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.

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.

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.

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.

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.

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.

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.

Do Strigolactones Regulate Bud Winter Dormancy and Charactrisitc Secondary Metabolism in Tea?

Tea(Camellia sinensis[L.]O.Kuntze.)is an important cash crop,which mainly uses tender shoots and young leaves for manufacturing.Due to the marketing characteristic that earlier made tea has higher price,the time of the breaking of winter dormancy buds in spring is extremely important in tea industry.Strigolactones are a group of carotenoids-derived metabolites which regulates bud outgrowth,shoot branching,tiller angle and environmental stress responses.The role of strigolactones in tea plant was briefly summarized in the current review,with an emphasis of the association of strigolactones on bud ecodormancy and shoot branching.The involvement of strigolactones on the biosynthesis of the tea characteristic metabolites flavonoids,caffeine and theanine were also discussed.Moreover,recent advances on the biosynthesis of strigolactones and its regulation by microRNAs and environmental stresses were also presented.This review provides a basis for future investigations underlying the mechanisms of strigolactones on bud winter dormancy and tea secondary metabolism.

Current Situations and Suggestions for Development of Oil Peony Industry in Hubei Province

Based on the investigation on the production of oil peony( Paeooia suffruticosa Andr.) in the main producing areas in Hubei Province,the current situations and problems faced by oil peony industry were analyzed.The oil peony industry is in the adjustment period after years of development in Hubei Province,and the following suggestions were proposed for its further development.First,make full use of the ornamental value of peony and carry out the theme eco-tourism of peony.Second,make full use of the advantages of local resources and develop resource evaluation and utilization.Third,promote the intensive processing of oil peony and extend the industrial chain of products.

Occurrence Regularity and Integrated Control Technology of Canker in Citrus

Canker is a quarantine bacterial disease that seriously harms leaves,branches and fruits of citrus,leading to a decrease in the production and affecting the commodity and sales of citrus.Citrus canker has the characteristics of fast spreading speed and difficult radical cure.Through the identification of symptoms and a summary of occurrence regularity,the integrated prevention and control technology for citrus canker is described in this article,in order to achieve effective prevention and control and reduce prevention and control cost.

Effects of Sinochem Microbial Organic Fertilizer on Tea Plants

[Objectives]This study was conducted to explore the application effects of Sinochem microbial organic fertilizer on tea plants.[Methods]Through the experiment and demonstration of Sinochem microbial organic fertilizer,its effects on the yield and quality of tea and the physical and chemical quality of soil were explored.[Results]Compared with the conventional organic fertilizer cake fertilizer,the fertilizer could increase the weight of freshly picked bud leaves,increase the yield of tea,and thus promote the growth of tea plants.It increased the contents of chlorophyll components,amino acids and tea polyphenols,the main functional substances of tea,which was conducive to improving the internal quality of tea.It improved the physical and chemical properties of soil,and increased the contents of organic matter,alkali-hydrolyzable nitrogen and available phosphorus in tea garden soil.It also had a good effect in improving soil environmental health indexes and physical and chemical properties,and did not contain heavy metals and plant growth hormones.[Conclusions]This study provides a theoretical basis for the popularization and application of Sinochem microbial organic fertilizer.

Applied Technology of Botanical Pesticides against Empoasca pirisuga Matumura

[Objectives] The paper was to explore the control effects of different botanical pesticides against Empoasca pirisuga Matumura. [Methods] 5% Eucalyptol SL, 0.5% matrine SL and 50% thiacloprid WDG were used to control E. pirisuga , and the decline rate of insect population was investigated. [Results] Eucalyptol had good control effect on E. pirisuga , with slow effect but long duration. It was harmless to natural enemies in tea gardens, with high safety and no chemical injury. [Conclusions] The study provides a theoretical basis for the application of botanical pesticides in tea production.

A bZIP transcription factor(CiFD) regulates drought-and low-temperature-induced flowering by alternative splicing in citrus

Drought and low temperature are two key environmental factors that induce adult citrus flowering. However, the underlying regulation mechanism is poorly understood. The bZIP transcription factor FD is a key component of the florigen activation complex(FAC) which is composed of FLOWERING LOCUS T(FT), FD, and 14-3-3 proteins. In this study, isolation and characterization of CiFD in citrus found that there was alternative splicing(AS) of CiFD, forming two different proteins(CiFDα and CiFDβ). Further investigation found that their expression patterns were similar in different tissues of citrus, but the subcellular localization and transcriptional activity were different. Overexpression of the CiFD DNA sequence(CiFD-DNA), CiFDα, or CiFDβ in tobacco and citrus showed early flowering, and CiFD-DNA transgenic plants were the earliest, followed by CiFDβ and CiFDα. Interestingly, CiFDα and CiFDβ were induced by low temperature and drought, respectively. Further analysis showed that CiFDαcan form a FAC complex with CiFT, Ci14-3-3, and then bind to the citrus APETALA1(CiAP1) promoter and promote its expression. However,CiFDβ can directly bind to the CiAP1 promoter independently of CiFT and Ci14-3-3. These results showed that CiFDβ can form a more direct and simplified pathway that is independent of the FAC complex to regulate drought-induced flowering through AS. In addition, a b HLH transcription factor(CibHLH96) binds to CiFD promoter and promotes the expression of CiFD under drought condition. Transgenic analysis found that CibHLH96 can promote flowering in transgenic tobacco. These results suggest that CiFD is involved in drought-and low-temperature-induced citrus flowering through different regulatory patterns.

Establishment of Self-incompatibility Gene cDNA Microarray to Identify S-genotypes of Pyrus pyrifolia

Based on the c DNA sequences from hyper variable(HV) regions of identified 52 S-alleles in Oriental pear cultivars, S-RNase c DNA probes were designed, and a c DNA microarray for S-RNase detections was established. Each microarray contained 240 sites from 55 c DNA probes, including all specific c DNA sequences from the HV regions of the S-alleles. Using the c DNA of pistils of tested pear cultivars as template and Cy3 fluorescently labeling primers by PCR amplification, microarray hybridization detected the S-genotype of each pear cultivar. The genotypes inferred from the c DNA microarray hybridization signals of pear cultivars such as ‘Lijiang Huangsuanli', ‘Xiuyu', ‘Midu Yuli', ‘Baimianli', and ‘Deshengxiang' were similar to the known genotypes of all tested cultivars. The S-RNase c DNA microarrays and the oligonucleotide gene chips were then used to conduct parallel testing of 24 P. pyrifolia cultivars with unknown S-genotypes. In conclusion, the construction of c DNA microarrays has further improved the pear S-RNase detection platform.