The Clausena lansium genome provides new insights into alkaloid diversity and the evolution of the methyltransferase family

Wampee(Clausena lansium)is an important evergreen fruit tree native to southern China that has a long history of use for medicinal purposes.Here,a chromosome-level genome of C.lansium was constructed with a genome size of 282.9 Mb and scaffold N50 of 30.75 Mb.The assembled genome contains 48.70%repetitive elements and 24,381 protein-coding genes.Comparative genomic analysis showed that C.lansium diverged from Aurantioideae 15.91-24.95 million years ago.Additionally,some expansive and specific gene families related to methyltransferase activity and S-adenosylmethionine-dependent methyltransferase activity were also identified.Further analysis indicated that N-methyltransferase(NMT)is mainly involved in alkaloid biosynthesis and O-methyltransferase(OMT)participates in the regulation of coumarin accumulation in wampee.This suggested that wampee's richness in alkaloids and coumarins might be due to the gene expansions of NMT and OMT.The tandem repeat event was one of the major reasons for the NMT expansion.Hence,the reference genome of C.lansium will facilitate the identification of some useful medicinal compounds from wampee resources and reveal their biosynthetic pathways.

Coupling of reduced inorganic fertilizer with plant-based organic fertilizer as a promising fertilizer management strategy for colored rice in tropical regions

Colored rice is a type of high-quality,high-added-value rice that has attracted increasing attention in recent years.The use of large amounts of inorganic nitrogen fertilizer in rice fields results in low fertilizer use efficiency and high environmental pollution.Organic fertilizer is a promising way to improve soil quality and sustain high yields.However,most studies focus on the effect of animal-based organic fertilizers.The effects of different ratios of plantbased organic fertilizer and inorganic fertilizer on the grain yield and quality of colored rice have rarely been reported.Therefore,a two-year field experiment was conducted in 2020 and 2021 to study the effects of replacing inorganic N fertilizers with plant-based organic fertilizers on the yield,nitrogen use efficiency(NUE),and anthocyanin content of two colored rice varieties in a tropical region in China.The experimental treatments included no nitrogen fertilization(T1),100% inorganic nitrogen fertilizer(T2),30%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T3),60%inorganic nitrogen fertilizer substitution with plant-based organic fertilizer(T4),and 100% plantbased organic fertilizer(T5).The total nitrogen provided to all the treatments except T1 was the same at 120 kg ha-1.Our results showed that the T3 treatment enhanced the grain yield and anthocyanin content of colored rice by increasing nitrogen use efficiency compared with T2.On average,grain yields were increased by 9 and 8%,while the anthocyanin content increased by 16 and 10% in the two colored rice varieties under T3 across the two years,respectively,as compared with T2.Further study of the residual effect of partial substitution of inorganic fertilizers showed that the substitution of inorganic fertilizer with plant-based organic fertilizer improved the soil physiochemical properties,and thus increased the rice grain yield,in the subsequent seasons.The highest grain yield of the subsequent rice crop was observed under the T5 treatment.Our results suggested that the application of plantbased organic fertilizers can sustain the production of colored rice with high anthocyanin content in tropical regions,which is beneficial in reconciling the relationship between rice production and environmental protection.

Recognition of the inducible,secretory small protein OsSSP1 by the membrane receptor OsSSR1 and the co-receptor OsBAK1 confers rice resistance to the blast fungus

The plant apoplast,which serves as the frontline battleground for long-term host–pathogen interactions,harbors a wealth of disease resistance resources.However,the identification of the disease resistance proteins in the apoplast is relatively lacking.In this study,we identified and characterized the rice secretory protein OsSSP1(Oryza sativa secretory small protein 1).OsSSP1 can be secreted into the plant apoplast,and either in vitro treatment of recombinant OsSSP1 or overexpression of OsSSP1 in rice could trigger plant immune response.The expression of OsSSP1 is suppressed significantly during Magnaporthe oryzae infection in the susceptible rice variety Taibei 309,and OsSSP1-overexpressing lines all show strong resistance to M.oryzae.Combining the knockout and overexpression results,we found that OsSSP1 positively regulates plant immunity in response to fungal infection.Moreover,the recognition and immune response triggered by OsSSP1 depend on an uncharacterized transmembrane OsSSR1(secretory small protein receptor 1)and the key co-receptor OsBAK1,since most of the induced immune response and resistance are lost in the absence of OsSSR1 or OsBAK1.Intriguingly,the OsSSP1 protein is relatively stable and can still induce plant resistance after 1 week of storage in the open environment,and exogenous OsSSP1 treatment for a 2-week period did not affect rice yield.Collectively,our study reveals that OsSSP1 can be secreted into the apoplast and percepted by OsSSR1 and OsBAK1 during fungal infection,thereby triggering the immune response to enhance plant resistance to M.oryzae.These findings provide novel resources and potential strategies for crop breeding and disease control.

Two gene clusters and their positive regulator SlMYB13 that have undergone domestication-associated negative selection control phenolamide accumulation and drought tolerance in tomato

Among plant metabolites,phenolamides,which are conjugates of hydroxycinnamic acid derivatives and polyamines,play important roles in plant adaptation to abiotic and biotic stresses.However,the molecular mechanisms underlying phenolamide metabolism and regulation as well as the effects of domestication and breeding on phenolamide diversity in tomato remain largely unclear.In this study,we performed a metabolite-based genome-wide association study and identified two biosynthetic gene clusters(BGC7 and BGC11)containing 12 genes involved in phenolamide metabolism,including four biosynthesis genes(two 4CL genes,one C3H gene,and one CPA gene),seven decoration genes(five AT genes and two UGT genes),and one transport protein gene(DTX29).Using gene co-expression network analysis we further discovered that SlMYB13 positively regulates the expression of two gene clusters,thereby promoting phenolamide accumulation.Genetic and physiological analyses showed that BGC7,BGC11 and SlMYB13 enhance drought tolerance by enhancing scavenging of reactive oxygen species and increasing abscisic acid content in tomato.Natural variation analysis suggested that BGC7,BGC11 and SlMYB13 were negatively selected during tomato domestication and improvement,leading to reduced phenolamide content and drought tolerance of cultivated tomato.Collectively,our study discovers a key mechanism of phenolamide biosynthesis and regulation in tomato and reveals that crop domestication and improvement shapes metabolic diversity to affect plant environmental adaptation.

Two imprinted genes primed by DEMETER in the central cell and activated by WRKY10 in the endosperm

The early development of the endosperm is crucial for balancing the allocation of maternal nutrients to offspring.This process is believed to be evolutionarily associated with genomic imprinting,resulting in parentally biased allelic gene expression.Beyond Fertilization Independent Seed(FIS)genes,the number of imprinted genes involved in early endosperm development and seed size determination remains limited.This study introduces early endosperm-expressed HAIKU(IKU)downstream Candidate F-box 1(ICF1)and ICF2 as maternally expressed imprinted genes(MEGs)in Arabidopsis thaliana.Although these genes are also demethylated by DEMETER(DME)in the central cell,their activation differs from the direct DME-mediated activation seen in classical MEGs such as the FIS genes.Instead,ICF maternal alleles carry pre-established hypomethylation in their promoters,priming them for activation by the WRKY10 transcription factor in the endosperm.On the contrary,paternal alleles are predominantly suppressed by CG methylation.Furthermore,we find that ICF genes partially contribute to the small seed size observed in iku mutants.Our discovery reveals a two-step regulatory mechanism that highlights the important role of conventional transcription factors in the activation of imprinted genes,which was previously not fully recognized.Therefore,the mechanism provides a new dimension to understand the transcriptional regulation of imprinting in plant reproduction and development.

Precision regulation of plant aromatic amino acid homeostasis

The aromatic amino acids(AAAs)phenylalanine(Phe),tyrosine(Tyr),and tryptophan(Trp)are not only building blocks of proteins,but also precursors of numerous primary and specialized metabolites(Schenck and Maeda,2018).For instance,Trp is a precursor of the phytohormone auxin and the plant defense compounds indole glucosinolates,while Phe serves as a precursor of lignin,coumarin and flavonoids.Some plant natural products such as morphine and vitamin E are derived from Tyr,and have been employed in human medicine and nutrition(Schenck and Maeda,2018;Wu et al.,2022;Yokoyama et al.,2021).

WTV2.0:A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode

Volatilomics is essential for understanding the biological functions and fragrance contributions of plant volatiles.However,the annotation coverage achieved using current untargeted and widely targeted volatomics(WTV)methods has been limited by low sensitivity and/or low acquisition coverage.Here,we introduce WTV 2.0,which enabled the construction of a high-coverage library containing 2111 plant volatiles,and report the development of a comprehensive selective ion monitoring(cSIM)acquisition method,including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method,that can acquire the smallest but sufficient number of ions for most plant volatiles,as well as the automatic qualitative and semi-quantitative analysis of cSIM data.Importantly,the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library,utilizing the obtained cSIM data.We showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method,doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit,and led to the discovery of menthofuran as a novel flavor compound in passion fruit.WTV 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.

A widely targeted metabolite modificomics strategy for modified metabolites identification in tomato

The structural and functional diversity of plant metabolites is largely created via chemical modification of a basic backbone.However,metabolite modifications in plants have still not been thoroughly investigated by metabolomics approaches.In this study,a widely targeted metabolite modificomics(WTMM)strategy was developed based on ultra-high performance liquid chromatography-quadrupole-linear ion trap(UHPLC-Q-Trap)and UHPLC-Q-Exactive-Orbitrap(UHPLC-QE-Orbitrap),which greatly improved the detection sensitivity and the efficiency of identification of modified metabolites.A metabolite modificomics study was carried out using tomato as a model,and over 34,000 signals with MS2 information were obtained from approximately 232 neutral loss transitions.Unbiased metabolite profiling was also performed by utilizing high-resolution mass spectrometry data to annotate a total of 2,118 metabolites with 125 modification types;of these,165 modified metabolites were identified in this study.Next,the WTMM database was used to assess diseased tomato tissues and 29 biomarkers were analyzed.In summary,the WTMM strategy is not only capable of large-scale detection and quantitative analysis of plant-modified metabolites in plants,but also can be used for plant biomarker development.

Leveraging a new thermosensor for heat-smart future agriculture

As global temperatures rise owing to climate change,crops are increasingly subjected to conditions that surpass their optimal temperature ranges,leading to heat stress(HS).HS impacts many morpho-physiological,biochemical,and molecular mechanisms in plants,ultimately affecting sustainable agricultural production worldwide(Ding et al.,2020;Kan et al.,2023;Raza et al.,2024).