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Improving error-correcting capability in DNA digital storage via soft-decision decoding

National Science Review 2024年第2期11卷 135-144页

作者：丁璐璐伍世刚候志浩李阿伦许亚苹冯虎潘玮华阮珏 Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences guangdong Provincial key laboratory of plant Molecular Breeding State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural University

Error-correcting codes(ECCs) employed in the state-of-the-art DNA digital storage(DDS) systems suffer from a trade-off between error-correcting capability and the proportion of redundancy. To address this issue, in this study, we introduce soft-decision decoding approach into DDS by proposing a DNA-specific error prediction model and a series of novel strategies. We demonstrate the effectiveness of our approach through a proof-of-concept DDS system based on Reed-Solomon(RS) code, named as Derrick. Derrick shows significant improvement in error-correcting capability without involving additional redundancy in both in vitro and in silico experiments, using various sequencing technologies such as Illumina, Pac Bio and Oxford Nanopore Technology(ONT). Notably, in vitro experiments using ONT sequencing at a depth of 7× reveal that Derrick, compared with the traditional hard-decision decoding strategy, doubles the error-correcting capability of RS code, decreases the proportion of matrices with decoding-failure by 229-fold, and amplifies the potential maximum storage volume by impressive 32 388-fold. Also, Derrick surpasses ‘state-of-the-art' DDS systems by comprehensively considering the information density and the minimum sequencing depth required for complete information recovery. Crucially, the soft-decision decoding strategy and key steps of Derrick are generalizable to other ECCs' decoding algorithms.

关键词： DNA digital storage (DDS) error-correcting code (ECC) soft-decision decoding error-correcting capability storage volume

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Wood of trees:Cellular structure,molecular formation,and genetic engineering

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Journal of Integrative plant Biology 2024年第3期66卷 443-467页

作者： Yingying Zhu Laigeng Li state key laboratory of Herbage Improvement and Grassland Agro-ecosystems and College of Ecology Lanzhou UniversityLanzhou 730000China National key laboratory of plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China

Wood is an invaluable asset to human society due to its renewable nature,making it suitable for both sustainable energy production and material manufacturing.Additionally,wood derived from forest trees plays a crucial role in sequestering a significant portion of the carbon dioxide fixed during photosynthesis by terrestrial plants.Nevertheless,with the expansion of the global population and ongoing industrialization,forest coverage has been substantially decreased,resulting in significant challenges for wood production and supply.Wood production practices have changed away from natural forests toward plantation forests.Thus,understanding the underlying genetic mechanisms of wood formation is the foundation for developing high-quality,fast-growing plantation trees.Breeding ideal forest trees for wood production using genetic technologies has attracted the interest of many.Tremendous studies have been carried out in recent years on the molecular,genetic,and cell-biological mechanisms of wood formation,and considerable progress and findings have been achieved.These studies and findings indicate enormous possibilities and prospects for tree improvement.This review will outline and assess the cellular and molecular mechanisms of wood formation,as well as studies on genetically improving forest trees,and address future development prospects.

关键词： cambium cell wall Populus wood formation xylem

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A booming field of large animal model research

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Zoological Research 2024年第2期45卷 311-313页

作者： Xiao-Jiang Li Liangxue Lai guangdong key laboratory of Non-human Primate Research Key Laboratory of CNS Regeneration(Ministry of Education)GHM Institute of CNS RegenerationJinan UniversityGuangzhouGuangdong 510632China state key laboratory of Bioactive Molecules and Druggability Assessment Jinan UniversityGuangzhouGuangdong 510632China cas key laboratory of Regenerative Biology Guangdong Provincial Key Laboratory of Stem Cell and Regenerative MedicineGuangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong 510530China

Animal models are integral to the study of fundamental biological processes and the etiology of human diseases.Small animal models,especially those involving mice,have yielded abundant and significant insights,greatly... 详细信息

关键词： mechanisms insight field

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plant virology in the 21st century in China:Recent advances and future directions

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Journal of Integrative plant Biology 2024年第3期66卷 579-622页

作者： Jianguo Wu Yongliang Zhang Fangfang Li Xiaoming Zhang Jian Ye Taiyun Wei Zhenghe Li Xiaorong Tao Feng Cui Xianbing Wang Lili Zhang Fei Yan Shifang Li Yule Liu Dawei Li Xueping Zhou Yi Li state key laboratory for Ecological Pest Control of Fujian and Taiwan Crops Vector-borne Virus Research CenterCollege of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhou 350002China state key laboratory of plant Environmental Resilience and Ministry of Agriculture key laboratory of Soil Microbiology College of Biological SciencesChina Agricultural UniversityBeijing 100193China state key laboratory for Biology of plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100193China state key laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China cas Center for Excellence in Biotic Interactions University of Chinese Academy of SciencesBeijing 100049China state key laboratory of plant Genomics Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China state key laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhou 310058China Department of plant Pathology The Key Laboratory of Plant ImmunityNanjing Agricultural UniversityNanjing 210095China state key laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products Institute of Plant VirologyNingbo UniversityNingbo 315211China MOE key laboratory of Bioinformatics Center for Plant BiologySchool of Life SciencesTsinghua UniversityBeijing 100084China state key laboratory of Protein and plant Gene Research School of Life SciencesPeking UniversityBeijing 100871China

plant viruses are a group of intracellular pathogens that persistently threaten global food security.Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years,including basic research and technologies for preventing and controlling plant viral diseases.Here,we review these milestones and advances,including the identification of new crop-infecting viruses,dissection of pathogenic mechanisms of multiple viruses,examination of multilayered interactions among viruses,their host plants,and virus-transmitting arthropod vectors,and in-depth interrogation of plantencoded resistance and susceptibility determinants.Notably,various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants.We also recommend future plant virology studies in China.

关键词： China emerging plant viruses plant virology plant resistance/susceptibility to viral infection plant-virus transmission vector interactions plant virus-based vectors viral pathogenesis

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Role of methoxy and C_(α)-based substituents in electrochemical oxidation mechanisms and bond cleavage selectivity of β-O-4 lignin model compounds

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Green Energy & Environment 2024年第1期9卷 114-125页

作者： Yang Zhou Qiang Zeng Hongyan He Kejia Wu Fuqiao Liu Xuehui Li School of Chemistry and Chemical Engineering The Guangdong Provincial Key Laboratory of Green Chemical Product TechnologyState Key Laboratory of Pulp and Paper EngineeringSouth China University of TechnologyGuangzhouGuangdong510640China cas key laboratory of Green Process and Engineering Institute of Process EngineeringChinese Academy of SciencesBeijing100190China

In order to better understand the specific substituent effects on the electrochemical oxidation process of β-O-4 bond, a series of methoxyphenyl type β-O-4 dimer model compounds with different localized methoxyl groups, including 2-(2-methoxyphenoxy)-1-phenylethanone, 2-(2-methoxyphenoxy)-1-phenylethanol, 2-(2-methoxyphenoxy)-1-(4-methoxyphenyl)ethanone, 2-(2-methoxyphenoxy)-1-(4-methoxyphenyl)ethanol, 2-(2,6-dimethoxyphenoxy)-1-(4-methoxyphenyl)ethanone, 2-(2,6-dimethoxyphenoxy)-1-(4-methoxyphenyl)ethanol have been selected and their electrochemical properties have been studied experimentally by cyclic voltammetry, and FT-IR spectroelectrochemistry. Combining with electrolysis products distribution analysis and density functional theory calculations, oxidation mechanisms of all six model dimers have been explored. In particular, a total effect from substituents of both para-methoxy(on the aryl ring closing to Cα) and Cα-OH on the oxidation mechanisms has been clearly observed, showing a significant selectivity on the Cα-Cβbond cleavage induced by electrochemical oxidations.

关键词： Lignin model compounds β-O-4 dimers Electrochemical oxidation Oxidation mechanisms Substituent effect

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Masculinizer gene controls sexual differentiation in Hyphantria cunea

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Insect Science 2024年第2期31卷 405-416页

作者： Xiaowei Li Huihui Liu Honglun Bi Yaohui Wang Jun Xu Sufang Zhang Zhen Zhang Ze Zhang Yongping Huang laboratory of Evolutionary and Functional Genomics School of Life SciencesChongqing UniversityChongqingChina cas key laboratory of Insect Developmental and Evolutionary Biology CAS Centerfor Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyShanghaiChina key laboratory of Forest Protection Research Institute of Forest EcologyEnvironment and ProtectionChinese Academy of ForestryState Forestry AdministrationBeijingChina

The Masculinizer gene,Masc,encodes a lepidopteran-specific novel CCCHtype zinc finger protein,which controls sex determination and dosage compensation in Bombyx mori.Considering the potential application of it in pest control,it is necessary to investigate the function of Masc gene in Hyphantria cunea,a globally invasive forest pest.In the present study,we identified and functionally characterized the Masc gene,HcMasc,in H.cunea.Sequence analysis revealed that HcMASC contained the conserved CCCH-type zinc finger domain,nuclear localization signal,and male determining domain,in which the last was confirmed to be required for its masculinization in BmN cell line.However,expression data showed that unlike male-biased expression in B.mori,Hc-Masc gene expresses in main all developmental stages or tissues in both sexes.Clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein 9-based disruption of the common exons 1 and 3 of the HcMasc gene resulted in imbalanced sex ratio and abnormal external genitalia of both sexes.Our results suggest that the HcMasc gene is required for both male and female sexual differentiation and dosage compensation in H.cunea and provide a foundation for developing better strategies to control this pest.

关键词： CRISPR/cas9 dosage compensation Hyphantria cunea Masc sexual differentiation

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Global characterization of OsPIP aquaporins reveals that the H_(2)O_(2)transporter OsPIP2;6 increases resistance to rice blast

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The Crop Journal 2024年第1期12卷 102-109页

作者： Gousi Li Jingluan Han Chen Yi Hao Luo Yuzhu Wang Fengpin Wang Xiaoyu Wang Letian Chen Yaling Zhang state key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources College of Life SciencesSouth China Agricultural UniversityGuangzhou 510642GuangdongChina guangdong laboratory for Lingnan Modern Agriculture Guangzhou 510642GuangdongChina National key laboratory of plant Molecular Genetics Shanghai Center for Plant Stress BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China

Plasma membrane intrinsic proteins(PIPs)are conserved plant aquaporins that transport small molecules across the plasma membrane to trigger instant stress responses and maintain cellular homeostasis under biotic and abiotic stress.To elucidate their roles in plant immunity to pathogen attack,we characterized the expression patterns,subcellular localizations,and H_(2)O_(2)-transport ability of 11 OsPIPs in rice(Oryza sativa),and identified OsPIP2;6 as necessary for rice disease resistance.OsPIP2;6 resides on the plasma membrane and facilitates cytoplasmic import of the immune signaling molecule H_(2)O_(2).Knockout of OsPIP2;6 increases rice susceptibility to Magnaporthe oryzae,indicating a positive function in plant immunity.OsPIP2;6 interacts with OsPIP2;2,which has been reported to increase rice resistance to pathogens via H_(2)O_(2)transport.Our findings suggest that OsPIP2;6 cooperates with OsPIP2;2 as a defense signal transporter complex during plant–pathogen interaction.

关键词： Aquaporin plant immunity Rice blast H_(2)O_(2)transport

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Arbuscular mycorrhizal fungi inoculation and exogenous indole-3-acetic acid application induce antioxidant defense response to alleviate cadmium toxicity in Broussonetia papyrifera

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Pedosphere 2024年第2期34卷 447-459页

作者： Xue LI Jingwei LIANG Hongjian WEI Yuxuan KUANG Hui CHEN Ming TANG Wentao HU state key laboratory of Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern AgricultureGuangdong Key Laboratory for Innovative Development and Utilization of Forest Plant GermplasmCollege of Forestry and Landscape ArchitectureSouth China Agricultural UniversityGuangzhou 510642China

Cadmium(Cd)contamination in soil poses a huge threat to plants even at low concentrations;Broussonetia papyrifera has great potential in remediation of soil heavy metal contamination.However,whether exogenous indole-3-acetic acid(IAA)application and arbuscular mycorrhizal fungi(AMF)have synergistic effects on Cd tolerance of B.papyrifera remains unclear.To investigate the effects of AMF inoculation and IAA application on the tolerance of B.papyrifera to Cd stress,two experiments were conducted:the first to investigate the effect of AMF(Rhizophagus irregularis)inoculation on the tolerance of B.papyrifera to Cd stress and the second to investigate the combined effects of AMF inoculation and IAA application on the tolerance of B.papyrifera to Cd stress.Parameters including endogenous hormone concentration,antioxidant defense response,malondialdehyde(MDA)content,and gene expression related to antioxidant enzyme system and hormone were measured.The results indicated that AMF alleviated Cd toxicity of B.papyrifera by reducing MDA content and improving antioxidant enzyme activities and Cd absorption capacity.Furthermore,the combination of AMF inoculation and IAA application had a synergetic effect on the tolerance of B.papyrifera to Cd stress through upregulating BpAUX1 and BpAUX2,which might contribute to root growth and root xylem synthesis,and by upregulating BpSOD2 and BpPOD34 to enhance the antioxidant enzyme system.This work provides a new insight into the application of IAA in the remediation of soil Cd pollution by mycorrhizal plants.

关键词： enzyme activity geneexpression heavy metal phytoremediation remediation Rhizophagus irregularis soil cadmium pollution stress tolerance

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Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

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Journal of Integrative plant Biology 2024年第4期66卷 824-843页

作者： Weihong Wu Xiao Feng Nan Wang Shao Shao Min Liu Fa Si Linhao Chen Chuanfeng Jin Shaohua Xu Zixiao Guo Cairong Zhong Suhua Shi Ziwen He state key laboratory of Biocontrol and guangdong Provincial key laboratory of plant resources School of Life SciencesSun Yat-sen UniversityGuangzhou 510275China Greater Bay Area Institute of Precision Medicine School of Life SciencesFudan UniversityGuangzhou 511462China Hainan Academy of Forestry(Hainan Academy of Mangrove) Haikou 571100China

Nypa fruticans(Wurmb),a mangrove palm species with origins dating back to the Late Cretaceous period,is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms.Here,we present a chromosome-level genome sequence and assembly for N.fruticans.We integrated the genomes of N.fruticans and other palm family members for a comparative genomic analysis,which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago,shaping the distinctive characteristics observed in this clade.We also inferred a low mutation rate for the N.fruticans genome,which underwent strong purifying selection and evolved slowly,thus contributing to its stability over a long evolutionary period.Moreover,ancient duplicates were preferentially retained,with critical genes having experienced positive selection,enhancing waterlogging tolerance in N.fruticans.Furthermore,we discovered that the pseudogenization of Early Methionine-labelled 1(EM1)and EM6 in N.fruticans underly its crypto-vivipary characteristics,reflecting its intertidal adaptation.Our study provides valuable genomic insights into the evolutionary history,genome stability,and adaptive evolution of the mangrove palm.Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

关键词： crypto-vivipary genome stability long-term adaptation mangrove Nypa fruticans palm

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Dt1 inhibits SWEET-mediated sucrose transport to regulate photoperiod-dependent seed weight in soybean

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Molecular plant 2024年第3期17卷 496-508页

作者： Xiaoming Li Zhonghui Chen Haiyang Li Lin Yue Cuirong Tan Hongjie Liu Yilong Hu Yuhua Yang Xiani Yao Lingping Kong Xiang Huangi Bin Yu Chunyu Zhang Yuefeng Guan Baohui Liu Fanjiang Kong Xingliang Hou guangdong Provincial key laboratory of Applied Botany&state key laboratory of plant Diversity and Specialty Crops South China Botanical GardenChinese Academyof SciencesGuangzhou510650China guangdong Provincial key laboratory of plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China University of Chinese Academy of Sciences Beijing 100049China College of Agronomy and Biotechnology China Agricultural UniversityBeijing 100193China

Soybean is a photoperiod-sensitive short-day crop whose reproductive period and yield are markedly affected by day-length changes.Seed weight is one of the key traits determining the soybean yield;how-ever,the prominent genes that control the final seed weight of soybean and the mechanisms underlying the photoperiod's effect on this trait remain poorly understood.In this study,we identify SwW19 as a major locus controlling soybean seed weight by QTL mapping and determine Dt1,an orthologous gene of Arabidopsis TFL1 that is known to govern the soybean growth habit,as the causal gene of the SW19 locus.We showed that Dt1 is highly expressed in developing seeds and regulates photoperiod-dependent seed weight in soybean.Further analyses revealed that the Dt1 protein physically interacts with the sucrose transporter GmSWEET10a to negatively regulate the import of sucrose from seed coat to the embryo,thus modulating seed weight under long days.However,Dt1 does not function in seed development under short days due to its very low expression.Importantly,we discovered a novel natural allelic variant of Dt1(H4 haplotype)that decouples its pleiotropic effects on seed size and growth habit;i.e.,this variant remains functional in seed development but fails to regulate the stem growth habit of soybean.Collectively,our findings provide new insights into how soybean seed development responds to photoperiod at different latitudes,offering an ideal genetic component for improving soybean's yield by manipulating its seed weightandgrowth habit.

关键词： soybean seed weight photoperiod dt1 sucrose transport

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