Transcriptome and metabolome analysis of preharvest internal browning in Nane plum fruit caused by high temperature

The preharvest internal browning of Nane plum fruit,with no visible effects on the appearance of the fruit,has become a serious problem in recent years in its production area in Guangdong Province,China.This study investigated the effects of environmental factors,including temperature,on Nane plum internal browning.Plum orchards at different elevations with different incidences of internal browning were selected.Using fruits with different internal browning incidence levels,the internal browning mechanism was analyzed with transcriptome and metabolome analyses.The results revealed decreased internal browning at high altitudes.Shading treatment significantly reduced internal browning,whereas bagging and insect-proof net-covering treatments significantly increased internal browning.Because bagging and net coverings increase the local ambient temperature,the findings suggest that high temperature is an important factor influencing the internal browning of Nane plum.The metabolome experiments showed that with increased internal browning,the levels of phenolic hydroxyls such as catechol increased,with simultaneous increases in hydrogen peroxide content and oxidase activity.It can be speculated that the oxidation of phenolic hydroxyl substances is the main cause of the preharvest browning of Nane plum.Transcriptome analysis revealed the increased expression of calcium signaling-related and downstream effector genes and indicated an important role of calcium in internal browning,possibly due to its increased content in the fruit.Further,with increasingly serious internal browning,genes related to photosynthesis were down-regulated,while genes related to senescence were up-regulated,thus suggesting the up-regulation of the process of cell senescence during internal browning.In conclusion,heat stress should be eliminated to reduce preharvest internal browning in Nane plum.

Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis

Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions.Here,we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv.‘Hongyang’,named Hongyang v4.0,which is the first to achieve two de novo haploid-resolved haplotypes,HY4P and HY4A.HY4P and HY4A have a total length of 606.1 and 599.6 Mb,respectively,with almost the entire telomeres and centromeres assembled in each haplotype.In comparison with Hongyang v3.0,the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions,resulting in∼38.6–39.5 Mb extra sequences,which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A,respectively.Furthermore,our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres.Globally,centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer(Ach-CEN153)with different copy numbers among chromosomes.Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids,but also have genetic features for participation in the regulation of cell division.The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.

Tissue distribution of cadmium and its effect on reproduction in Spodoptera exigua

Vegetable fields are often contaminated by heavy metals,and Spodoptera exigua is a major vegetable pest which is stressed by heavy metals mainly by feeding.In this study,cadmium accumulation in the tissues of S.exigua exposed to cadmium and its effects on the growth and development of the parents and the offspring were investigated.Under the stress of different concentrations of cadmium(0.2,3.2,and 51.2 mg kg^(-1)),the cadmium content in each tissue of S.exigua increased in a dose-dependent manner.At the larval stage,the highest cadmium accumulation was found in midgut in all three cadmium treatments,but at the adult stage,the highest cadmium content was found in fat body.In addition,the cadmium content in ovaries was much higher than in testes.When F1S.exigua was stressed by cadmium and the F_(2)generation was not fed a cadmium-containing diet,the larval survival,pupation rate,emergence rate and fecundity of the F_(2)generation were significantly reduced in the 51.2 mg kg^(-1)treatment compared to the corresponding F1generation.Even in the F_(2)generation of the 3.2 mg kg^(-1)treatment,the fecundity was significantly lower than in the parental generation.The fecundity of the only-female stressed treatment was significantly lower than that of the only-male stressed treatment at the 3.2 and 51.2 mg kg^(-1)cadmium exposure levels.When only mothers were stressed at the larval stage,the fecundity of the F_(2)generation was significantly lower than that of the F1generation in the 51.2 mg kg^(-1)treatment,and it was also significantly lower than in the 3.2 and 0.2 mg kg^(-1)treatments.The results of our study can provide useful information for forecasting the population increase trends under different heavy metal stress conditions and for the reliable environmental risk assessment of heavy metal pollution.

Flavonoid content and radical scavenging activity in fruits of Chinese dwarf cherry(Cerasus humilis) genotypes

The Chinese dwarf cherry（Cerasus humilis（Bge.） Sok.） is a small shrub with edible fruits. It is native to northern and western China. This species was included as a medicinal plant in the ‘‘Chinese Pharmacopeia’’ and has emerged as an economically important crop for fresh fruit consumption, processing into juice and wine and nutraceutical products as well. To gain a better understanding of flavonoid biosynthesis and help develop value added products and better cultivars with greater health benefits, we analyzed total flavonoid content（TFC）, composition, and radical scavenging activities in fruit extracts of 16 Chinese dwarf cherry genotypes. Fruit peel TFC ranged from 33.5 to72.8 mg/g REáFW（RE： rutin equivalent, FW： fresh weight）while fruit flesh TFC ranged from 4.3 to 16.9 mg/g REáFW.An HPLC analysis revealed that fruit extracts contained 14 flavonoids with considerable variation in their profiles across genotypes. The most abundant flavonoids in most genotypes were proanthocyanidin B1（PA-B1）, proanthocyanidin B2（PA-B2）, phloretin 20-O-glucoside（PG）, and phloretin 20,40-O-diglucoside（PDG）. Principal component analysis showed that PG, PA-B1, and PA-B2 had large,positive factor loading values in the first principal component for each genotype. Increased scavenging activity of2,2-diphenyl-1-picrylhydrazyl（DPPH） radicals was apparent in genotypes ‘Nongda 4’, ‘Nongda 3’, ‘Nongda 6’,‘Wenfenli’, and ’10-32’, suggesting promising applications in the production of nutraceutical products. In summary, our results will aid in breeding, fruit processing, and developing medicinal uses of the Chinese dwarf cherry.

Genome-wide analysis of cytochrome P450 genes in Citrus clementina and characterization of a CYP gene encoding f lavonoid 3′-hydroxylase

Cytochrome P450s(CYPs)are the largest family of enzymes in plant and play multifarious roles in development and defense but the available information about the CYP superfamily in citrus is very limited.Here we provide a comprehensive genome-wide analysis of the CYP superfamily in Citrus clementina genome,identifying 301 CYP genes grouped into ten clans and 49 families.The characteristics of both gene structures and motif compositions strongly supported the reliability of the phylogenetic relationship.Duplication analysis indicated that tandem duplication was the major driving force of expansion for this superfamily.Promoter analysis revealed numerous cis-acting elements related to various responsiveness.RNA-seq data elucidated their expression patterns in citrus fruit peel both during development and in response to UV-B.Furthermore,we characterize a UV-B-induced CYP gene(Ciclev10019637m,designated CitF3′H)as a f lavonoid 3-hydroxylase for the first time.CitF3 H catalyzed numerous f lavonoids and favored naringenin in yeast assays.Virusinduced silencing of CitF3′ H in citrus seedlings significantly reduced the levels of 3′-hydroxylated f lavonoids and their derivatives.These results together with the endoplasmic reticulum-localization of CitF3 H in plant suggest that this enzyme is responsible for the biosynthesis of 3-hydroxylated f lavonoids in citrus.Taken together,our findings provide extensive information about the CYP superfamily in citrus and contribute to further functional verification.

Genome-wide profiling of histone H3 lysine 27 trimethylation and its modification in response to chilling stress in grapevine leaves

Histone H3 lysine 27 trimethylation(H3K27me3) is a histone modification associated with transcriptional repression. However, insights into the genome-wide pattern of H3K27me3 in grapevines are limited. Here, anti-H3K27 chromatin immunoprecipitation(ChIP), high-throughput sequencing, and transcriptome analysis were performed using leaves of Vitis amurensis. The leaves were treated at 4°C for 2 h and 24 h and used to investigate changes in H3K27me3 under chilling treatment. The results show that H3K27me3 is well-distributed both in gene regions(-50%) and in the intergenic region(-50%) in the grapevine genome(Vitis vinifera ‘Pinot Noir PN40024'). H3K27me3 was found to be localized in8 368 annotated gene regions in all detected samples(leaves at normal temperature and under chilling treatments) and mainly enriched in gene bodies with the adjacent promoter and downstream areas. The short-term chilling treatments(4°C for 2 h) induced 2 793 gains and 305losses in H3K27me3 modification. Subsequently, 97.3% of the alterations were restored to original levels after 24 h treatment. The ChIP-qPCR for five differential peaks showed similar results to the data for ChIP-seq, indicating that the chilling-induced H3K27me3 modification is reliable.Integrative analysis of transcriptome and ChIP-seq results showed that the expression of H3K27me3 target genes was significantly lower than those of non-target genes, indicating transcriptional repression of H3K27me3 in grapevine leaves. Furthermore, histone methylation alterations were detected in 82 genes and were related to either repression or activation of their expression during chilling stress. The findings provide the genome-wide H3K27me3 patterns in grapevines and shed light on uncovering its regulation in chilling stress responses.

Transcriptomic analysis reveals the defense mechanisms of citrus infested with Diaphorina citri

Huanglongbing(HLB) is a devastating disease that has led to an acute crisis for growers of citrus, one of the world's most important fruit crops. The phloem-feeding Asian citrus psyllid(ACP), Diaphorina citri, is the main pest at the new shoot stage and is the only natural vector of HLB pathogenic bacteria. Little is known about how plants perceive and defend themselves from this destructive pest. Here, we characterized changes in the expression of various genes in citrus plants that were continuously infested by D. citri for different durations(12, 24, and 48 h). A total of 5 219 differentially expressed genes(DEGs) and 643 common DEGs were identified across all time points. Several pathways related to defense were activated, such as peroxisome, alpha-linolenic acid metabolism, and phenylpropanoid and terpenoid biosynthesis, and some pathways related to growth and signal transduction were suppressed in response to D. citri infestation. The expression of genes including kinases(CML44, CIPK6, and XTH6), phytohormones(SAMT, LOX6, and NPR3), transcription factors(bHLH162, WRKY70, and WRKY40), and secondary metabolite synthesis-related genes(PAL, 4CL2, UGT74B1 and CYP82G1) was significantly altered in response to D. citri infestation. The findings of this study greatly enhance our understanding of the mechanisms underlying the defense response of citrus plants to D. citri infestation at the molecular level. Functional characterization of the candidate defense-related genes identified in this study will aid the molecular breeding of insect-resistant citrus varieties.

Direct evidence for dynamics of cell heterogeneity in watercored apples: turgor-associated metabolic modifications and within-fruit water potential gradient unveiled by single-cell analyses

Watercore is a physiological disorder in apple(Malus×domestica Borkh.)fruits that appears as water-soaked tissues adjacent to the vascular core,although there is little information on what exactly occurs at cell level in the watercored apples,particularly from the viewpoint of cell water relations.By combining picolitre pressure-probe electrospray-ionization mass spectrometry(picoPPESI-MS)with freezing point osmometry and vapor pressure osmometry,changes in cell water status and metabolisms were spatially assayed in the same fruit.In the watercored fruit,total soluble solid was lower in the watercore region than the normal outer parenchyma region,but there was no spatial difference in the osmotic potentials determined with freezing point osmometry.Importantly,a disagreement between the osmotic potentials determined with two methods has been observed in the watercore region,indicating the presence of significant volatile compounds in the cellular fluids collected.In the watercored fruit,cell turgor varied across flesh,and a steeper water potential gradient has been established from the normal outer parenchyma region to the watercore region,retaining the potential to transport water to the watercore region.Site-specific analysis using picoPPESI-MS revealed that together with a reduction in turgor,remarkable metabolic modifications through fermentation have occurred at the border,inducing greater production of watercore-related volatile compounds,such as alcohols and esters,compared with other regions.Because alcohols including ethanol have low reflection coefficients,it is very likely that these molecules would have rapidly penetrated membranes to accumulate in apoplast to fill.In addition to the water potential gradient detected here,this would physically contribute to the appearance with high tissue transparency and changes in colour differences.Therefore,it is concluded that these spatial changes in cell water relations are closely associated with watercore symptoms as well as with metabolic alterations.

Morphological, physiological and molecular characteristics of the seedless 'Hongjiangcheng' sweet orange

Seedless citrus has become one of the breeding goals due to its high edible ratio and convenience in fresh consumption and processing.In this study, the ‘Hongjiangcheng' sweet orange(WT) and its seedless mutant(MT) after cobalt-60 radiation were selected to study the formation metabolism of citrus seedless phenotype. Compared with WT, the MT had altered primary metabolite contents, as indicated by GC-MS analysis. The mature pollen of the MT was mostly distorted and shrunken, and the orange mutant exhibited significantly lower fertility than the WT. Through pollination experiments and paraffin sectioning of the MT, we observed self-compatibility during pollen tube germination in situ, in combination with the absence of natural parthenocarpy and arrested zygotic embryo development at the fourth week after pollination. From transcriptomic analyses of ovules in the fourth week, 815 differentially expressed genes(DEGs) were identified.Furthermore, according to the annotation of gene function and qRT-PCR analysis, Cs4g10930, Cs5g21900 and orange1.1t02243 were identified as candidate genes that may govern the mechanism of seedlessness. Finally, Agrobacterium-mediated transformation verified that the overexpression of Cs4g10930 and Cs5g21900 in Newhall navel orange calli inhibited embryoid production. This study provides a better understanding of seedless formation in citrus and two key genes that may play an important role in the early selection of seedless lines in citrus breeding programs.

OsNPF3.1,a nitrate,abscisic acid and gibberellin transporter gene,is essential for rice tillering and nitrogen utilization efficiency

Low-affinity nitrate transporter genes have been identified in subfamilies 4-8 of the rice nitrate transporter 1(NRT1)/peptide transporter family(NPF),but the OsNPF3 subfamily responsible for nitrate and phytohormone transport and rice growth and development remains unknown.In this study,we described OsNPF3.1 as an essential nitrate and phytohormone transporter gene for rice tillering and nitrogen utilization efficiency(NUtE).OsNPF3.1 possesses four major haplotypes of its promoter sequence in 517 cultivars,and its expression is positively associated with tiller number.Its expression was higher in the basal part,culm,and leaf blade than in other parts of the plant,and was strongly induced by nitrate,abscisic acid(ABA)and gibberellin 3(GA_3)in the root and shoot of rice.Electrophysiological experiments demonstrated that OsNPF3.1 is a pH-dependent low-affinity nitrate transporter,with rice protoplast uptake assays showing it to be an ABA and GA_3 transporter.OsNPF3.1 overexpression significantly promoted ABA accumulation in the roots and GA accumulation in the basal part of the plant which inhibited axillary bud outgrowth and rice tillering,especially at high nitrate concentrations.The NUtE of OsNPF3.1-overexpressing plants was enhanced under low and medium nitrate concentrations,whereas the NUtE of OsNPF3.1 clustered regularly interspaced short palindromic repeats(CRISPR)plants was increased under high nitrate concentrations.The results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate concentrations.The altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations,respectively.

Strategies for timing nitrogen fertilization of pear trees based on the distribution, storage, and remobilization of ^(15)N from seasonal application of (^(15)NH_4)_2SO_4

In order to improve the management of nitrogen(N) fertilization in pear orchards, we investigated the effects of application timing on the distribution, storage, and remobilization of N in mature pear trees in a field experiment at Jingtai County, Gansu Province, China. Nine trees were selected for the experiment and each received equal aliquots of 83.33 g N in the autumn, spring, and summer, with ^(15)N-labeled(NH_4)_2SO_4 used in one of the aliquots each season. Results showed that the(^(15)NH_4)_2SO_4 applied in the autumn remained in the soil during the winter. In the following spring this N was absorbed and rapidly remobilized into each organ, especially new organs(leaves, fruit and new shoots). The ^(15)N supplied in spring was rapidly transported to developing fruit between the young fruit and fruit enlargement stages. ^(15)N from the summer application of fertilizer was mainly stored in the coarse roots over the winter, then was mobilized to support growth of new organs in spring. In conclusion, for pear trees we recommend that the autumn application of N-fertilizer be soon after fruit harvest in order to increase N stores in fine roots. Spring application should be between full bloom and the young fruit stages to meet the high N demands of developing fruit. Summer application of fertilizer at the fruit enlargement stage does not contemporaneously affect the growth of pears, but increases the N stored in coarse roots, and in turn the amount available for remobilization in spring.

Expressing p20 hairpin RNA of Citrus tristeza virus confers Citrus aurantium with tolerance/resistance against stem pitting and seedling yellow CTV strains

The Citrus tristeza virus (CTV) uses 3 silencing suppressor genes, p20, p23 and p25, to resist the attacks from its Citrus hosts. Inactivating these genes is therefore obviously a potential defensive option in addition to the current control strat-egies including aphid management and the use of mild strain cross protection. In this study, we cloned partial DNA frag-ments from the three genes, and used them to construct vectors for expressing hairpin RNAs (hpRNAs). To facilitate the formation of hpRNAs, the constructs were introduced in a loop structure. Fol owing transformation of sour orange (Citrus aurantium) with these constructs, 8 p20 hpRNA (hp20) and 1 p25 hpRNA (hp25) expressing lines were obtained. The 7 hp20 transgenic lines were further characterized. Their reactions to CTV were tested fol owing inoculation with CT14A and/or TR-L514, both of which are severe strains. Results showed that 3 lines (hp20-5, hp20-6 and hp20-8) were completely resistant to TR-L514 under greenhouse conditions for no detectable viral load was found in their leaves by PCR. However, they exhibited only partial suppression of TR-L514 under screen house conditions since the virus was detected in their leaves, though 2 months later compared to non-transgenic controls. Further tests showed that hp20-5 was tolerant also to CT14A under screen house conditions. The growth of hp20-5 was much better than others including the controls that were concurrently chal enged with CT14A. These results showed that expressing p20 hpRNA was sufifcient to confer sour orange with CTV resistance/tolerance.

The Variation of Stone Cell Content in 236 Germplasms of Sand Pear(Pyrus pyrifolia)and Identification of Related Candidate Genes

Stone cells have been described to substantially influence pear fruit quality,as lignin and cellulose are the main components of stone cells.However,there are limited studies on the relationship between the variation and molecular basis of stone cells,lignin and cellulose content among different pear varieties.Here,to reveal the variation of stone cell content within different cultivated species,we collected 236 germplasms of sand pear(Pyrus pyrifolia)at 50 days after flower blooming(DAFB),the key stage of stone cell formation.In our results,we measured the content of stone cells,lignin and cellulose and found that these contents ranged from2.82%to 29.00%,8.84%to 55.30%and 11.52%to 30.55%,respectively.Further analysis showed that the variation coefficient of stone cell,lignin and cellulose content was 39.10%,28.03%and 16.71%,respectively.Additionally,a significant correlation between stone cell,lignin and cellulose content were detected,and the correlation coefficient between the contents of stone cell and lignin(0.912)was higher than between the contents of stone cell and cellulose(0.796).Moreover,the average lignin content(29.73%)was higher than the average cellulose content(18.03%)in stone cells in pear fruits,indicating that lignin is the main component of stone cell in pears.Finally,on the basic of the transcriptome data,we identified 10 transcription factors belonging to bHLH,ERF,MYB,and NAC transcript families,which might be involved in lignin formation in stone cells.qRT-PCR experiments verified coincident trends between expression of candidate genes and stone cell content.This research laid foundation for future studies on genetic variation of stone cells in pear fruits and provided important gene resources for stone cell regulation.

Effects of short-term heat stress on PSII and subsequent recovery for senescent leaves of Vitis vinifera L. cv. Red Globe

Heat stress occurs frequently in energy-saving sunlight greenhouses(ESSG) at the late growth stage. Three-year delayed cultivation(DC) of the Red Globe cultivar of Vitis vinifera L. was used to clarify the physiological mechanisms of short-term heat stress on PSII and subsequent recovery from heat stress. By November, the photosynthetic function had declined and the fall in transpiration rate(E) with heating time increased the possibility of heat damage. In July, the most obvious increase was in the relative variable fluorescence at J point at 40°C, and in November it changed to K point. The 5 min of heat treatment resulted in a significant increase of the relative variable fluorescence at 0.3 ms(W), and after 10 min of heat treatment, the number of reactive centres per excited cross section(RC/CS), probability that a trapped exciton moves an electron into the electron transport chain beyond Q–(at t=0)(Ψ) and quantum yield of electron transport at t=0(φ) decreased significantly(P<0.05), suggesting that the reaction centre, donor and acceptor side of photosystem II(PSII) were all significantly inhibited(P<0.05) and that the thermal stability of the photosynthetic mechanism was reduced. The inhibition of energy fluxes for senescent leaves in November was earlier and more pronounced than that for healthy leaves, which did not recover from heat stress of more than 15 min after 2 h recovery at room temperature.

Transcriptome profiling reveals regulatory mechanisms underlying corolla senescence in petunia

The genetic regulatory mechanisms that govern natural corolla senescence in petunia are not well understood.To identify key genes and pathways that regulate the process,we performed a transcriptome analysis in petunia corolla at four developmental stages,including corolla fully opening without anther dehiscence(D0),corolla expansion,2 days after anthesis(D2),corolla with initial signs of senescence(D4),and wilting corolla(D7).We identified large numbers of differentially expressed genes(DEGs),ranging from 4626 between the transition from D0 and D2,1116 between D2 and D4,a transition to the onset of flower senescence,and 327 between D4 and D7,a developmental stage representing flower senescence.KEGG analysis showed that the auxin-and ethylene-related hormone biosynthesis and signaling transduction pathways were significantly activated during the flower development and highly upregulated at onset of flower senescence.Ethylene emission was detected at the D2 to D4 transition,followed by a large eruption at the D4 to D7 transition.Furthermore,large numbers of transcription factors(TFs)were activated over the course of senescence.Functional analysis by virus-induced gene silencing(VIGS)experiments demonstrated that inhibition of the expression of TFs,such as ethylene-related ERF,auxin-related ARF,bHLH,HB,and MADS-box,significantly extended or shortened flower longevity.Our data suggest that hormonal interaction between auxin and ethylene may play critical regulatory roles in the onset of natural corolla senescence in petunia.

Tracing founder haplotypes of Japanese apple varieties: application in genomic prediction and genome-wide association study

Haplotypes provide useful information for genomics-based approaches,genomic prediction,and genome-wide association study.As a small number of superior founders have contributed largely to the breeding history of fruit trees,the information of founder haplotypes may be relevant for performing the genomics-based approaches in these plants.In this study,we proposed a method to estimate 14 haplotypes from 7 founders and automatically trace the haplotypes forward to apple parental(185 varieties)and breeding(659 F 1 individuals from 16 full-sib families)populations based on 11,786 single-nucleotide polymorphisms,by combining multiple algorithms.Overall,92%of the single-nucleotide polymorphisms information in the parental and breeding populations was characterized by the 14 founder haplotypes.The use of founder haplotype information improved the accuracy of genomic prediction in 7 traits and the resolution of genome-wide association study in 13 out of 27 fruit quality traits analyzed in this study.We also visualized the significant propagation of the founder haplotype with the largest genetic effect in genome-wide association study over the pedigree tree of the parental population.These results suggest that the information of founder haplotypes can be useful for not only genetic improvement of fruit quality traits in apples but also for understanding the selection history of founder haplotypes in the breeding program of Japanese apple varieties.

High-level expression and purification of Plutella xylostella acetylcholinesterase in Pichia pastoris and its potential application

The acetylcholinesterase 2（AChE2）cloned from Plutella xylostella was first successfully expressed in methylotrophic yeast Pichia pastoris GS115.One transformant with high-level expression of the recombinant AChE（rAChE,23.2 U mL-1in supernatant）was selected by plating on increasing concentrations of antibiotic G418 and by using a simple and specific chromogenic reaction with indoxyl acetate as a substrate.The maximum production of r ACh E reached about 11.8 mg of the enzyme protein per liter of culture.The r ACh E was first precipitated with ammonium sulfate（50%saturation）and then purified with procainamide affinity column chromatography.The enzyme was purified 12.1-fold with a yield of 22.8%and a high specific activity of 448.3 U mg-1.It was sensitive to inhibition by methamidophos and pirimicarb,the calculated 50% inhibitory concentration（IC50）values of the two pesticides were 0.357 and 0.888 mg L-1,respectively,and the calculated 70% inhibitory concentration（IC70）values were 0.521 and 0.839 mg L-1,respectively.The results suggested that it has a potential application in the detection of pesticide residues.

A chromosome-scale genome sequence of pitaya (Hylocereus undatus) provides novel insights into the genome evolution and regulation of betalain biosynthesis

Pitaya(Hylocereus)is the most economically important fleshy-fruited tree of the Cactaceae family that is grown worldwide,and it has attracted significant attention because of its betalain-abundant fruits.Nonetheless,the lack of a pitaya reference genome significantly hinders studies focused on its evolution,as well as the potential for genetic improvement of this crop.Herein,we employed various sequencing approaches,namely,PacBio-SMRT,Illumina HiSeq paired-end,10×Genomics,and Hi-C(high-throughput chromosome conformation capture)to provide a chromosome-level genomic assembly of‘GHB’pitaya(H.undatus,2n=2x=22 chromosomes).The size of the assembled pitaya genome was 1.41 Gb,with a scaffold N50 of~127.15 Mb.In total,27,753 protein-coding genes and 896.31Mb of repetitive sequences in the H.undatus genome were annotated.Pitaya has undergone a WGT(whole-genome triplication),and a recent WGD(whole-genome duplication)occurred after the gamma event,which is common to the other species in Cactaceae.A total of 29,328 intact LTR-RTs(~696.45Mb)were obtained in H.undatus,of which two significantly expanded lineages,Ty1/copia and Ty3/gypsy,were the main drivers of the expanded genome.A high-density genetic map of F1 hybrid populations of‘GHB’בDahong’pitayas(H.monacanthus)and their parents were constructed,and a total of 20,872 bin markers were identified(56,380 SNPs)for 11 linkage groups.More importantly,through transcriptomic and WGCNA(weighted gene coexpression network analysis),a global view of the gene regulatory network,including structural genes and the transcription factors involved in pitaya fruit betalain biosynthesis,was presented.Our data present a valuable resource for facilitating molecular breeding programs of pitaya and shed novel light on its genomic evolution,as well as the modulation of betalain biosynthesis in edible fruits.

Isolation and Characterization of a Cinnamoyl CoA Reductase Gene(CCR) in Pear(Pyrus pyrifolia)

Pear is a popular and commercially important fresh fruit, and its texture is related to the presence of sclereid formatted by parenchyma cell with lignification in vascular plants. Previous studies have demonstrated that content of lignin may be regulated by cinnamoyl CoA reductase(CCR) in various plants. However, the function of CCR in pears remains very limited. In the present study, we isolated a cDNA encoding CCR(PpCCR, GenBank accession No. KF999958) and its promoter(proPpCCR) from Whangkeumbae pear to investigate the function of CCR in lignin biosynthesis. PpCCR-GFP expressed in rice mesophyll protoplast demonstrated that PpCCR-GFP was localized in the cytoplasm, indicating that CCR may function in cytoplasm without localization signals. In transgenic plants carrying PpCCR, we observed higher lignin content compared with that in wild type plants, further suggesting that PpCCR can affect the lignin contents through regulating lignin biosynthesis in Arabidopsis thaliana. More studies in other plants are needed to confirm our conclusion.

Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database

Cultivated strawberry(Fragaria×ananassa)is an important fruit crop species whose fruits are enjoyed by many worldwide.An octoploid of hybrid origin,the complex genome of this species was recently sequenced,serving as a key reference genome for cultivated strawberry and related species of the Rosaceae family.The current annotation of the F.ananassa genome mainly relies on ab initio predictions and,to a lesser extent,transcriptome data.Here,we present the structure and functional reannotation of the F.ananassa genome based on one PacBio full-length RNA library and ninety-two Illumina RNA-Seq libraries.This improved annotation of the F.ananassa genome,v1.0.a2,comprises a total of 108,447 gene models,with 97.85%complete BUSCOs.The models of 19,174 genes were modified,360 new genes were identified,and 11,044 genes were found to have alternatively spliced isoforms.Additionally,we constructed a strawberry genome database(SGD)for strawberry gene homolog searching and annotation downloading.Finally,the transcriptome of the receptacles and achenes of F.ananassa at four developmental stages were reanalyzed and qualified,and the expression profiles of all the genes in this annotation are also provided.Together,this study provides an updated annotation of the F.ananassa genome,which will facilitate genomic analyses across the Rosaceae family and gene functional studies in cultivated strawberry.