A comparative study on the role of conventional,chemical,and nanopriming for better salt tolerance during seed germination of direct seeding rice

Salinity is one of the most significant risks to crop production and food security as it harms plant physiology and biochemistry.The salt stress during the rice emergence stages severely hampers the seed germination and seedling growth of direct-seeded rice.Recently,nanoparticles(NPs)have been reported to be effectively involved in many plant physiological processes,particularly under abiotic stresses.To our knowledge,no comparative studies have been performed to study the efficiency of conventional,chemical,and seed nanopriming for better plant stress tolerance.Therefore,we conducted growth chamber and field experiments with different salinity levels(0,1.5,and 3‰),two rice varieties(CY1000 and LLY506),and different priming techniques such as hydropriming,chemical priming(ascorbic acid,salicylic acid,and γ-aminobutyric acid),and nanopriming(zinc oxide nanoparticles).Salt stress inhibited rice seed germination,germination index,vigor index,and seedling growth.Also,salt stress increased the over accumulation of reactive oxygen species(H_(2)O_(2) and O_(2)^(-)·)and malondialdehyde(MDA)contents.Furthermore,salt-stressed seedlings accumulated higher sodium(Na^(+))ions and significantly lower potassium(K^(+))ions.Moreover,the findings of our study demonstrated that,among the different priming techniques,seed nanopriming with zinc oxide nanoparticles(NanoZnO)significantly contributed to rice salt tolerance.ZnO nanopriming improved rice seed germination and seedling growth in the pot and field experiments under salt stress.The possible mechanism behind ZnO nanopriming improved rice salt tolerance included higher contents of α-amylase,soluble sugar,and soluble protein and higher activities of antioxidant enzymes to sustain better seed germination and seedling growth.Moreover,another mechanism of ZnO nanopriming induced rice salt tolerance was associated with better maintenance of(K^(+))ions content.Our research concluded that NanoZnO could promote plant salt tolerance and be adopted as a practical nanopriming technique,promoting global crop production in saltaffected agricultural lands.

Visualization Analysis of the Impact of Rubber Agroforestry Ecosystem on Soil Microbial Community

Rubber agroforestry systems positively impact soil microbial communities. This study employed a bibliometric approach to explore the research status, hotspots, and development trends related to these effects. Using CiteSpace software, we visually analyzed research literature from the Web of Science (WOS) core database, spanning 2004 to 2024. The focus was on the impact of rubber agroforestry ecosystems on soil microbial communities. The results indicate significant attention from Chinese researchers, who have published numerous influential papers in this field. Authors Liu Wenjie have contributed the most papers, although no stable core author group exists. The Chinese Academy of Sciences is the leading research institution in terms of publication volume. While there is close collaboration between different institutions and countries, the intensity of researcher cooperation is low. The most cited literature emphasizes soil nutrients and structure in rubber agroforestry, laying a foundation for soil microorganism studies. Most cited journals are from countries like Netherlands and the United Kingdom. Key research areas include the effects of rubber intercropping on soil microbial communities, agroforestry management, and soil health. Research development can be divided into three stages: the initial stage (2010-2015), the development stage (2015-2020), and the mature stage (2020-2024). Current studies show that rubber intercropping and rubber-based agroforestry systems enhance soil microbial communities, positively impacting soil health. This paper provides a theoretical basis for the sustainable development of rubber agroforestry systems and improved management plans. Future research could explore the effects of species composition on soil microbiological characteristics and develop methods for species interactions. An in-depth study of the soil microbial community’s structure and function, and its relationship with rubber trees, is crucial. Developing effective, rationally designed rubber agroforestry systems and underground soil microbiome technology will promote sustainability and improve plantation productivity.

The telomere-to-telomere genome of Fragaria vesca reveals the genomic evolution of Fragaria and the origin of cultivated octoploid strawberry

Fragaria vesca,commonly known as wild or woodland strawberry,is the most widely distributed diploid Fragaria species and is native to Europe and Asia.Because of its small plant size,low heterozygosity,and relative ease of genetic transformation,F.vesca has been a model plant for fruit research since the publication of its Illumina-based genome in 2011.However,its genomic contribution to octoploid cultivated strawberry remains a long-standing question.Here,we de novo assembled and annotated a telomere-to-telomere,gap-free genome of F.vesca‘Hawaii 4’,with all seven chromosomes assembled into single contigs,providing the highest completeness and assembly quality to date.The gap-free genome is 220785082 bp in length and encodes 36173 protein-coding gene models,including 1153 newly annotated genes.All 14 telomeres and seven centromeres were annotated within the seven chromosomes.Among the three previously recognized wild diploid strawberry ancestors,F.vesca,F.iinumae,and F.viridis,phylogenomic analysis showed that F.vesca and F.viridis are the ancestors of the cultivated octoploid strawberry F.×ananassa,and F.vesca is its closest relative.Three subgenomes of F.×ananassa belong to the F.vesca group,and one is sister to F.viridis.We anticipate that this high-quality,telomere-to-telomere,gap-free F.vesca genome,combined with our phylogenomic inference of the origin of cultivated strawberry,will provide insight into the genomic evolution of Fragaria and facilitate strawberry genetics and molecular breeding.

Identification and profile of phenolamides with anthracnose resistance potential in tea(Camellia sinensis)

Tea anthracnose is a prevalent disease in China that can lead to reduced tea production and lower quality,yet there is currently a lack of effective means for controlling this disease.In this study,we identified 46 phenolamides(including 27 isomers)in different tissues and organs of tea plants based on a developed workflow,and the secondary mass spectra of all these compounds have been documented.It was revealed that tea plants predominantly accumulate protonated aliphatic phenolamides,rather than aromatic phenolamides.The profile of phenolamides indicate that their buildup in tea plants is specific to certain tissues and acyl-acceptors,and this distribution is associated with the extent of phenolamide acyl-modification.Additionally,it was observed that N-Feruloylputrescine(Fer-Put,a type of phenolamides)was responsive to the stimulated accumulation of the tea anthracnose pathogen.The findings of anti-anthracnose experiments in vitro and on tea leaf demonstrated that Fer-Put was capable of significantly inhibiting the growth of anthracnose pathogen colony,effectively prevented tea leaf disease.Furthermore,it was observed that Fer-Put treatment can enhance the antioxidant enzyme activity of tea leaves.TEA002780.1 and TEA013165.1 gene may be responsible for the biosynthesis of Fer-Put in the disease resistance process in tea plants.Through these studies,the types and distribution of phenolamides in tea plants have been elucidated,and Fer-Put’s ability to resist anthracnose has been established,providing new insights into the resistance of tea anthracnose.

Significant reduction of ammonia emissions while increasing crop yields using the 4R nutrient stewardship in an intensive cropping system

Ammonia (NH_3) emissions should be mitigated to improve environmental quality.Croplands are one of the largest NH_3sources,they must be managed properly to reduce their emissions while achieving the target yields.Herein,we report the NH_3 emissions,crop yield and changes in soil fertility in a long-term trial with various fertilization regimes,to explore whether NH_3 emissions can be significantly reduced using the 4R nutrient stewardship (4Rs),and its interaction with the organic amendments (i.e.,manure and straw) in a wheat–maize rotation.Implementing the 4Rs significantly reduced NH_3 emissions to 6 kg N ha~(–1) yr~(–1) and the emission factor to 1.72%,without compromising grain yield (12.37 Mg ha~(–1) yr~(–1))and soil fertility (soil organic carbon of 7.58 g kg~(–1)) compared to the conventional chemical N management.When using the 4R plus manure,NH_3 emissions (7 kg N ha~(–1) yr~(–1)) and the emission factor (1.74%) were as low as 4Rs,and grain yield and soil organic carbon increased to 14.79 Mg ha~(–1) yr~(–1) and 10.09 g kg~(–1),respectively.Partial manure substitution not only significantly reduced NH_3 emissions but also increased crop yields and improved soil fertility,compared to conventional chemical N management.Straw return exerted a minor effect on NH_3 emissions.These results highlight that 4R plus manure,which couples nitrogen and carbon management can help achieve both high yields and low environmental costs.

Pyramiding of multiple genes generates rapeseed introgression lines with clubroot and herbicide resistance, high oleic acid content, and early maturity

Clubroot and herbicide resistance,high oleic acid(OA)content,and early maturity are targets of rapeseed(Brassica napus L.)breeding.The objective of this study was to develop new male-fertility restorer lines by pyramiding favorable genes to improve these traits simultaneously.Seven elite alleles for the four traits were introduced into the restorer line 621R by speed breeding with marker-assisted and phenotypic selection.Six introgression lines(ILs)were developed with four-to seven-gene combinations and crossed with two elite parents to develop hybrids.All ILs and their corresponding hybrids displayed high resistance to both clubroot pathotype 4 and sulfonylurea herbicides.Three ILs and their hybrids showed large increases in OA contents and four showed earlier maturity.These new ILs may be useful in rapeseed hybrid breeding for the target traits.

Reduction of N2O emissions by DMPP depends on the interactions of nitrogen sources(digestate vs. urea) with soil properties

The inhibition of nitrification by mixing nitrification inhibitors(NI)with fertilizers is emerging as an effective method to reduce fertilizer-induced nitrous oxide(N_(2)O)emissions.The additive 3,4-dimethylpyrazole phosphate(DMPP)apparently inhibits ammonia oxidizing bacteria(AOB)more than ammonia oxidizing archaea(AOA),which dominate the nitrification in alkaline and acid soil,respectively.However,the efficacy of DMPP in terms of nitrogen sources interacting with soil properties remains unclear.We therefore conducted a microcosm experiment using three typical Chinese agricultural soils with contrasting pH values(fluvo-aquic soil,black soil and red soil),which were fertilized with either digestate or urea in conjunction with a range of DMPP concentrations.In the alkaline fluvo-aquic soil,fertilization with either urea or digestate induced a peak in N_(2)O emission(60μg N kg^(-1)d^(-1))coinciding with the rapid nitrification within 3 d following fertilization.DMPP almost eliminated this peak in N_(2)O emission,reducing it by nearly 90%,despite the fact that the nitrification rate was only reduced by 50%.In the acid black soil,only the digestate induced an N_(2)O emission that increased gradually,reaching its maximum(20μg N kg^(-1)d^(-1))after 5–7 d.The nitrification rate and N_(2)O emission were both marginally reduced by DMPP in the black soil,and the N_(2)O yield(N_(2)O-N per NO2–+NO3–-N produced)was exceptionally high at 3.5%,suggesting that the digestate induced heterotrophic denitrification.In the acid red soil,the N_(2)O emission spiked in the digestate and urea treatments at 50 and 10μg N kg^(-1)d^(-1),respectively,and DMPP reduced the rates substantially by nearly 70%.Compared with 0.5%DMPP,the higher concentrations of DMPP(1.0 to 1.5%)did not exert a significantly(P<0.05)better inhibition effect on the N_(2)O emissions in these soils(either with digestate or urea).This study highlights the importance of matching the nitrogen sources,soil properties and NIs to achieve a high efficiency of N_(2)O emission reduction.

Down-regulation of MeMYB2 leads to anthocyanin accumulation and increases chilling tolerance in cassava(Manihot esculenta Crantz)

Chilling-induced accumulation of reactive oxygen species(ROS) is harmful to plants,which usually produce anthocyanins to scavenge ROS as protection from chilling stress.As a tropical crop,cassava is hypersensitive to chilling,but the biochemical basis of this hypersensitivity remains unclear.We previously generated Me MYB2-RNAi transgenic cassava with increased chilling tolerance.Here we report that Me MYB2-RNAi transgenic cassava accumulated less ROS but more cyanidin-3-O-glucoside than the wild type under early chilling stress.Under this stress,the anthocyanin biosynthesis pathway was more active in Me MYB2-RNAi lines than in the wild type,and several genes involved in the pathway,including Me TT8,were up-regulated by Me MYB2-RNAi in the transgenic cassava.Me MYB2 bound to the Me TT8 promoter and blocked its expression under both normal and chilling conditions,thereby inhibiting anthocyanin accumulation.Me TT8 was shown to bind to the promoter of Dihydroflavonol 4-reductase(Me DFR-2)and increased Me DFR-2 expression.Me MYB2 appears to act as an inhibitor of chilling-induced anthocyanin accumulation during the rapid response of cassava to chilling stress.

Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato

MicroTom has a short growth cycle and high transformation efficiency,and is a prospective model plant for studying organ development,metabolism,and plant–microbe interactions.Here,with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments,we constructed multiple gene co-expression networks,which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth,e.g.arbuscular mycorrhizal symbiosis and fruit development.Additionally,non-coding RNAs,including miRNAs,lncRNAs,and circRNAs were also identified,together with their potential targets.Interacting networks between different types of non-coding RNAs(miRNA-lncRNA),and non-coding RNAs and genes(miRNA-mRNA and lncRNA-mRNA)were constructed as well.Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit.Lastly,we established a database(http://eplant.njau.edu.cn/microTomBase/)with genomic and transcriptomic data,as well as details of gene co-expression and interacting networks on MicroTom,and this database should be of great value to those who want to adopt MicroTom as a model plant for research.

Deep placement of nitrogen fertilizer increases rice yield and nitrogen use efficiency with fewer greenhouse gas emissions in a mechanical direct-seeded cropping system

Deep placement of nitrogen fertilizer is a key strategy for improving nitrogen use efficiency. A two-year field experiment was conducted during the early rice growing seasons(March–July) of 2016 and 2017.The experimental treatments comprised two rice cultivars: Wufengyou 615(WFY 615) and Yuxiangyouzhan(YXYZ), and three N treatments: mechanical deep placement of all fertilizers as basal dose at 10 cm soil depth(one-time deep-placement fertilization, namely OTDP fertilization);manual surface broadcast(the common farmer practice) of 40% N fertilizer at one day before sowing(basal fertilizer)followed by broadcast application of 30% each at tillering and panicle initiation stages;and no fertilizer application at any growth stage as a control. One-time deep-placement fertilization increased grain yield of both rice cultivars by 11.8%–19.6%, total nitrogen accumulation by 10.3%–13.1%, nitrogen grain production efficiency by 29.7%–31.5%, nitrogen harvest index by 27.8%–30.0%, nitrogen agronomic efficiency by 71.3%–77.2%, and nitrogen recovery efficiency by 42.4%–56.7% for both rice cultivars, compared with the multiple-broadcast treatment. One-time deep-placement fertilization reduced CH4-induced global warming potential(GWP) by 20.7%–25.3%, N2O-induced GWP by 7.2%–12.3%, and total GWP by 14.7%–22.9% for both rice cultivars relative to the multiple-broadcast treatment. The activities of glutamine synthetase and nitrate reductase were increased at both panicle-initiation and heading stages in both rice cultivars following one-time deep-placement fertilization treatment. Larger leaf area index at heading stage and more favorable root morphological traits expressed as larger total root length, mean root diameter, and total root volume per hill were also observed. One-time deep-placement fertilization could be an effective strategy for increasing grain yield and nitrogen use efficiency and lowering greenhouse-gas emissions under mechanical direct-seeded cropping systems.

Anti-Obesity, Anti-Atherosclerotic and Anti-Oxidant Effects of Pu-Erh Tea on a High Fat Diet-Induced Obese Rat Model

Pu-erh tea, a traditional Chinese beverage, has been believed to have many benefits to human health and without side effects. In this study, we systematically analyzed the main active components of Pu-erh tea and investigated its anti-obesity, anti-atherosclerotic and anti-oxidant effects using an obese rat model. Obesity was induced by feeding a high-fat diet and subsequently the experimental obese mice were fed with high-fat diet supplemented with low (2.5%), medium (5%) or high (7.5%) doses of Pu-erh tea powder for 6 weeks respectively. As result, the body weight gain of the rats was decreased by medium and high doses of Pu-erh tea treatments. Furthermore, the levels of serum total cholesterol (TC), triglyceride (TG) and atherosclerosis index (AI) were significantly lowered by Pu-erh tea compared to the control group. Conversely, high density lipoproteincholesterol (HDL-C) level of the rats was significantly elevated by Pu-erh tea treatments. In addition, Pu-erh tea treatments increased the activities of anti-oxidative enzymes such as superoxide dismutase (SOD) and glutathione peroxides (GSH-Px), whereas reduced the level of lipid peroxidation product malondialdehyde (MDA) in obese rats. Collectively, our find-ings revealed that Pu-erh tea exerts comprehensive benefits in anti-obesity, anti-atherosclerotic and anti-oxidant effects, therefore can be used as a promising functional food in obesity management.

Identification and characterization of MeERF genes and their targets in pathogen response by cassava(Manihot esculenta)

Cassava,Manihot esculenta Crantz (Me),is a major dietary source of calories for over 700 million people in tropical regions.The production of cassava is constantly threatened by cassava bacterial blight (CBB),caused by Xanthomonas axonopodis pv.manihotis (Xam).The gene resources for CBB-resistant breeding of cassava are limited.In model plant species,ethylene response factors play important roles in response to pathogen infection.In this study,cassava ethylene response factors (MeERFs) were identified and characterized as the first step in studying their potential for CBB-resistant breeding of cassava.In the cassava genome 155 MeERFs were identified,of which 23 were induced by Xam infection.The promoter regions of204 genes harbored GCC-box that had the potential to interact with MeERFs.Using 37 transcriptomes derived from Xam infection treatment,four gene co-expression modules for the MeERFs and GCC-box containing genes were constructed.Six MeERFs were associated with two GCC-box containing genes:transcription initiation factor TFIIE subunit beta (MeTFIIE),and histone-lysine N-methyltransferase ASHR1 (MeASHR1).Dual-luciferase reporter assays showed that MeERF10 and MeERF58 positively regulated Me TFIIE;MeERF137 negatively regulated Me TFIIE;MeERF10 and MeERF137 positively regulated Me ASHR1;and MeERF35 negatively regulated Me ASHR1.The four MeERFs may mediate pathogen response by regulating the expression of the two GCC-box containing genes.

Chromosomal-level genome of macadamia(Macadamia integrifolia)

Macadamia from the family Proteaceae is a plant native to Australia and has long been favoured by people for its crispy and high nutritional and medicinal value.Here,the genome of GUIRE 1(GR1),a highly heterozygous superior cultivar of macadamia nut,was sequenced and assembled using nanopore sequencing,and a 807-Mb genome(contig N50,1.9 Mb;scaffold N50,54.70 Mb)and 14 chromosomes were obtained.A total of 453 Mb(about 55.95%)repetitive sequences and 37,657 protein-coding genes were obtained by gene annotation and homologous protein comparison.Proteaceae diverged from Nelumbonaceae nearly 115.37 million years ago and from Rubiaceae about 140 million years ago.A genome-wide duplication(WGD)event occurred in macadamia 41 million years ago based on the WGD analysis.The functional enrichment analysis of M.integrifolia-specific gene families revealed their roles in signal transduction,protein phosphorylation,protein binding,and defense response.Here,a highly heterozygous genome of M.integrifolia was unlocked to provide a database for breeding and molecular mechanism research.

Challenges and opportunities to improve tropical fruits in Hainan,China

Tropical fruits play a major role in the economic and social development of Hainan(China).Despite favorable climatic conditions,the yield of tropical fruits in Hainan remains low,in part due to the low genetic potential of currently grown tropical fruit varieties.Consequently,there is a need to improve yield potential by exploiting the genome and germplasm resources of tropical fruit species,minimizing post-harvest losses,and improving transportation standards.In this study,we intend to collect germplasm resources from a wide range of domestic and exotic sources to evaluate the genetic yield potential and nutritional quality of fruit using plant morphology,taxonomy and physiological parameters.In this review,we aim to identify current bottlenecks in the Hainan tropical fruit industry and propose solutions through the use of conventional breeding and new biotechnological tools,including the use of omics and CRISPR to enhance yield and tackle biotic and abiotic stresses of tropical fruit species.Producing new fruit cultivars in Hainan,either through conventional strategies or the use of genome editing technology such as CRISPR,could help improve the socioeconomic status of this region.Furthermore,increasing the genetic potential and production of new cultivars can help in meeting the demands of new trade agreements with various nations under the'One Belt,One Road'initiative,Boao Forum for Asia,ASEAN agreements,and the Shanghai Cooperation Organization.

Distinct root system acclimation patterns of seagrass Zostera japonica in sediments of different trophic status:a research by X-ray computed tomography

Conspecific seagrass living in differing environments may develop different root system acclimation patterns.We applied X-ray computed tomography(CT)for imaging and quantifying roots systems of Zostera japonica collected from typical oligotrophic and eutrophic sediments in two coastal sites of northern China,and determined sediment physicochemical properties that might influence root system morphology,density,and distribution.The trophic status of sediments had little influence on the Z.japonica root length,and diameters of root and rhizome.However,Z.japonica in oligotrophic sediment developed the root system with longer rhizome node,deeper rhizome distribution,and larger allocation to below-ground tissues in order to acquire more nutrients and relieve the N deficiency.And the lower root and rhizome densities of Z.japonica in eutrophic sediment were mainly caused by fewer shoots and shorter longevity,which was resulted from the more serious sulfide inhibition.Our results systematically revealed the effect of sediment trophic status on the phenotypic plasticity,quantity,and distribution of Z.japonica root system,and demonstrated the feasibly of X-ray CT in seagrass root system research.

Differentially Expressed Genes Related to Fertility Conversion in Thermo-sensitive Genic Male Sterile(TGMS) Lines of Brassica juncea

[Objective] This study was performed to screen functional genes related to the fertility conversion of thermo-sensitive genic male sterile （TGMS） lines of Brassica juncea L. [Method] A B. juncea TGMS line K121S was selected as the experimental material. The total RNAs were isolated from fertile and sterile pollens at different development stages, including mother cell stage, tetrad stage, tricellular pollen stage and maturity stage. DDRT-PCR was carried out to identify differentially expressed genes. [Result] A total of 44 differentially expressed cDNA fragments were identified with Dot blot. And seven candidate genes related to fertility conversion of K121S were screened out by BLASTN, including callose synthase gene, aldehyde dehydrogenase gene and RNA polymerase I transcription factor RRN3 gene which were differentially expressed at the transcriptional level, H＇-ATPase gene, fructose diphosphate aldolase -class I gene, teucine-rich repeat receptor-Jike serine/threonine- protein kinase gene and alkaline/neutral invertase gene, which were differentially expressed at the post-transcriptional level. [Conclusion] The results of this study will help to explain the molecular mechanism of thermo-sensitive genic male sterility of B. juncea.

Accumulation of Sugars and Liquid in Apoplast of Fruit Flesh Result in Pineapple Translucency

Translucency is a recurring problem for pineapple industry. Translucent fruit contained more sucrose, glucose and fructose in apoplast than those in apoplast of normal fruit. There were more liquid in intercellular space of translucent fruit than that of normal flesh. The contents of alcohol and ethylene in translucent fruit were higher than those in normal fruit. Translucent fruit contained less calcium than normal fruit. Electrolyte leakage of translucent flesh was more than that of normal flesh. There were 205 proteins of which the expressions in translucent flesh were higher than those in normal flesh. Calcium-ions-binding protein EF-hand domain-containing protein, ethylene-synthesizing enzyme 1-aminpcyclopropane-1-carboxylate oxidase, ROS-producing protein universal stress protein A-like protein were the top three proteins of which the expressions in translucent flesh were higher than those in normal fruit. When much sugar was transferred into fruit pulp and accumulated in intercellular space, water will be absorbed from cells around and translucence formed. The accumulation of sugar and liquid in apoplast were due to that cell wall and membrane were degraded, which was from being attacked by ROS. There might be more and larger pores in cell wall and membranes of translucent flesh. These data played foundations for researching methods for controlling pineapple translucency.

Effects of Storage Temperature on Postharvest Physiology of Amorphophallus cormifer Microbulb

[Objectives]The paper was to explore the optimum storage temperature of Amorphophallus cormifer microbulbs.[Methods]With A.cormifer as the raw material,the effects of different storage temperatures(4,12 and 20℃)on postharvest physiology of A.cormifer during the storage period of 80 d were investigated.[Results]There was no significant difference in starch content among the treatments,and the content of reducing sugar at 4℃was significantly higher than those of other treatments during the storage period.There was no significant difference in total water content among treatments,and the specific gravity of free water at 4℃was significantly lower than those at 12 and 20℃,respectively.At 60 d post storage,the POD activity at 4℃was significantly higher than those at 12 and 20℃,respectively.At the 80th day of storage,the PPO activity at 4℃was significantly lower than those at 12 and 20℃,respectively.[Conclusions]The low temperature of 4℃is more conducive to the storage of A.cormifer microbulbs,and the results also provide the theoretical basis for long-term storage of A.cormifer bulbs.

Identification and functional analysis of transcription factors related to coconut(Cocos nucifera L.)endosperm development based on ATAC-seq

Coconut(Cocos nucifera L.)is a member of the palm tree family(Arecaceae)and the only living species of the genus Cocos.In this paper,the regulatory relationship pathways between multiple transcription factors and functional genes were identified by combining ATAC-seq and RNAseq in coconut endosperm at four different developmental stages(fruit after pollination:7 months,8 months,9 months and 10 months,respectively).The results indicated that the peaks detected in the promoter-TSS area accounted for the largest proportion(11.99%)in the third stage.These results suggest that the chromatin open region of cells in this period is more functional and that there are more functional genes with active transcription.In addition,a large number of potential regulatory relationships between transcription factors and functional genes were detected via bioinformatics analysis at the genomic level.Among them,CnGATA20 was predicted to be an important transcription factor with a binding site on the promoter region of the CnOLE18 gene.The regulatory pathway by which CnGATA20 positively regulates the expression of CnOLE18 was further confirmed by yeast one-hybrid,protoplast transient expression and dual-luciferase reporter system experiments.The results provide a new research strategy for exploring the regulation at both the transcriptional and posttranscriptional levels during coconut endosperm growth and development.

De novo assembly of plant complete genomes

Plant genomes encode the mysteries of how plants cope with complex environments over long evolutionary histories.Over the past 20 years,rapidly developing technologies have allowed the decoding of hundreds of plant draft or reference genomes.The diversity,polyploidy and heterozygosity of plants make it technically challenging and time-consuming to generate high-quality plant genome assemblies.Recently invented ultra-long read sequencing technologies have achieved a milestone where several plant genomes have been gapless and assembled into telomere to telomere.Telomere-to-telomere(T2T)genome refers to a high-quality complete genome with high genomic accuracy,high continuity,and high integrity.With the release of the completed human genome and Arabidopsis thaliana genome,the era of complete T2T species genome has arrived.In this review,we summarize the history leading up to the gap free plant genomes based on emerging ultra-long read sequencing technologies.We discuss to close gaps relying on targeted genome sequencing and assembling technologies.However,there are still quite a lot of challenges in super large,polyploidy,and unstable genomes.Nevertheless,these complete genomes have already provided unprecedented information,which will certainly deepen our understanding of plant genomes and the exploration of more functional sequences.By taking advantage of the complete genomes,a series of important genes could be annotated,which will help achieve the goal of genome design in crop species.