Light intensity regulates the sexual behaviors of oriental fruit fly Bactrocera dorsalis under laboratory conditions

The oriental fruit fly,Bactrocera dorsalis(Hendel),is a devastating pest of citrus fruits.After successful mating,adult females insert their eggs into the ripened fruit,resulting in moldy and rotten fruit and causing great economic losses for the citrus industry.In the field,flies initiate copulatory behaviors as twilight approaches,and decreasing light intensity in this period is the normal stimulus for copulation.In this study,ten light intensities ranging from 0–30000 lux were set to identify the typical intensity that strongly regulates the copulation behavior of B.dorsalis.Three light intensities found to regulate the copulation behavior were then selected to verify their effects on adult male wing fanning and female chemotaxis towards 2,3,5-trimethylpyrazine(TMP).At last,strong light and complete darkness were artificially combined in the lab to verify whether they could prevent copulation to inform behavioral manipulation of oriental flies in the future.The results indicated that adult flies generally initiated copulatory behaviors at low light intensity(<1000 lux).Stronger light significantly prevented copulation in proportion to intensity,with nearly no copulation events initiated when light intensity was above 20000 lux.Both male wing fanning and female chemotaxis towards TMP were attenuated as light intensity became stronger.However,at 10000 lux,males still fanned their wings to a certain extent while TMP completely lost its attractiveness to females.In the darkness,adults did not initiate any sexual behaviors,e.g.,copulation,wing fanning,or chemotaxis to TMP.One hour of strong light(10000 lux)combined with continuous darkness completely prevented mating.These results show that light condition is an essential factor for copulatory behaviors in the oriental fruit fly.Researchers could thus manipulate light conditions artificially or disrupt the molecular target in flies’light transduction pathway to develop environmentally-friendly techniques to control this pest.

Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism

Amycolatopsis mediterranei is used for industry-scale production of rifamycin, which plays a vital role in antimyco- bacterial therapy. As the first sequenced genome of the genus Amycolatopsis, the chromosome of strain U32 comprising 10 236 715 base pairs, is one of the largest prokaryotic genomes ever sequenced so far. Unlike the linear topology found in streptomycetes, this chromosome is circular, particularly similar to that of Saccharopolyspora erythraea and Nocardia farcinica, representing their close relationship in phylogeny and taxonomy. Although the predicted 9 228 protein-coding genes in the A. mediterranei genome shared the greatest number of orthologs with those of S. erythraea, it was unexpectedly followed by Streptomyces coelicolor rather than N. farcinica, indicating the distinct metabolic characteristics evolved via adaptation to diverse ecological niches. Besides a core region analogous to that common in streptomycetes, a novel ＇quasicore＇ with typical core characteristics is defined within the non-core region, where 21 out of the total 26 gene clusters for secondary metabolite production are located. The rifamycin biosynthesis gene cluster located in the core encodes a cytochrome P450 enzyme essential for the conversion of rifamycin SV to B, revealed by comparing to the highly homologous cluster of the rifamycin B-producing strain S699 and further confirmed by genetic complementation. The genomic information of A. mediterranei demonstrates a metabolic network orchestrated not only for extensive utilization of various carbon sources and inorganic nitrogen compounds but also for effective funneling of metabolic intermediates into the secondary antibiotic synthesis process under the control of a seemingly complex regulatory mechanism.

Effects of ceramsite on methane and hydrogen sulphide productions from macroalgae biomass

The easy acidification and high hydrogen sulfide （H2S） production during anaerobic digestion of macroalgae limited its application in biomethane production. In order to investigate the effects of ceramsite on methane and HzS productions during anaerobic digestion of macroalgae, batch experiments ofMacrocystis pyrifera were carried out. Four groups named C0, C1, C2 and C3 added with 0, 1.5, 3.0 and 4.5 g/g substrate of ceramsite, respectively, were studied and compared. The highest cumulative methane yield of 286.3 mL/g substrate is obtained in C2, which is 40.11% higher than that of CO. The cumulative HzS yields of C1, C2 and C3 are 32.67%, 44.66% and 53.21% lower than that of CO, respectively. Results indicate that ceramsite addition permits higher methane yields, shorter lag-phase time and lower HzS yields during anaerobic digestion of Macrocystispyrifera.

Optimization of Wickerhamomyces anomalus Fermentation Conditions for Pectinase Production Based on Wet Processing of Arabica Coffee in Yunnan Province

In order to improve the pectin-degrading efficiency in wet processing of Arabica coffee in Yunnan, Box-Behnken design and single factor experiment were used to optimize the fermentation conditions of five pectinolytic Wickerhamomyces anomalus strains from the fermentation broth of Arabica coffee in Baoshan, Yunnan during wet processing with pectase activity as an indicator. The results showed that the five strains all synthesized pectin lyase(PL), polygalacturonase(PG), and pectin methylesterase(PM).Among them, strain CAP5 had strong ability to produce PG and PL,while strain CAP4 secreted a large amount of PM. Under optimized conditions, the activity of PG, PL, and PM of the five strains came in at 250.17~411.20 U/mL, 12.98~16.55 U/mL, and 208.52~322.83 U/mL,respectively. The four factors of nitrogen source concentration,fermentation time, Mn2+ concentration, and pH value were optimized and the optimal pectinase-producing fermentation conditions for five strains were as follows: peptone 2.2 g/L, fermentation time 30 h, Mn2+ 1.5 mmol/L, and pH 4.3. After fermentation under the optimized conditions, the maximum PG activity of CAP5 amounted to 411.20 U/mL, 114.03% higher than that before optimization.Meanwhile, the PG activity of strains CAP3, CAP4, CAP8, and CAP10 increased by 86.74%, 114.55%, 65.79%, and 66.07%,respectively, and the activity of PL and PM of the five strains rose 150.35%~218.56% and 341.07%~418.52%, respectively. These findings suggested that W. anomalus strains could be used as coffee starter and had great potential for the lysis of pectin.

Multiomics comparison among populations of three plant sources of Amomi Fructus

Amomi Fructus(Sharen,AF)is a traditional Chinese medicine(TCM)from three source species(or varieties),including Wurfbainia villosa var.villosa(WVV),W.villosa var.xanthioides(WVX),or W.longiligularis(WL).Among them,WVV has been transplanted from its top-geoherb region,Guangdong,to its current main production area,Yunnan,for>50 years in China.However,the genetic and transcriptomic differentiation among multiple AF source species(or varieties)and between the origin and transplanted populations of WVV is unknown.In our study,the observed overall higher expression of terpenoid biosynthesis genes in WVV than in WVX provided possible evidence for the better pharmacological effect of WVV.We also screened six candidate borneol dehydrogenases(BDHs)that potentially catalyzed borneol into camphor in WVV and functionally verified them.Highly expressed genes at the P2 stage of WVV,Wv05G1424 and Wv05G1438,were capable of catalyzing the formation of camphor from(+)-borneol,(-)-borneol and DL-isoborneol.Moreover,the BDH genes may experience independent evolution after acquiring the ancestral copies,and the following tandem duplications might account for the abundant camphor content in WVV.Furthermore,four populations of WVV,WVX,and WL are genetically differentiated,and the gene flow from WVX to WVV in Yunnan contributed to the greater genetic diversity in the introduced population(WVV-JH)than in its top-geoherb region(WVV-YC),which showed the lowest genetic diversity and might undergo genetic degradation.In addition,terpene synthesis(TPS)and BDH genes were selected among populations of multiple AF source species(or varieties)and between the top-and non-top-geoherb regions,which might explain the difference in metabolites between these populations.Our findings provide important guidance for the conservation,genetic improvement,and industrial development of the three source species(or varieties)and for identifying top-geoherbalism with molecular markers,and proper clinical application of AF.

Multi-Omics-Guided Discovery of Omicsynins Produced by Streptomyces sp.1647:Pseudo-Tetrapeptides Active Against Influenza A Viruses and Coronavirus HCoV-229E

Many microorganisms have mechanisms that protect cells against attack from viruses.The fermentation components of Streptomyces sp.1647 exhibit potent anti-influenza A virus(IAV)activity.This strain was isolated from soil in southern China in the 1970s,but the chemical nature of its antiviral substance(s)has remained unknown until now.We used an integrated multi-omics strategy to identify the antiviral agents from this streptomycete.The antibiotics and Secondary Metabolite Analysis Shell(antiSMASH)analysis of its genome sequence revealed 38 biosynthetic gene clusters(BGCs)for secondary metabolites,and the target BGCs possibly responsible for the production of antiviral components were narrowed down to three BGCs by bioactivity-guided comparative transcriptomics analysis.Through bioinformatics analysis and genetic manipulation of the regulators and a biosynthetic gene,cluster 36 was identified as the BGC responsible for the biosynthesis of the antiviral compounds.Bioactivity-based molecular networking analysis of mass spectrometric data from different recombinant strains illustrated that the antiviral compounds were a class of structural analogues.Finally,18 pseudo-tetrapeptides with an internal ureido linkage,omicsynins A1–A6,B1–B6,and C1–C6,were identified and/or isolated from fermentation broth.Among them,11 compounds(omicsynins A1,A2,A6,B1–B3,B5,B6,C1,C2,and C6)are new compounds.Omicsynins B1–B4 exhibited potent antiviral activity against IAV with the 50%inhibitory concentration(IC_(50))of approximately 1μmol·L^(-1)and a selectivity index(SI)ranging from 100 to 300.Omicsynins B1–B4 also showed significant antiviral activity against human coronavirus HCoV-229E.By integrating multi-omics data,we discovered a number of novel antiviral pseudo-tetrapeptides produced by Streptomyces sp.1647,indicating that the secondary metabolites of microorganisms are a valuable source of novel antivirals.

Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization

Water caltrop(Trapa spp.,Lythraceae)is a traditional but currently underutilized non-cereal crop.Here,we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa.natans(4x,AABB),i.e.,diploid T.natans(2x,AA)and Trapa incisa(2x,BB).In conjunction with four published(sub)genomes of Trapa,we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element(TE)library to develop Trapa genomic resources.The pangenome displayed substantial gene-content variationwith dispensable and private gene clusters occupying a large proportion(51.95%)of the total cluster sets in the six(sub)genomes.Genotyping of presence-absence variation(PAVs)identified 40453 PAVs associated with 2570 genes specific to A-or B-lineages,of which 1428were differentially expressed,andwere enriched in organ development process,organic substancemetabolic process and response to stimulus.Comparative genome analyses showed that the allotetraploid T.natans underwent asymmetric subgenome divergence,with the B-subgenome being more dominant than the A-subgenome.Multiple factors,including PAVs,asymmetrical amplification of TEs,homeologous exchanges(HEs),and homeolog expression divergence,together affected genome evolution after polyploidization.Overall,this study sheds lights on the genome architecture and evolution of Trapa,and facilitates its functional genomic studies and breeding program.

The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes

Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin,flesh,and vegetative tissues,endowing them with high utility value in red wine blending and nutrient-enriched foods developing.However,due to the lack of genome information,the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient.Here,the cultivar‘Yan73’was used for assembling the telomere-to-telomere(T2T)genome of teinturier grapes by combining the High Fidelity(HiFi),Hi-C and ultralong Oxford Nanopore Technologies(ONT)reads.Two haplotype genomes were assembled,at the sizes of 501.68 Mb and 493.38 Mb,respectively.In the haplotype 1 genome,the transposable elements(TEs)contained 32.77%of long terminal repeats(LTRs),while in the haplotype 2 genome,31.53%of LTRs were detected in TEs.Furthermore,obvious inversions were identified in chromosome 18 between the two haplotypes.Transcriptome profiling suggested that the gene expression patterns in‘Cabernet Sauvignon’and‘Yan73’were diverse depending on tissues,developmental stages,and varieties.The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages,whereas the expression levels of numerous genes showed significant differences.Compared with other genes,the expression levels of VvMYBA1 and VvUFGT4 in all samples,VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of‘Yan73’were higher than those of‘Cabernet Sauvignon’.Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of‘Yan73’haplotype 2 genome.The‘Yan73’T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.

Impact of COVID-19-related nonpharmaceutical interventions on diarrheal diseases and zoonotic Salmonella

Non-pharmaceutical interventions(NPIs)have been proven effective in reducing the spread of the coronavirus disease 2019(COVID-19),but their broader impact on gastrointestinal disorders remains poorly studied.Here,we report an observational analysis and retrospective study that compares the incidence of acute diarrheal diseases in Hangzhou,Zhejiang,China,between 2019 and 2020,with an examination of the antimicrobial resistance and genetic spectrum of non-typhoidal Salmonella(NTS)from 2015 to 2022,before and during the COVID-19 pandemic.Our findings underscore that NPIs related to COVID-19 effectively reduced the incidence of acute diarrhea,with a substantial decrease in most enteric pathogens.Notably,NTS exhibited an unexpected surge.Further genomic investigations of NTS isolates revealed an overall reduction in antimicrobial-resistant(AMR),disinfection-tolerant,and virulent capabilities,but with marked variations detected between human and animal isolates.Additional genome-based analysis confirmed a decrease in the scale of zoonotic transmission in response to NPIs,suggesting particular NTS types may contribute to human infections via alternative pathways.The collective findings manifested that COVID-19-related NPIs had a mixed impact on NTS infections,which may inform AMR NTS mitigation policy.

Telomere-to-telomere haplotype-resolved reference genome reveals subgenome divergence and disease resistance in triploid Cavendish banana

Banana is one of the most important crops of the world.Cavendish-type bananas,which have a monospecific Musa acuminata origin(AAA),account for around half of the global banana production,thereby are of great significance for human societies.However,until now,the high-quality haplotype-resolved reference genome was still undecoded for banana cultivars.Here,we reported the telomere-to-telomere(T2T)and haplotype-resolved reference genome of‘Baxijiao’(Cavendish)consisting of three haploid assemblies.The sizes of the three haploid assemblies were estimated to be 477.16 Mb,477.18 Mb,and 469.57 Mb,respectively.Although with monospecific origins,the three haploid assemblies showed great differences with low levels of sequence collinearity.Several large reciprocal translocations were identified among chromosomes 1,4,and 7.An expansion of gene families that might affect fruit quality and aroma was detected,such as those belonging to sucrose/disaccharide/oligosaccharide catabolic processes,sucrose metabolic process,starch metabolic process,and aromatic compound biosynthetic process.Besides,an expansion of gene families related to anther and pollen development was observed,which could be associated with parthenocarpy and sterility of the Cavendish cultivar.Finally,much fewer resistance genes were identified in‘Baxijiao’than in M.acuminata,particularly in the gene clusters in chromosomes 3 and 10,providing potential targets to explore for molecular analysis of disease resistance in banana.This T2T haplotype-resolved reference genome will thus be a valuable genetic resource for biological studies,molecular breeding,and genetic improvement of banana.

A novel transposable Mu-like prophage in Bacillus alcalophilus CGMCC 1.3604(ATCC 27647)

Dear Editor,Transposable phages,which are reproduced by transposition(Harshey,2012;Taylor,1963),have been widely applied in the field of biotechnology to manipulate operon/gene fusions,in vivo cloning,randomion mutagenesis,and integration of DNA into bacterial genomes(Abalakina et al.,2008;Akhverdyan et al.,2011).One of the best-studied transposable phages is

The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Grapevine is one of the most economically important crops worldwide.However,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these regions.Here,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads.The T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 version.We annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T assembly.We detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease resistance.Even though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein phosphorylation.The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually,a process that can be time-consuming and prone to errors.The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations.The processing of a large number of sequences,however,remains a time-consuming task.To conquer this challenge,we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis(ORPA).ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST,completing the task just in 1 min.With increasing data volume,the efficiency of ORPA is even more pronounced,over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes.The phylogenetic tree outputs from ORPA are equivalent to HomBlocks,indicating its outstanding efficiency.Due to its speed and accuracy,ORPA can identify species-level evolutionary conflicts,providing valuable insights into evolutionary cognition.

Efficient control of root-knot nematodes by expressing Bt nematicidal proteins in root leucoplasts

Root-knot nematodes(RKNs)are plant pests that infect the roots of host plants.Bacillus thuringiensis(Bt)nematicidal proteins exhibited toxicity to nematodes.However,the application of nematicidal proteins for plant protection is hampered by the lack of effective delivery systems in transgenic plants.In this study,we discovered the accumulation of leucoplasts(root plastids)in galls and RKN-induced giant cells.RKN infection causes the degradation of leucoplasts into small vesicle-like structures,which are responsible for delivering proteins to RKNs,as observed through confocal microscopy and immunoelectron microscopy.We showed that different-sized proteins from leucoplasts could be taken up by Meloidogyne incognita female.To further explore the potential applications of leucoplasts,we introduced the Bt crystal protein Cry5Ba2 into tobacco and tomato leucoplasts by fusing it with a transit peptide.The transgenic plants showed significant resistance to RKNs.Intriguingly,RKN females preferentially took up Cry5Ba2 protein when delivered through plastids rather than the cytosol.The decrease in progeny was positively correlated with the delivery efficiency of the nematicidal protein.In conclusion,this study offers new insights into the feeding behavior of RKNs and their ability to ingest leucoplast proteins,and demonstrates that root leucoplasts can be used for delivering nematicidal proteins,thereby offering a promising approach for nematode control.

A faster killing effect of plastid-mediated RNA interference on a leaf beetle through induced dysbiosis of the gut bacteria

The expression of double-stranded RNAs(dsRNAs)from the plastid genome has been proven to be an effective method for controlling herbivorous pests by targeting essential insect genes.However,there are limitations to the efficiency of plastid-mediated RNA interference(PM-RNAi)due to the initial damage caused by the insects and their slow response to RNA interference.In this study,we developed transplastomic poplar plants that express dsRNAs targeting the b-Actin(dsACT)and Srp54k(dsSRP54K)genes of Plagiodera versicolora.Feeding experiments showed that transplastomic poplar plants can cause significantly higher mortality in P.versicolora larvae compared with nuclear transgenic or wild-type poplar plants.The efficient killing effect of PM-RNAi on P.versicolora larvae was found to be dependent on the presence of gut bacteria.Importantly,foliar application of a gut bacterial strain,Pseudomonas putida,will induce dysbiosis in the gut bacteria of P.versicolora larvae,leading to a significant acceleration in the speed of killing by PM-RNAi.Overall,our findings suggest that interfering with gut bacteria could be a promising strategy to enhance the effectiveness of PM-RNAi for insect pest control,offering a novel and effective approach for crop protection based on RNAi technology.

Chemoproteomics reveals the epoxidase enzyme for the biosynthesis of camptothecin in Ophiorrhiza pumila

Camptothecin is one of the most commonly used anticancer drugs worldwide,yet the downstream biosynthetic route from strictosidine to camptothecin has remained unclear for more than half a century.Here,we searched for proteins involved in camptothecin biosynthesis from the camptothecin-producing plant Ophiorrhiza pumila by chemoproteomics and identified Op CYP716E111.

Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

Given the escalating impact of climate change on agriculture and food security,gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate change.Alfalfa(Medicago sativa subsp.sativa),the queen of forages,shows remarkable adaptability across diverse global environments,making it an excellent model for investigating species responses to climate change.In this study,we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa’s climatic adaptation and genetic susceptibility to future climate change.We found that interspecific genetic exchange has contributed to the gene pool of alfalfa,particularly enriching defense and stress-response genes.Intersubspecific introgression between M.sativa subsp.falcata(subsp.falcata)and alfalfa not only aids alfalfa’s climatic adaptation but also introduces genetic burden.A total of 1671 genes were associated with climatic adaptation,and 5.7%of them were introgressions from subsp.falcata.By integrating climate-associated variants and climate data,we identified populations that are vulnerable to future climate change,particularly in higher latitudes of the Northern Hemisphere.These findings serve as a clarion call for targeted conservation initiatives and breeding efforts.We also identified preadaptive populations that demonstrate heightened resilience to climate fluctuations,illuminating a pathway for future breeding strategies.Collectively,this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars,contributing to effective agricultural strategies for facing future climate change.

Treating Chronic Diseases by Regulating the Gut Microbiota

Chronic diseases comprise a wide range of abnormal conditions and illnesses that impair patients’physical and/or mental functioning,and last for a long time.Largely a contemporary plague,chronic diseases are responsible for the observed morbidity and mortality in developed countries as well as in some developing countries [1,2].

VvBBX44 and VvMYBA1 form a regulatory feedback loop to balance anthocyanin biosynthesis in grape

Anthocyanins are essential for the quality of perennial horticultural crops,such as grapes.In grapes,ELONGATED HYPOCOTYL 5(HY5)and MYBA1 are two critical transcription factors that regulate anthocyanin biosynthesis.Our previous work has shown that Vitis vinifera B-box protein 44(VvBBX44)inhibits anthocyanin synthesis and represses VvHY5 expression in grape calli.However,the regulatory mechanism underlying this regulation was unclear.In this study,we found that loss of VvBBX44 function resulted in increased anthocyanin accumulation in grapevine callus.VvBBX44 directly represses VvMYBA1,which activates VvBBX44.VvMYBA1,but not VvBBX44,directly modulates the expression of grape UDP flavonoid 3-O-glucosyltransferase(VvUFGT).We demonstrated that VvBBX44 represses the transcriptional activation of VvUFGT and VvBBX44 induced by VvMYBA1.However,VvBBX44 and VvMYBA1 did not physically interact in yeast.The application of exogenous anthocyanin stimulated VvBBX44 expression in grapevine suspension cells and tobacco leaves.These findings suggest that VvBBX44 and VvMYBA1 form a transcriptional feedback loop to prevent overaccumulation of anthocyanin and reduce metabolic costs.Our work sheds light on the complex regulatory network that controls anthocyanin biosynthesis in grapevine.

Genomic investigation and nationwide tracking of pediatric invasive nontyphoidal Salmonella in China

Impact Statement。Invasive nontyphoidal Salmonella(iNTS)causes significant concern with~15%morbidity,affecting populations mainly in African countries.