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A centromere map based on super pan-genome highlights the structure and function of rice centromeres

Journal of Integrative Plant Biology 2024年第2期66卷 196-207页

作者： Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen Longbo Yang xiaofan dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang Hongge Qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang Qiang Xu Yan Cui Qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou Qian Qian Longbiao Guo Lianguang Shang State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China 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 SciencesShenzhen 518120China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya City 572024China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary factors.Rice centromeres are crucial for chromosome segregation,and contain some unreported genes.Due to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is needed.We constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice.We showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary patterns.We also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution.Furthermore,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging.We investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 methods.By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement.

关键词： centromere super pan-genome CentoO satellite repeat rice

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Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo xiaofan dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang 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 Institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences State Key Laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National Laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

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A complete assembly of the rice Nipponbare reference genome

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Molecular Plant 2023年第8期16卷 1232-1236页

作者： Lianguang Shang Wenchuang He Tianyi Wang Yingxue Yang Qiang Xu Xianjia Zhao Longbo Yang Hong Zhang Xiaoxia Li Yang Lv Wu Chen Shuo Cao Xianmeng Wang Bin Zhang Xiangpei Liu Xiaoman Yu Huiying He Hua Wei Yue Leng Chuanlin Shi Mingliang Guo Zhipeng Zhang Bintao Zhang Qiaoling Yuan Hongge Qian Xinglan Cao Yan Cui Qianqian Zhang xiaofan dai Congcong Liu Longbiao Guo Yongfeng Zhou Xiaoming Zheng Jue Ruan Zhukuan Cheng Weihua Pan Qian Qian 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 SciencesShenzhen 518120China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Co-Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhou 225009China

Dear Editor,In 2005,the current commonly used rice reference genome(Oryza sativa ssp.japonica cv.Nipponbare)was initially released by the International Rice Genome Sequencing Project(International Rice Genome Sequencing Project,2005).Thereafter,the reference genome was further updated in 2013 with improved genome assembly(IRGSP-1.0)and gene annotations(MSU7,RAP-DB)(Kawahara et al.,2013;Sakai et al.,2013).In the past 10 years,this reference has been serving as one of the most important genetic resources for subsequent rice functional genomics efforts.As several rice genomes had been assembled into gapless chromosomes with only 2–5 telomeres absent(Li et al.,2021;Song et al.,2021;Zhang et al.,2022),the IRGSP1.0 and its annotations still performed as the most widely used reference.However,limitations of sequencing technology and intricate genomic organization led to an under-representation of complex regions in this reference,leaving a total of 72 major gaps(including 19 telomeres),167 minor gaps,and 779 unknown bases(Kawahara et al.,2013),with an estimated length of3%of the genome unsolved.

关键词： Sakai bases assembly

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Biohythane production from two-stage anaerobic digestion of food waste:A review

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Journal of Environmental Sciences 2024年第5期139卷 334-349页

作者： Xiaona An Ying Xu Xiaohu dai State Key Laboratory of Pollution Control and Resource Reuse School of Environmental Science and EngineeringTongji UniversityShanghai 200092China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China

The biotransformation of food waste(FW)to bioenergy has attracted considerable research attention as a means to address the energy crisis and waste disposal problems.To this end,a promising technique is two-stage anaerobic digestion(TSAD),in which the FW is transformed to biohythane,a gaseous mixture of biomethane and biohydrogen.This review summarises the main characteristics of FW and describes the basic principle of TSAD.Moreover,the factors influencing the TSAD performance are identified,and an overview of the research status;economic aspects;and strategies such as pre-treatment,co-digestion,and regulation of microbial consortia to increase the biohythane yield from TSAD is provided.Additionally,the challenges and future considerations associated with the treatment of FW by TSAD are highlighted.This paper can provide valuable reference for the improvement and widespread implementation of TSAD-based FW treatment.

关键词： Two-stage anaerobic digestion(TSAD) Food waste(FW) Methane production Hydrogen production

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Neighborhood predictors of short sleep duration and bedtime irregularity among children in the United States: results from the 2019-2020 National Surveyof Children's Health

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World Journal of Pediatrics 2024年第1期20卷 73-81页

作者： Ying dai Jianghong Liu School of Nursing University of Pennsylvania418 Curie Blvd.Room 426Claire M.Fagin HallPhiladelphiaPA19104-6096USA

Background Environmental factors may contribute to short sleep duration and irregular bedtime in children.Neighborhood factors and children's sleep duration and bedtime regularity remain a less investigated area.The aim of this study was to investigate the national and state-level proportions of children with short sleep duration and irregular bedtime and their neighborhood predictors.Methods A total of 67,598 children whose parents completed the National Survey of Children's Health in 2019-2020 were included in the analysis.Survey-weighted Poisson regression was used to explore the neighborhood predictors of children's short sleep duration and irregular bedtime.Results The prevalence of short sleep duration and irregular bedtime among children in the United States(US)was 34.6%[95%confidence interval(CI)=33.8%-35.4%]and 16.4%(95%CI=15.6%-17.2%)in 2019-2020,respectively.Safe neighborhoods,supportive neighborhoods,and neighborhoods with amenities were found to be protective factors against children's short sleep duration,with risk ratios ranging between 0.92 and 0.94,P<0.05.Neighborhoods with detracting elements were associated with an increased risk of short sleep duration[risk ratio(RR)=1.06,95%CI=1.00-1.12]and irregular bedtime(RR=1.15,95%CI=1.03-1.28).Child race/ethnicity moderated the relationship between neighborhood with amenities and short sleepduration.Conclusions Insufficient sleep duration and irregular bedtime were highly prevalent among US children.A favorable neighborhood environment can decrease children's risk of short sleep duration and irregular bedtime.Improving the neighborhood environment has implications for children's sleep health,especially for children from minority racial/ethnic groups.

关键词： Child National Survey of Children's Health Neighborhood.Sleep Social determinants of health

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Seismic performance evaluation of water supply pipes installed in a full-scale RC frame structure based on a shaking table test

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Earthquake Engineering and Engineering Vibration 2024年第1期23卷 163-178页

作者： Wu Houli Guo Endong Wang Jingyi dai Xin dai Chenxi Key Laboratory of Earthquake Engineering and Engineering Vibration Institute of Engineering MechanicsChina Earthquake AdministrationHarbin 150080China Key Laboratory of Earthquake Disaster Mitigation Ministry of Emergency ManagementHarbin 150080China

As an important part of nonstructural components,the seismic response of indoor water supply pipes deserves much attention.This paper presents shaking table test research on water supply pipes installed in a full-scale reinforced concrete(RC)frame structure.Different material pipes and different methods for penetrating the reinforced concrete floors are combined to evaluate the difference in seismic performance.Floor response spectra and pipe acceleration amplification factors based on test data are discussed and compared with code provisions.A seismic fragility study of displacement demand is conducted based on numerical simulation.The acceleration response and displacement response of different combinations are compared.The results show that the combination of different pipe materials and different passing-through methods can cause obvious differences in the seismic response of indoor riser pipes.

关键词： water supply pipe different materials shaking table test amplification factor seismic fragility

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Near-field wideband beam training for ELAA with uniform circular array

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Science China(Information Sciences) 2024年第6期67卷 370-383页

作者： Yuhao CHEN Linglong dai Department of Electronic Engineering Tsinghua UniversityBeijing National Research Center for Information Science and Technology (BNRist)

Extremely large-scale antenna array(ELAA) at millimeter wave(mmWave) and Terahertz(THz)band has been considered a key technology for combating high attenuation in high-frequency bands in future6G communications. Uniform circular arrays(UCAs) have attracted much attention because of their ability to provide flat beamforming gain at all angles. To realize efficient beamforming, beam training is widely used to acquire channel state information. However, with a large antenna number, the beam training overhead in ELAA systems becomes overwhelming. Moreover, with a large bandwidth, the beam defocus effect severely degrades beam training accuracy. To address these issues, this paper proposes a frequency-dependent focusing(FDF)-based beam training scheme to realize effective beam training in near-field wideband ELAA systems with UCA. Specifically, we first analyze the FDF property of UCA, where signals at different subcarriers can simultaneously focus on different distances. Then, by exploiting the FDF property to search different distances using different subcarriers simultaneously, we design a hierarchical codebook and propose an FDFbased beam training scheme. To reveal the effectiveness of the proposed scheme, we compare its necessary beam training overhead with that of existing schemes. Finally, the simulation results demonstrate that the proposed scheme can achieve accurate beam training in near-field wideband UCA systems with a low beam training overhead.

关键词： extremely large-scale antenna array (ELAA) uniform circular array (UCA) near-field wideband beam training

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Prenatal cadmium exposure impairs neural tube closure via inducing excessive apoptosis in neuroepithelium

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Journal of Environmental Sciences 2024年第4期138卷 572-584页

作者： Shiyong Zhu Xuenan Li Xueyan dai Jinlong Li College of Veterinary Medicine Northeast Agricultural UniversityHarbin 150030China Key Laboratory of the Provincial Education Department of Heilongjiang for Common Animal Disease Prevention and Treatment Northeast Agricultural UniversityHarbin 150030China Heilongjiang Key Laboratory for Laboratory Animals and Comparative Medicine Northeast Agricultural UniversityHarbin 150030China

Birth defects have become a public health concern.The hazardous environmental factors exposure to embryos could increase the risk of birth defects.Cadmium,a toxic environmental factor,can cross the placental barrier during pregnancy.Pregnant woman may be subjected to cadmium before taking precautionary protective actions.However,the link between birth defects and cadmium remains obscure.Cadmium exposure can induce excessive apoptosis in neuroepithelium during embryonic development progresses.Cadmium exposure activated the p53 via enhancing the adenosine 5‘-monophosphate(AMP)-activated protein kinase(AMPK)and reactive oxygen species'(ROS)level.And cadmium decreases the level of Paired box 3(Pax3)and murine double minute 2(Mdm2),disrupting the process of p53 ubiquitylation.And p53 accumulation induced excessive apoptosis in neuroepithelium during embryonic development progresses.Excessive apoptosis led to the failure of neural tube closure.The study emphasizes that environmental materials may increase the health risk for embryos.Cadmium caused the failure of neural tube closure during early embryotic day.Pregnant women may be exposed by cadmium before taking precautionary protective actions,because of cadmium concentration-containing foods and environmental tobacco smoking.This suggests that prenatal cadmium exposure is a threatening risk factor for birth defects.

关键词： Cadmium Neural tube closure Excessive apoptosis p53 Embryogenesis

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How plants sense and respond to osmotic stress

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Journal of Integrative Plant Biology 2024年第3期66卷 394-423页

作者： Bo Yu dai-Yin Chao Yang Zhao Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesThe Chinese Academy of SciencesShanghai 200032China Key Laboratory of Plant Carbon Capture The Chinese Academy of SciencesShanghai 200032China National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyThe Chinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100049China

Drought is one of the most serious abiotic stresses to land plants.Plants sense and respond to drought stress to survive under water deficiency.Scientists have studied how plants sense drought stress,or osmotic stress caused by drought,ever since Charles Darwin,and gradually obtained clues about osmotic stress sensing and signaling in plants.Osmotic stress is a physical stimulus that triggers many physiological changes at the cellular level,including changes in turgor,cell wall stiffness and integrity,membrane tension,and cell fluid volume,and plants may sense some of these stimuli and trigger downstream responses.In this review,we emphasized water potential and movements in organisms,compared putative signal inputs in cell wall-containing and cell wall-free organisms,prospected how plants sense changes in turgor,membrane tension,and cell fluid volume under osmotic stress according to advances in plants,animals,yeasts,and bacteria,summarized multilevel biochemical and physiological signal outputs,such as plasma membrane nanodomain formation,membrane water permeability,root hydrotropism,root halotropism,Casparian strip and suberin lamellae,and finally proposed a hypothesis that osmotic stress responses are likely to be a cocktail of signaling mediated by multiple osmosensors.We also discussed the core scientific questions,provided perspective about the future directions in this field,and highlighted the importance of robust and smart root systems and efficient source-sink allocations for generating future high-yield stress-resistant crops and plants.

关键词： cell volume drought membrane tension osmotic stress turgor

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Metagenomics reveals the microbial community and functional metabolism variation in the partial nitritation-anammox process:From collapse to recovery

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Journal of Environmental Sciences 2024年第1期135卷 210-221页

作者： Hong Wang Hui Gong Xiaohu dai Min Yang State Key Laboratory of Pollution Control and Resource Reuse College of Environmental Science and EngineeringTongji UniversityShanghai 200092China BIOMATH Department of Data Analysis and Mathematical ModellingGhent UniversityGhent 9000Belgium

Mainstream partial nitritation-anammox(PNA)process easily suffers from performance instability and even reactor collapse in application.Thus,it is of great significance to unveil the characteristic of performance recovery,understand the intrinsic mechanism and then propose operational strategy.In this study,we combined long-term reactor operation,batch tests,and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery.Proper aeration control(0.10-0.25mg O_(2)/L)was critical for performance recovery.It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5%to 11.0%.Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery,and the genes abundance related to signal transduction was dramatically increased.The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins,thereby possibly improving the activity and abundance of AnAOB,which was conducive to the performance recovery.Moreover,the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process.Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery.The achievement of performance recovery was driven by anammox,nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium.These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.

关键词： Partial nitritation-anammox Metagenomics Microbial community Functional metabolism Recovery

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