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Physiological,transcriptome and gene functional analysis provide novel sights into cadmium accumulation and tolerance mechanisms in kenaf

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Journal of Environmental Sciences 2024年第3期137卷 500-514页

作者： Shan Cao Meng Wang Jiao Pan Dengjie Luo Samavia Mubeen Caijin Wang Jiao Yue Xia Wu Qijing Wu Hui Zhang Canni Chen Muzammal Rehman Sichen Xie Ru Li Peng Chen Guangxi key laboratory of agro-environment and Agric-products safety Key Laboratory of Plant Genetics and BreedingCollege of AgricultureGuangxi UniversityNanning 530004China state key laboratory for conservation and utilization of subtropical agro-bioresources College of Life Science and TechnologyGuangxi UniversityNanning 530004China

Kenaf is considered to have great potential for remediation of heavy metals in ***,studies on molecular mechanisms of root Cd accumulation and tolerance are still *** this study,two differently tolerant kenaf cultivars were selected as materials and the physiological and transcriptomic effects were evaluated under Cd *** study showed that 200μmol/L CdCl_(2) treatment triggered the reactive oxygen species(ROS)explosion and membrane lipid *** with the Cd-sensitive cultivar‘Z',the Cd-tolerant cultivar‘F'was able to resist oxidative stress in cells by producing higher antioxidant enzyme activities and increasing the contents of ascorbic acid(AsA)and glutathione(GSH).The root cell wall of‘F'exhibited higher polysaccharide contents under Cd treatment,providing more Cd-binding *** were 3,439 differentially expressed genes(DEGs)that were co-regulated by Cd treatment in two *** biosynthesis and plant hormone signal transduction pathways were significantly enriched by functional annotation *** associated with pectin,cellulose,and hemi-cellulose metabolism were involved in Cd chelation of root cell wall;V-ATPases,ABCC3 and Narmp3 could participated in vacuolar compartmentalization of Cd;PDR1 was responsible for Cd effux;the organic acid transporters contributed to the absorption of Cd in *** genes might have played key roles in kenaf Cd tolerance and Cd ***,HcZIP2 was identified to be involved in Cd uptake and transport in *** findings provide a deeper understanding of the molecular pathways underlying Cd accumulation and detoxification mechanisms in kenaf.

关键词： Kenaf Cd stress Physiological Transcriptome HcZIP2

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 ***,whether exogenous indole-3-acetic acid(IAA)application and arbuscular mycorrhizal fungi(AMF)have synergistic effects on Cd tolerance of *** remains *** investigate the effects of AMF inoculation and IAA application on the tolerance of *** to Cd stress,two experiments were conducted:the first to investigate the effect of AMF(Rhizophagus irregularis)inoculation on the tolerance of *** to Cd stress and the second to investigate the combined effects of AMF inoculation and IAA application on the tolerance of *** to Cd *** including endogenous hormone concentration,antioxidant defense response,malondialdehyde(MDA)content,and gene expression related to antioxidant enzyme system and hormone were *** results indicated that AMF alleviated Cd toxicity of *** by reducing MDA content and improving antioxidant enzyme activities and Cd absorption ***,the combination of AMF inoculation and IAA application had a synergetic effect on the tolerance of *** 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 *** 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

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

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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

Insertion sequence transposition activates antimycobacteriophage immunity through an Isr2-silenced lipid metabolism gene island

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mLife 2024年第1期3卷 87-100页

作者： Yakun Li Yuyun Wei Xiao Guo Xiaohui Li Lining Lu Lihua Hu Zheng-Guo He state key laboratory for conservation and utilization of subtropical agro-bioresources Guangxi Research Center for Microbial and Enzyme Engineering TechnologyCollege of Life Scienceand TechnologyGuangxi UniversityNanningChina

Insertion sequences(ISs)exist widely in bacterial genomes,but their roles in the evolution of bacterial antiphage defense remain to be ***,we report that,under the pressure of phage infection,the IS1o96 transposition of Mycobacterium smegmatis into the Isr2 gene can occur at high frequencies,which endows the mutant mycobacterium with a broad-spectrum antiphage ***2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related *** complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium,thus defending against phage ***,a phage that has evolved mutations in two tail-filament genes can re-escape from the Isr2 inactivation-triggered host *** study uncovered a new signaling pathway for activating antimycobacteriophage immunity by Is transposition and provided insight into the natural evolution of bacterial antiphage defense.

关键词： antiphage defense bacteriophage gene island insertion sequence mycobacteria

Lipid concentration and composition in xylem sap of woody angiosperms from a tropical savanna and a seasonal rainforest

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Plant Diversity 2024年第1期46卷 126-133页

作者： Ling-Bo Huang Xinyi Guan Amy Ny Aina Aritsara Jun-Jie Zhu Steven Jansen Kun-Fang Cao state key laboratory for conservation and utilization of subtropical agro-bioresources Guangxi Key Laboratory of Forest Ecology and ConservationGuangxi UniversityDaxuedong Road 100NanningGuangxi 530004China Institute of Botany Ulm UniversityAlbert-Einstein-Allee 11Ulm89081Germany

Lipids may play an important role in preventing gas embolisms by coating nanobubbles in xylem *** studies on xylem sap lipids have been reported for temperate plants,and it remain unclear whether sap lipids have adaptational significance in tropical *** this study,we quantify the lipid composition of xylem sap for angiosperm species from a tropical savanna(seven species)and a seasonal rainforest(five species)using mass *** found that all twelve species studied contained lipids in their xylem sap,including galactolipids,phospholipids and triacylglycerol,with a total lipid concentration ranging from 0.09 to 0.26 nmol/*** was no difference in lipid concentration or composition between plants from the two sites,and the lipid concentration was negatively related to species’open vessel ***,savanna species showed little variation in lipid composition between the dry and the rainy *** results support the hypothesis that xylem sap lipids are derived from the cytoplasm of individual conduit cells,remain trapped inside individual conduits,and undergo few changes in composition over consecutive seasons.A xylem sap lipidomic data set,which includes 12 tropical tree species from this study and 11 temperate tree species from literature,revealed no phylogenetic signals in lipid composition for these *** study fills a knowledge gap in the lipid content of xylem sap in tropical trees and provides additional support for their common distribution in xylem sap of woody *** appears that xylem sap lipids have no adaptive significance.

关键词： Xylem sap Lipids Tropical savanna Tropical rainforest Vessels

DNA methylation in poultry:a review

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Journal of Animal Science and Biotechnology 2024年第2期15卷 509-518页

作者： Xing Ju Zhijun Wang Danfeng Cai Semiu Folaniyi Bello Qinghua Nie state key laboratory for conservation and utilization of subtropical agro‑bioresources Lingnan Guangdong Laboratory of AgricultureCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdong 510642China Guangdong Provincial key Lab of agro‑Animal Genomics and Molecular Breeding and key Lab of Chicken Genetics Breeding and ReproductionMinistry of AgricultureGuangzhouGuangdong 510642China college of Animal Science and Technology Zhejiang Agriculture and Forestry University666 Wusu RoadLin’an 311300China

As an important epigenetic modification,DNA methylation is involved in many biological processes such as animal cell differentiation,embryonic development,genomic imprinting and sex chromosome *** DNA methylation sequencing becomes more sophisticated,it becomes possible to use it to solve more zoological *** paper reviews the characteristics of DNA methylation,with emphasis on the research and application of DNA methylation in poultry.

关键词： CpG islands Differentially methylated genes Differentially methylated regions DNA methylation Poultry

SapBase:A central portal for functional and comparative genomics of Sapindaceae species

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Journal of Integrative Plant Biology 2024年第8期66卷 1561-1570页

作者： Jiawei Li Chengjie Chen Zaohai Zeng Fengqi Wu Junting Feng Bo Liu Yingxiao Mai Xinyi Chu Wanchun Wei Xin Li Yanyang Liang YuanLong Liu Jing Xu Rui Xia state key laboratory for conservation and utilization of subtropical agro-bioresources College of HorticultureSouth China Agricultural UniversityGuangzhou 510640China Guangdong laboratory for Lingnan Modern agriculture South China Agricultural UniversityGuangzhou 510640China key laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China at the Ministry of agriculture and Rural Affairs South China Agricultural UniversityCollege of HorticultureGuangzhou 510640China

The Sapindaceae family,encompassing a wide range of plant forms such as herbs,vines,shrubs,and trees,is widely distributed across tropical and subtropical *** family includes economically important crops like litchi,longan,rambutan,and *** the wide application of genomic technologies in recent years,several Sapindaceae plant genomes have been decoded,leading to an accumulation of substantial omics data in this *** surge in data highlights the pressing need for a unified genomic data center capable of storing,sharing,and analyzing these ***,we introduced SapBase,that is,the Sapindaceae Genome *** houses seven published plant genomes alongside their corresponding gene structure and functional annotations,small RNA annotations,gene expression profiles,gene pathways,and synteny block *** offers user-friendly features for gene information mining,co-expression analysis,and interspecies comparative genomic ***,we showcased SapBase's extensive capacities through a detailed bioinformatic analysis of a MYB gene in ***,Sap Base could serve as an integrative genomic resource and analysis platform for the scientific exploration of Sapinaceae species and their comparative studies with other plants.

关键词： functional crops unified

Rice GWAS-to-Gene uncovers the polygenic basis of traits

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Science China Life Sciences 2024年

作者： Xianrong Xie Qunjie Zhang Yao-Guang Liu state key laboratory for conservation and utilization of subtropical agro-bioresources Guangdong Laboratory for Lingnan Modern Agriculture College of Agriculture College of Life Sciences South China Agricultural University college of agriculture South China Agricultural University

For over a century, researchers have worked to develop methodologies to identify the causal genes contributing to phenotypic variations in organisms from humans to important crops such as rice(Oryza sativa L.). In contrast to discrete and monogenic qualitative phenotypes such as the green or yellow color of pea(Pisum sativum) seeds, quantitative traits such as plant height are polygenic (Robinson et al., 2015). In the past 30 years,genetic mapping experiments, especially genome-wide association studies (GWAS),have enhanced our understanding of the genetic bases of many complex traits,especially in humans and other model organisms (Abdellaoui et al., 2023).

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Aboveground biomass stocks of species-rich natural forests in southern China are influenced by stand structural attributes,species richness and precipitation

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Plant Diversity 2024年第4期46卷 530-536页

作者： Wen-Hao Zeng Shi-Dan Zhu Ying-Hua Luo Wei Shi Yong-Qiang Wang Kun-Fang Cao state key laboratory for conservation and utilization of subtropical agro-bioresources College of ForestryGuangxi UniversityNanning 530004China Guangxi key laboratory of Forest Ecology and conservation College of ForestryGuangxi UniversityNanning 530004China key laboratory of National Forestry and Grassland Administration on Biodiversity conservation in Karst Mountainous Areas of Southwestern China School of Life SciencesGuizhou Normal UniversityHuaxi College TownGui'an DistrictGuiyang 550025China

Forests,the largest terrestrial carbon sinks,play an important role in carbon sequestration and climate change *** forest attributes and environmental factors have been shown to impact aboveground biomass,their influence on biomass stocks in species-rich forests in southern China,a biodiversity hotspot,has rarely been *** this study,we characterized the effects of environmental factors,forest structure,and species diversity on aboveground biomass stocks of 30 plots(1 ha each) in natural forests located within seven nature reserves distributed across subtropical and marginal tropical zones in Guangxi,*** results indicate that forest aboveground biomass stocks in this region are lower than those in mature tropical and subtropical forests in other ***,we found that aboveground biomass was positively correlated with stand age,mean annual precipitation,elevation,structural attributes and species richness,although not with species *** we compared stands with the same basal area,we found that aboveground biomass stock was higher in communities with a higher coefficient of variation of diameter at breast *** findings highlight the importance of maintaining forest structural diversity and species richness to promote aboveground biomass accumulation and reveal the potential impacts of precipitation changes resulting from climate warming on the ecosystem services of subtropical and northern tropical forests in ***,many natural forests in southern China are not fully ***,their continued growth will increase their carbon storage over time.

关键词： subtropical forest Marginal tropical forest Aboveground biomass Species diversity Forest structural attribute Environment factor