetic improvement of tomato salt tolerance in future.

Exogenous Spermidine Promotes Germination of Aged Sorghum Seeds by Mediating Sugar Metabolism

Starch, a substance stored in seeds, is the main source of energy for germination in sorghum seeds. However, as the seeds age, the catabolism of seed starch is affected, thereby seriously damaging germination ability. In this study, we aimed to understand how exogenous spermidine promoted germination in aged sorghum seed. Our phenotypic analysis indicated that exogenous spermidine not only significantly improved the germination rate, germination potential, germination index, and vigor index of aged seeds, but also increased the root and shoot length after germination. Further, physiological analysis showed that exogenous spermidine increased the content of soluble sugar by upregulating the activity of amylase and sucrose invertase. Exogenous spermidine also improved the activities of key enzymes in glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway of aged sorghum seeds. Interestingly, exogenous spermidine protected the mitochondrial structure of aged seeds, which was consistent with the increase in the respiration rate and ATP content during seed germination. Moreover, qRT-PCR analysis revealed that exogenous spermidine induced the expression of key genes related to starch and sugar metabolism in aged sorghum seeds. In conclusion, our study demonstrated that exogenous spermidine promoted aged sorghum seed germination by regulating starch and sugar metabolism.

Efficient regeneration of mature castanopsis hystrix from in vitro stem explants

Castanopsis hystrix is one of the main timber trees grown in China. However, severe shortage of natural seeds and the difficulty of explant regeneration has limited seedling supply. As such, there is a need for research on asexual multiplication of C. hystrix. This study established a rapid propagation technology system for C. hystrix genotypes, including explant treatment, proliferation, and rooting. HZ (a modified MS medium) supplemented with 4.4 μM BA and 0.5 μM IBA was found to be the optimal medium for shoot sprouting. The maximum proliferation coefficient and the number of effective shoots was obtained on HZ medium supplemented with 2.6 μM BA and 1.0 μM IBA, were 3.00 and 5.63, respectively. A rooting rate of 83.33% was achieved using half-strength HZ medium supplemented with 3.2 μM NAA. Adding vitamin C (80 mg⋅l-1) for 7 days in a dark environment reduced the browning rate, while increasing the proliferation rate. Additionally, through cytological observation, we established how and where adventitious roots occur. The survival rate of transplanted plantlets was > 90%. This is the first report of an in vitro regeneration technique that uses stem segments of mature C. hystrix as explants.

Artemisia argyi allelopathy: a generalist compromises hormone balance, element absorption, and photosynthesis of receptor plants

BACKGROUND

Allelopathy is expressed through the release of plant chemicals and is considered a natural alternative for sustainable weed management. Artemisia argyi (A. argyi) is widely distributed throughout Asia, and often dominates fields due to its strong allelopathy. However, the mechanism of A. argyi allelopathy is largely unknown and need to be elucidated at the physiological and molecular levels.

RESULTS

In this study, we used electron microscopy, ionomics analysis, phytohormone profiling, and transcriptome analysis to investigate the physiological and molecular mechanisms of A. argyi allelopathy using the model plant rice (Oryza sativa) as receptor plants. A. argyi water extract (AAWE)-treated rice plants grow poorly and display root morphological anomalies and leaf yellowing. We found that AAWE significantly inhibits rice growth by destroying the root and leaf system in multiple ways, including the integrity of ultrastructure, reactive oxygen species (ROS) homeostasis, and the accumulation of soluble sugar and chlorophyll synthesis. Further detection of the hormone contents suggests that AAWE leads to indole-3-acetic acid (IAA) accumulation in roots. Moreover, ionomics analysis shows that AAWE inhibits the absorption and transportation of photosynthesis-essential mineral elements, especially Mg, Fe, and Mn. In addition, the results of transcriptome analysis revealed that AAWE affects a series of crucial primary metabolic processes comprising photosynthesis in rice plants.

CONCLUSIONS

This study indicates that A. argyi realizes its strongly allelopathy through comprehensive effects on recipient plants including large-scale IAA synthesis and accumulation, ROS explosion, damaging the membrane system and organelles, and obstructing ion absorption and transport, photosynthesis and other pivotal primary metabolic processes of plants. Therefore, AAWE could potentially be developed as an environmentally friendly botanical herbicide due to its strong allelopathic effects.

Pan-genome analysis of three main Chinese chestnut varieties

Chinese chestnut (Castanea mollissima Blume) is one of the earliest domesticated plants of high nutritional and ecological value, yet mechanisms of C. mollissima underlying its growth and development are poorly understood. Although individual chestnut species differ greatly, the molecular basis of the formation of their characteristic traits remains unknown. Though the draft genomes of chestnut have been previously released, the pan-genome of different variety needs to be studied. We report the genome sequence of three cultivated varieties of chestnut herein, namely Hei-Shan-Zhai-7 (H7, drought-resistant variety), Yan-Hong (YH, easy-pruning variety), and Yan-Shan-Zao-Sheng (ZS, early-maturing variety), to expedite convenience and efficiency in its genetics-based breeding. We obtained three chromosome-level chestnut genome assemblies through a combination of Oxford Nanopore technology, Illumina HiSeq X, and Hi-C mapping. The final genome assemblies are 671.99 Mb (YH), 790.99 Mb (ZS), and 678.90 Mb (H7), across 12 chromosomes, with scaffold N50 sizes of 50.50 Mb (YH), 65.05 Mb (ZS), and 52.16 Mb (H7). Through the identification of homologous genes and the cluster analysis of gene families, we found that H7, YH and ZS had 159, 131, and 91 unique gene families, respectively, and there were 13,248 single-copy direct homologous genes in the three chestnut varieties. For the convenience of research, the chestnut genome database was constructed. Based on the results of gene family identification, the presence/absence variations (PAVs) information of the three sample genes was calculated, and a total of 2,364, 2,232, and 1,475 unique genes were identified in H7, YH and ZS, respectively. Our results suggest that the GBSS II-b gene family underwent expansion in chestnut (relative to nearest source species). Overall, we developed high-quality and well-annotated genome sequences of three C. mollissima varieties, which will facilitate clarifying the molecular mechanisms underlying important traits, and shortening the breeding process.

Seed Germination Mechanism of Carex rigescens Under Variable Temperature Determinded Using Integrated Single-Molecule Long-Read and Illumina Sequence Analysis

The turfgrass species Carex rigescens has broad development and utilization prospects in landscaping construction. However, seed dormancy and a low germination rate have inhibited its application. Furthermore, the molecular mechanisms of seed germination in C. rigescens have not been thoroughly studied. Therefore, in the present study, PacBio full-length transcriptome sequencing combined with Illumina sequencing was employed to elucidate the germination mechanism of C. rigescens seeds under variable temperatures. In general, 156,750 full-length non-chimeric sequences, including those for 62,086 high-quality transcripts, were obtained using single-molecule long read sequencing. In total, 40,810 high-quality non-redundant, 1,675 alternative splicing, 28,393 putative coding sequences, and 1,052 long non-coding RNAs were generated. Based on the newly constructed full-length reference transcriptome, 23,147 differentially expressed genes were identified. We screened four hub genes participating in seed germination using weighted gene co-expression network analysis. Combining these results with the physiological observations, the important roles of sucrose and starch metabolic pathways in germination are further discussed. In conclusion, we report the first full-length transcriptome of C. rigescens, and investigated the physiological and transcriptional mechanisms of seed germination under variable temperatures. Our results provide valuable information for future transcriptional analyses and gene function studies of C. rigescens.

Caffeic Acid, an Allelochemical in Artemisia argyi, Inhibits Weed Growth via Suppression of Mitogen-Activated Protein Kinase Signaling Pathway and the Biosynthesis of Gibberellin and Phytoalexin

Artemisia argyi is widely distributed in Asia, and it often becomes the dominant population in the field because of its strong ecological niche competitiveness. Allelochemicals secreted by plants are generally considered an important reason for their dominance in ecological competition. In this study, the allelochemicals in A. argyi were screened by a series of experiments and their mechanisms were explored via transcriptomics. First, the inhibitory effects of A. argyi on Echinochloa crusgalli, Setaria viridis, Portulaca oleracea and Amaranthus retroflexus were evaluated. Then, we carried out a qualitative and quantitative analysis of the chemical composition of the aqueous extract of A. argyi to screen for potential allelochemicals that can inhibit weed growth. Four potential allelochemicals were quantified: neochlorogenic acid (5-CQA), chlorogenic acid (3-CQA), cryptochlorogenic acid (4-CQA), and caffeic acid (CA). Coincidentally, their allelopathic effects on weeds seemed to be identical to their content, in the order CA>4-CQA>5-CQA>3-CQA. These findings suggested that CA might be the main allelopathic compound in the aqueous extract of A. argyi. Subsequently, the allelopathic effect and molecular mechanism of CA on S. viridis leaves were investigated. The physiological results showed that CA significantly induced reactive oxygen species (ROS) production, led to malondialdehyde (MDA) accumulation, and disrupted enzyme activities (POD, SOD, CAT) in S. viridis leaves. Moreover, transcriptome results revealed that CA inhibited S. viridis growth by downregulating multiple genes involved in gibberellin (GA) and phytoalexin biosynthesis and Mitogen-activated protein kinase (MAPK) signaling pathways. In addition, differentially expressed genes (DEGs) related to the biosynthesis and signaling pathways of phytohormones were verified by Quantitative Real-Time PCR (RT-qPCR). Taken together, this study may be the first to identify allelochemicals and explore their molecular mechanism about A. argyi. Importantly, the ecological advantages of A. argyi could be applied to ecological regulation and the development of botanical herbicides.

Regulation Mechanism of Exogenous Brassinolide on Bulbil Formation and Development in Pinellia ternata

The bulbil is the propagative organ of the P. ternata, which has a great effect on the yield of P. ternata. It is well known that plant hormones play important roles in bulbil formation and development. However, there is not clear about brassinolide (BR) regulation on bulbil formation and development. In this study, we revealed the effects of BR and BR biosynthesis inhibitors (propiconazole, Pcz) application on the histological observation, starch and sucrose metabolism, photosynthesis pathway, and hormone signaling pathway of P. ternata. The results showed that BR treatment reduced starch catabolism to maltodextrin and maltose in bulbil by decreasing BAM and ISA genes expression and increased cellulose catabolism to D-glucose in bulbil by enhancing edg and BGL genes expression. BR treatment enhanced the photosynthetic pigment content and potential maximum photosynthetic capacity and improved the photoprotection ability of P. ternata by increasing the dissipation of excess light energy to heat, thus reduced the photodamage in the PSII center. BR treatment increased the GA and BR content in bulbil of P. ternata, and decreased the ABA content in bulbil of P. ternata. Pcz treatment increased the level of GA, SL, ABA, and IAA in bulbil of P. ternata. BR regulated the signal transduction of BR, IAA, and ABA to regulate the formation and development of bulbil in P. ternata. These results provide molecular insight into BR regulation on bulbil formation and development.

Deciphering Rhizosphere Microbiome Assembly of Castanea henryi in Plantation and Natural Forest

Based on the importance and sensitivity of microbial communities to changes in the forest ecosystem, soil microorganisms can be used to indicate the health of the forest system. The metagenome sequencing was used to analyze the changes of microbial communities between natural and plantation Castanea henryi forests for understanding the effect of forest types on soil microbial communities. Our result showed the soil microbial diversity and richness were higher in the natural forests than in the plantation. Proteobacteria, Actinobacteria, and Acidobacteria are the dominant categories in the C. henryi rhizosphere, and Proteobacteria and Actinobacteria were significantly enriched in the natural forest while Acidobacteria was significantly enriched in the plantation. Meanwhile, the functional gene diversity and the abundance of functions in the natural forest were higher than that of the plantation. Furthermore, we found that the microbial network in the natural forests had more complex than in the plantation. We also emphasized the low-abundance taxa may play an important role in the network structure. These results clearly showed that microbial communities, in response to different forest types, provide valuable information to manipulate microbiomes to improve soil conditions of plantation.

Allelopathic effect of Artemisia argyi on the germination and growth of various weeds

Allelopathy means that one plant produces chemical substances to affect the growth and development of other plants. Usually, allelochemicals can stimulate or inhibit the germination and growth of plants, which have been considered as potential strategy for drug development of environmentally friendly biological herbicides. Obviously, the discovery of plant materials with extensive sources, low cost and markedly allelopathic effect will have far-reaching ecological impacts as the biological herbicide. At present, a large number of researches have already reported that certain plant-derived allelochemicals can inhibit weed growth. In this study, the allelopathic effect of Artemisia argyi was investigated via a series of laboratory experiments and field trial. Firstly, water-soluble extracts exhibited the strongest allelopathic inhibitory effects on various plants under incubator conditions, after the different extracts authenticated by UPLC-Q-TOF-MS. Then, the allelopathic effect of the A. argyi was systematacially evaluated on the seed germination and growth of Brassica pekinensis, Lactuca sativa, Oryza sativa, Portulaca oleracea, Oxalis corniculata and Setaria viridis in pot experiments, it suggested that the A. argyi could inhibit both dicotyledons and monocotyledons not only by seed germination but also by seedling growth. Furthermore, field trial showed that the A. argyi significantly inhibited the growth of weeds in Chrysanthemum morifolium field with no adverse effect on the growth of C. morifolium. At last, RNA-Seq analysis and key gene detection analysis indicated that A.argyi inhibited the germination and growth of weed via multi-targets and multi-paths while the inhibiting of chlorophyll synthesis of target plants was one of the key mechanisms. In summary, the A. argyi was confirmed as a potential raw material for the development of preventive herbicides against various weeds in this research. Importantly, this discovery maybe provide scientific evidence for the research and development of environmentally friendly herbicides in the future.

Functional characterization of a starch synthesis-related gene AmAGP in Amorphophallus muelleri

has attracted tremendous interest because of its high contents of glucomannan and starch. Very few genes regulating glucomannan and starch were reported in Amorphophallus. In this study, an ADP-glucose pyrophosphorylase (AGP) gene that plays a significant role in plant starch synthesis was cloned from Amorphophallus muelleri. It was shown that it encoded a predicted protein containing a conserved plant ADP-Glucose-PP repeat domain and seven potential ligand-binding sites. The real-time quantitative PCR showed that AmAGP was most abundant in tubers, and it was positively correlated with starch content. Additionally, its influencers about temperature and exogenous plant hormone were also discussed, showing that AmAGP expressed highly in tubers under treatments using 25°C and IAA. Furthermore, starch content was closely related to AmAGP expression level, suggesting that AmAGP was involved in the regulation of starch synthesis in A. muelleri. Therefore, identifying the sequence of AmAGP and its expression pattern during tuber enlarging and the changes of its transcript levels in response to temperature and plant hormones would contribute to a better understanding of starch synthesis, and also providing a reference information for future preferable breeding for obtaining more starch or more glucomannan in Amorphophallus.