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

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Journal of Integrative Agriculture 2024年第4期23卷 1087-1104页

作者： Junnan Hang Bowen Wu Diyang Qiu Guo Yang Zhongming Fang Mingyong Zhang Institute of Rice Industry Technology Research/key laboratory of Functional Agriculture Guizhou Provincial Department of Education/Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous RegionMinistry of Education/Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province/College of Agricultural SciencesGuizhou UniversityGuiyang 550025China key laboratory of south china agricultural plant molecular analysis and Genetic improvement/Guangdong Provincial key laboratory of Applied Botany/south china Botanical Garden Chinese Academy of SciencesGuangzhou 510650China Institute of Fruit Tree Research Guangdong Academy of Agricultural SciencesGuangzhou 510640China

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 *** 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 *** 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 *** 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 ***3.1 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 *** 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 *** results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate *** altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations,respectively.

关键词： rice tillering grain yield phytohormone nitrate transporter nitrogen utilization efficiency

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Structure,bioavailability and physicochemical properties of icariin-soymilk nanoparticle

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Food Science and Human Wellness 2024年第2期13卷 972-981页

作者： Jinping Wang Lingrong Wen Yueming Jiang Hong Zhu Weizheng Sun Guangyi Dai Bao Yang Guangdong Provincial key laboratory of Applied Botany Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic ImprovementSouth China Botanical GardenChinese Academy of SciencesGuangzhou 510650China south china National Botanical Garden Guangzhou 510650China College of Food Science and Engineering Jilin Agricultural UniversityChangchun 130118China University of Chinese Academy of Sciences Beijing 100049China School of Food Sciences and Engineering South China University of TechnologyGuangzhou 510640China

Soymilk is a natural ***,the performance of flavonoid-soymilk nano-complex remains *** this work,icariin-soymilk nano-complexes(ISNCs)were successfully fabricated and *** effects of high-pressure homogenization(HPH)treatment on structure and physicochemical properties of soymilk and nano-complexes were *** treatment could significantly improve the surface hydrophobicity and interfacial activity of *** soymilk with HPH treatment could significantly improve the water solubility(20 folds),thermal stability and bioavailability of *** highest encapsulation efficiency(93.28%),loading capacity(39.09μg/mg),ζ-potentia(absolute value,31.20 mV)and bioavailability(72.14%)were observed in HSI-200(200 bar of homogenization pressure).While HSI-500(500 bar of homogenization pressure)showed the smallest particle size(183.73 nm).ISNCs showed a rougher surface and an irregular lamellar structure with large amount of fine particles by using Cryo-SEM,suggesting that icariin was encapsulated in *** data supplied a novel strategy to improve the performance of icariin in functional foods.

关键词： Encapsulation efficiency Flavonoid High pressure homogenization Loading capacity Nano-complex

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Rice gene OsUGT75A regulates seedling emergence under deep-sowing conditions

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The Crop Journal 2024年第1期12卷 133-141页

作者： Jia Zhao Siyu Liu Xiaoqian Zhao Zhibo Huang Shan Sun Zixuan Zeng Yongqi He Zhoufei Wang The laboratory of Seed Science and Technology Guangdong Key Laboratory of Plant Molecular BreedingNational Engineering Research Center of Plant Space BreedingSouth China Agricultural UniversityGuangzhou 510642GuangdongChina

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field *** we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot *** of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing *** of free abscisic acid(ABA)and jasmonates(JA)were higher in shoots of OsUGT75A mutants than in those of wild-type plants,and OsUGT75A mutants were more sensitive to ABA and JA *** shoot length was attributed to higher ABA INSENSITIVE 3(OsABI3)expression and lower JASMONATE-ZIM domain protein(OsJAZ)expression in *** extension by OsUGT75A is achieved mainly by promotion of cell *** elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice ***75A acts to increase seedling emergence under deep-sowing conditions.

关键词： Abscisic acid Deep-sowing Jasmonic acid Rice Shoot length

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Rice stripe mosaic virus hijacks rice heading‐related gene to promote the overwintering of its insect vector

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Journal of Integrative plant Biology 2024年第9期66卷 2000-2016页

作者： Siping Chen Xinyi Zhong Zhiyi Wang Biao Chen Xiuqin Huang Sipei Xu Xin Yang Guohui Zhou Tong Zhang Guangdong Province key laboratory of Microbial Signals and Disease Control College of Plant ProtectionSouth China Agricultural UniversityGuangzhou 510642China State key laboratory of Green Pesticide South China Agricultural UniversityGuangzhou 510642China

Rice stripe mosaic virus(RSMV)is an emerging pathogen which significantly reduces rice yields in the southern region of *** is transmitted by the leafhopper Recilia dorsalis,which overwinters in rice *** field investigations revealed that RSMV infection causes delayed rice heading,resulting in a large number of green diseased plants remaining in winter rice *** creates a favorable environment for leafhoppers and viruses to overwinter,potentially contributing to the rapid spread and epidemic of the ***,we explored the mechanism by which RSMV manipulates the developmental processes of the rice plant.A rice heading‐related E3 ubiquitin ligase,Heading date Associated Factor 1(HAF1),was found to be hijacked by the RSMV‐encoded *** impairment of HAF1 function affects the ubiquitination and degradation of downstream proteins,HEADING DATE 1 and EARLY FLOWERING3,leading to a delay in rice *** results provide new insights into the development regulation‐based molecular interactions between virus and plant,and highlights the importance of understanding virus‐vector‐plant tripartite interactions for effective disease management strategies.

关键词： HAF1 heading leafhoppers overwintering RSMV

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Strigolactone regulates nitrogen-phosphorus balance in rice

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Science china(Life Sciences) 2024年第2期67卷 428-430页

作者： Huwei Sun Hanyun Wang Chengcai Chu Guangdong Provincial key laboratory of plant molecular Breeding College of AgricultureSouth China Agricultural UniversityGuangzhou 510642China key laboratory for Enhancing Resource Use Efficiency of Crops in south china Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510642China Guangdong laboratory for Lingnan Modern Agriculture Guangzhou 510642

Phosphorus(P) is one of the essential elements for growth and development of *** agriculture depends heavily on the application of large amounts of fertilizers,including P *** application of P fertilizers causes sever... 详细信息

关键词： pollution phosphorus fertilizers

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Juvenile hormone induces reproduction via miR-1175-3p in the red imported fire ant, Solenopsis invicta

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Insect Science 2024年第2期31卷 371-386页

作者： Jie Chen Ziying Guan Yunjie Ma Qingxing Shi Ting Chen Muhammad Irfan WarisLihua Lyu Lihua Lyu Yongyue Lu Guojun Qi Institute of plant Protection Guangdong Academy of Agricultural SciencesKey Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of High Technology for Plant ProtectionGuangzhouChina Department of Entomology College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina

Juvenile hormone(JH)acts in the regulation of caste differentiation between queens and workers(i.e.,with or without reproductive capacity)during vitellin synthesis and oogenesis in social ***,the regulatory mechanisms have not yet been ***,we identified a highly expressed microRNA(miRNA),miR-1175-3p,in the red imported fire ant,Solenopsis *** found that miR-1175-3p is prominently present in the fat bodies and ovaries of ***,miR-1175-3p interacts with its target gene,broad-complex core(Br-C),in the fat *** utilizing miR-1175-3p agomir,we successfully suppressed the expression of the Br-C protein in queens,resulting in reduced vitellogenin expression,fewer eggs,and poorly developed ***,decreasing miR-1175-3p levels led to the increased expression of Br-C and vitellogenin in workers,triggering the“re-development”of the ***,when queens were fed with JH,the expression of miR-1175-3p decreased,whereas the expression of vitellogenin-2 and vitellogenin-3 ***,the suppression of fertility in queens caused by treatment with agomir miR-1175-3p was completely rescued by the increased vitellogenin expression induced by being fed with *** results suggest the critical role of miR-1175-3p in JH-regulated reproduction,shedding light on the molecular mechanism underlying miRNA-mediated fecundity in social insects and providing a novel strategy for managing ***.

关键词： juvenile hormone miR-1175-3p red imported fire ant reproduction social insects vitellogenin

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Rice seed germination priming by salicylic acid and the emerging role of phytohormones in anaerobic germination

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Journal of Integrative plant Biology 2024年第8期66卷 1537-1539页

作者： Yongqi He Jia Zhao Zhoufei Wang The laboratory of Seed Science and Technology Guangdong Key Laboratory of Plant Molecular BreedingSouth China Agricultural UniversityGuangzhou 510642China key laboratory for Enhancing Resource Use Efficiency of Crops in south china Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhou 510642China National Engineering Research Center of plant Space Breeding South China Agricultural UniversityGuangzhou 510642China

Direct seeding has been increasingly adopted under both rainfed and irrigated conditions due to its low cost and *** only to suppress weed germination and reduce the cost of manual weeding and/or dependence on herbicides,but also to control pests and reduce pesticide usage,farmers usually flood the direct-seeded field,resulting in inadequate seed germination and seedling establishment.

关键词： seedling weed germination

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The temporal-spatial expression and functional analysis of three gustatory receptor genes in Solenopsis invicta using sweet and bitter compounds

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Insect Science 2024年第2期31卷 448-468页

作者： Muhammad Irfan Waris Yanyuan Lei Guojun Qi Ziying Guan Abdul Rashied Jie Chen Lihua Lyu Institute of plant Protection Guangdong Academy of Agricultural SciencesGuangdong Provincial Key Laboratory of High Technology for Plant ProtectionGuangzhouChina Department of Entomology College of Plant ProtectionSouth China Agricultural UniversityGuangzhouChina

The insect gustatory system participates in identifying potential food sources and avoiding toxic *** this process,gustatory receptors(GRs)recognize feeding stimulant and deterrent ***,the GRs involved in recognizing stimulant and deterrent compounds in the red imported fire ant,Solenopsis invicta,remain ***,we conducted a study on the genes SinvGR1,SinvGR32b,and SinvGR28a to investigate the roles of GRs in detecting feeding stimulant and deterrent *** this current study,we found that sucrose and fructose are feeding stimulants and the bitter compound quinine is a feeding *** fire ant workers showed significant behavior changes to avoid the bitter taste in feeding stimulant *** transcription quantitative real-time polymerase chain reaction results from developmental stages showed that the SinvGR1,SinvGR32b,and SinvGR28a genes were highly expressed in fire ant ***-specific expression profiles indicated that SinvGR1,SinvGR32b,and SinvGR28a were specifically expressed in the antennae and foreleg tarsi of workers,whereas SinvGR32b gene transcripts were also highly accumulated in the male ***,the silencing of SinvGRI or SinvGR32b alone and the co-silencing of both genes disrupted worker stimulation and feeding on sucrose and *** results also showed that SinvGR28a is required for avoiding quinine,as workers with knockdown of the SinvGR28a gene failed to avoid and fed on *** study first identified stimulant and deterrent compounds of fire ant workers and then the GRs involved in the taste recognition of these *** study could provide potential target gustatory genes for the control of the fire ant.

关键词： behavioral responses feeding assays gustatory receptors RNA interference Solenopsis invicta temporal-spatial expression

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Phytochrome B interacts with LIGULELESS1 to control plant architecture and density tolerance in maize

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molecular plant 2024年第8期17卷 1255-1271页

作者： Qingbiao Shi Ying Xia Qibin Wang Kaiwen Lv Hengjia Yang Lianzhe Cui Yue Sun Xiaofei Wang Qing Tao Xiehai Song Di Xu Wenchang Xu Xingyun Wang Xianglan Wang Fanying Kong Haisen Zhang Bosheng Li Pinghua Li Haiyang Wang Gang Li State key laboratory of Wheat improvement College of Life SciencesShandong Agricultural UniversityTai'an 271018China State key laboratory of Wheat improvement College of AgronomyShandong Agricultural UniversityTai'an 271018China Peking University Institute of Advanced agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangShandong 261000China Guandong laboratory for Lingnan Modern Agriculture State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural UniversityGuangzhou510642China

Over the past few decades,significant improvements in maize yield have been largely attributed to increased plant density of upright hybrid varieties rather than increased yield per ***,dense planting triggers shade avoidance responses(SARs)that optimize light absorption but impair plant vigor and performance,limiting yield improvement through increasing plant *** this study,we demonstrated that high-density-induced leaf angle narrowing and stem/stalk elongation are largely dependent on phytochrome B(phyB1/B2),the primaryphotoreceptor responsible for perceiving red(R)and far-red(FR)light in *** found that maize phyB physically interacts with the LIGULELESS1(LG1),a classical key regulator of leaf angle,to coordinately regulate plant architecture and density *** abundance of LG1 is significantly increased by phyB under high R:FR light(low density)but rapidly decreases under low R:FR light(high density),correlating with variations in leaf angle and plant height under various *** addition,we identified the homeobox transcription factor HB53 as a target co-repressed by both phyB and LG1 but rapidly induced by canopy *** and cellular analyses showed that HB53 regulates plant architecture by controlling the elongation and division of ligular adaxial and abaxial *** together,these findings uncover the phyB-LG1-HB53 regulatory module as a key molecular mechanism governing plant architecture and density tolerance,providing potential genetic targets for breeding maize hybrid varieties suitable for high-density planting.

关键词： maize phytochrome B LIGULELESS1 HB53 leaf angle density tolerance

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