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WTV2.0:A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode

Molecular Plant 2024年第6期17卷 972-985页

作者： Honglun Yuan Yiding Jiangfang Zhenhuan Liu Rongxiu Su Qiao Li Chuanying Fang Sishu Huang Xianqing Liu Alisdair R.Fernie Jie Luo School of breeding and Multiplication(Sanya Institute of breeding and Multiplication)and College of Tropical Agriculture and Forestry Hainan UniversitySanya Hainan 572025China Yazhouwan National Laboratory(YNL) Sanya Hainan 572025China department of Molecular Physiology Max-Planck-Institute of Molecular Plant PhysiologyAm Mühlenberg 1Potsdam-Golm 14476Germany

Volatilomics is essential for understanding the biological functions and fragrance contributions of plant ***,the annotation coverage achieved using current untargeted and widely targeted volatomics(WTV)methods has been limited by low sensitivity and/or low acquisition ***,we introduce WTV 2.0,which enabled the construction of a high-coverage library containing 21.1.plant volatiles,and report the development of a comprehensive selective ion monitoring(cSIM)acquisition method,including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method,that can acquire the smallest but sufficient number of ions for most plant volatiles,as well as the automatic qualitative and semi-quantitative analysis of cSIM ***,the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library,utilizing the obtained cSIM *** showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method,doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit,and led to the discovery of menthofuran as a novel flavor compound in passion *** 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.

关键词： volatilomics widely targeted methods GC-MS selective ion monitoring plant volatiles

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The anthocyanin formation of purple leaf is associated with the activation of LfiHY5 and LfiMYB75 in crape myrtle

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Horticultural Plant Journal 2024年第5期10卷 1230-1246页

作者： Lu Feng Ping Shen Xiufeng Chi Yang Zhou Jieru Liu Tangren Cheng Jia Wang Qixiang Zhang Ming Cai Huitang Pan State Key Laboratory of Efficient Production of Forest Resources Beijing Key Laboratory of Ornamental Plants Germplasm Innovation&Molecular BreedingNational Engineering Research Center for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape ArchitectureBeijing Forestry UniversityBeijing 100083China

Purple-leafed plants not only have a higher resistance to biotic and abiotic stresses,but also have higher ornamental *** are vital for leaf color formation,growth and development of purple ***,the molecular mechanism underlying purple leaf formation in Lagerstroemia indica remains *** and transcriptomic analysis of purple-leafed cultivar‘Ebony Embers’and greenleafed cultivar‘Arapahoe’showed that the high expression of anthocyanin structure genes induced hyperaccumulation of cyanidin and pelargonidin derivatives,making the leaves ***5,LfiMYB75 and LfibHLH1.were identified using correlation analysis and weighted gene co-expression network ***‘Arapahoe’‘Ebony Embers’population,LfiHY5 and LfiMYB75 showed significant positive correlation with leaf anthocyanin *** expression of LfiMYB75 and LfiHY5 in tobacco and purple-leafed crape myrtle indicated that the two genes activated anthocyanin *** two-hybrid analysis showed that LfiMYB75 and LfibHLH1.could form a complex that enhanced anthocyanin *** monohybrid and dual-luciferase assays confirmed that LfiHY5 activated the expression of LfiMYB75,to activate the transcription of anthocyanin structural genes LfiCHS and ***,there were three alleles of LfiHY5 in crape myrtle,and the different sequences had different activation effects on *** conclusion,the results showed that LfiHY5 led to upregulate the transcription of LfiMYB75,and LfiMYB75 formed a complex with LfibHLH1.which increased the transcription level of LfiCHS and LfiANS to affect anthocyanin synthesis in crape myrtle.

关键词： Lagerstroemia indica Leaf color Anthocyanin HY5 MYB bHLH

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MiR-1.6a targets ATG7 to inhibit autophagy and angiogenesis after myocardial infarction

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animal Models and Experimental Medicine 2024年第4期7卷 408-418页

作者： Guofeng Bai Jinghao Yang Weili Liao Xiaofeng Zhou Yingting He Nian Li Liuhong Zhang Yifei Wang Xiaoli Dong Hao Zhang Jinchun Pan Liangxue Lai Xiaolong Yuan Xilong Wang Guangdong Provincial Key Laboratory of Laboratory animals Guangdong Laboratory Animals Monitoring InstituteGuangzhouChina Guangdong Laboratory of Lingnan Modern Agriculture National Engineering Research Center for Breeding Swine IndustryState Key Laboratory of Swine and Poultry Breeding IndustryGuangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular BreedingCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdongChina Huidong County animal Quarantine and Inspection Institute HuizhouGuangdongChina department of Cardiology Hainan General HospitalHainan Affiliated Hospital of Hainan Medical UniversityHainan Clinical Medicine Research InstitutionHaikouPeople's Republic of China Key Laboratory of Regenerative Biology Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdongChina

Background:Myocardial infarction(MI)is an acute condition in which the heart mus-cle dies due to the lack of blood *** research has suggested that au-tophagy and angiogenesis play vital roles in the prevention of heart failure after MI,and miR-1.6a is considered to be an important regulatory factor in *** the specific mechanism remains *** this study,using cultured venous endothelial cells and a rat model of MI,we aimed to identify the potential target genes of miR-1.6a and discover the mechanisms of inhibiting autophagy and ***:We first explored the biological functions of miR-1.6a on autophagy and angiogenesis on endothelial *** we identified ATG7,which was the down-stream target gene of *** expression of miR-1.6a and ATG7 was investi-gated in the rat model of ***:We found that miR-1.6a inhibits the proliferation,cell cycle,autophagy and angiogenesis,but promoted the apoptosis of vein endothelial ***,ATG7 was identified as the target of miR-1.6a,and ATG7 rescued the inhibition of autophagy and angiogenesis by *** expression of miR-1.6a in the rat model of MI was decreased but the expression of ATG7 was increased in the infarction ***:Our results indicate that miR-1.6a may inhibit autophagy and angiogenesis by targeting *** mechanism may be a potential therapeutic treatment for MI.

关键词： angiogenesis ATG7 autophagy miR-1.6a miRNAs myocardial infarction

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Brassinosteroid biosynthesis and signaling:Conserved and diversified functions of core genes across multiple plant species

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Plant Communications 2024年第9期5卷 72-100页

作者： Brian Zebosi Erik Vollbrecht Norman B.Best department of {1. Development and Cell BiologyIowa State UniversityAmesIA 50011USA Interdepartmental {1. and Genomics Graduate Program Iowa State UniversityAmesIA 50011USA USDA-ARS Plant Genetics Research UnitColumbiaMO 65201USA

Brassinosteroids(BRs)are important regulators that control myriad aspects of plant growth and development,including biotic and abiotic stress responses,such that modulating BR homeostasis and signaling presents abundant opportunities for plant breeding and crop *** and other proteins involved in the biosynthesis and signaling of BRs are well understood from molecular {1. and phenotypic analysis in Arabidopsis thaliana;however,knowledge of the molecular functions of these genes in other plant species,especially cereal crop plants,is *** this manuscript,we comprehensively review functional studies of BR genes in Arabidopsis,maize,rice,Setaria,Brachypodium,and soybean to identify conserved and diversified functions across plant species and to highlight cases for which additional research is in *** performed phylogenetic analysis of gene families involved in the biosynthesis and signaling of BRs and re-analyzed publicly available transcriptomic *** trees coupled with expression data provide a valuable guide to supplement future research on BRs in these important crop species,enabling researchers to identify gene-editing targets for BR-related functional studies.

关键词： brassinosteroids maize rice Setaria soybean Brachypodium Arabidopsis

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Unveiling the distinctive traits of functional rye centromeres:minisatellites,retrotransposons,and R-loop formation

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Science China(Life Sciences) 2024年第9期67卷 1989-2002页

作者： Chang Liu Shulan Fu Congyang Yi Yang Liu Yuhong Huang Xianrui Guo Kaibiao Zhang Qian Liu James A.Birchler Fangpu Han State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory for Plant genetics and {1. Sichuan Agricultural UniversityChengdu 611130China Division of Biological Science University of MissouriColumbia 65211-7400USA

Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle *** their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting diverse sizes and compositions across *** functional significance of rye centromeric DNA sequences,particularly in centromere identity,remains *** this study,we comprehensively characterized the sequence composition and organization of rye *** findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs)and interspersed *** systematically classified LTR-RTs into five categories,highlighting the prevalence of younger CRS1.CRS2,and CRS3 of CRSs(centromeric retrotransposons of Secale cereale)were primarily located in the core centromeres and exhibited a higher association with CENH3 *** minisatellites,mainly derived from retrotransposons,along with CRSs,played a pivotal role in establishing functional centromeres in ***,we observed the formation of R-loops at specific regions of CRS1.CRS2,and CRS3,with both rye pericentromeres and centromeres exhibiting enrichment in ***,these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres,suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere *** work provides insights into the DNA sequence composition,distribution,and potential function of R-loops in rye *** knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres,offering implications for the development of synthetic centromeres in future plant modifications and beyond.

关键词： centromere LTR-RTs minisatellite rye R-loop

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Exploring the molecular landscape of NNK-induced transformation:A comprehensive genome-wide CRISPR/Cas9 screening

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Genes & Diseases 2024年第4期11卷 42-44页

作者： Trang Dinh Mira Rahm Zhenghe Wang Christopher McFarland Athar Khalil department of {1. and Genome Sciences Case WesternReserve UniversityClevelandOH44106USA

Lung cancer is the leading cause of cancer-related deaths worldwide,with an estimated 1.8 million deaths in 2020 alone.1.While several risk factors are associated with lung cancer,smoking remains the most significant environmental cause of the disease.1.One of the most potent carcinogens in tobacco smoke is 4-(methylnitrosoamino)-1.(3-pyridyl)-1.butanone(NNK),which is produced from nicotine through a series of metabolic reactions.

关键词： CRISPR/Cas9 NNK lung

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Transcriptomic Analysis Reveals the Formation Mechanism of Anthocyanins Light-Independent Synthesis in Chrysanthemum

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1599-1621页

作者： Fangye Liu Jiaping Qu Yajun Li Jiawei Fan Yumeng Cui Jingwen Wu Xueqi Gu Xia Li He Huang Beijing Advanced Innovation Center for Tree breeding by Molecular Design Beijing Key Laboratory of Ornamental Plants Germplasm Innovation&Molecular BreedingNational Engineering Research Center for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Education MinistrySchool of Landscape ArchitectureBeijing Forestry UniversityBeijing100083China Urban Construction School Beijing City UniversityBeijing100083China

Chrysanthemum×morifolium is a horticultural crop which plays a vital role in theﬂower industry with signiﬁ-cant economic value and has a cultivation history of over three thousand years in *** accumulation of anthocyanins is always affected by ***,we revealed that anthocyanin accumulation is highly dependent on light in‘2021.35’genotype chrysanthemum,while it is light-independent in‘2001.02’genotype ***,no literature has been reported regarding the non-photosensitive chrysanthemum in anthocya-nins light-independent synthesis *** the phenotype analysis of 44 F1.generations,we found that light-independence is a dominant trait which can be stable inherited by *** transcriptome of the rayﬂorets of‘2021.35’and‘2001.02’under light and bagging treatment were sequenced and *** on weighted gene co-expression network analysis(WGCNA),K-means analysis,and Real-Time Quantitative Poly-merase Chain Reaction(RT-qPCR)analysis,1. genes were highly correlated with the anthocyanin *** anthocyanin content of rayﬂorets treated with different light-quality conditions indicated that blue light signiﬁ-cantly affected anthocyanin *** Yeast one-hybrid analysis,CmBIC1.1.and CmBIC1.2 can directly regulate the anthocyanin structural gene *** our study,we revealed the important characteristics of light-independent anthocyanin synthesis in chrysanthemums and screened regulatory factors in light-depen-dent and light-independent anthocyanin synthesis *** results laid the groundwork for subsequent ana-lysis of the molecular mechanism involved in the light-independent synthesis of anthocyanins in chrysanthemums.

关键词： Chrysanthemum non-photosensitive transcriptome anthocyanin biosynthesis

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GINS1.as a Novel Biomarker of Survival in Colon Adenocarcinoma Patients-A Secondary Publication

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Proceedings of Anticancer Research 2024年第3期8卷 60-67页

作者： Muhammad Umair Abid Yasir Hameed department of Plant {1. and genetics University of Agriculture FaisalabadFaisalabadPakistan department of Biochemistry and Biotechnology The Islamia University of BahawalpurBahawalpurPakistan

The study focused on elaborating the role of GINS1.expression and its regulatory mechanisms in colon adenocarcinoma (COAD). Using the UALCAN informational index, GINS1.expression assessment unveiled a critical up- regulation in malignant cells that stood out from normal controls, suggesting its contribution to COAD expansion. Further dismantling GINS1.expression across various boundaries revealed unsurprising up-regulation in different malignant development stages, racial groups, genders, and age classes in COAD patients, characteristics for its imperative role in cancer progression. Moreover, this study investigated the promoter methylation status of GINS1. uncovering a critical uniqueness between COAD samples and normal controls. Analyzing promoter methylation across various clinical boundaries uncovered powerful variations, with particular methylation patterns seen across cancer stages, race groups, genders, and age groups. Survival analysis using the Kaplan-Meier (KM) plotter tool showed a colossal connection between GINS1.expression levels and overall survival (OS) in COAD patients, with low GINS1.expression interfacing with higher OS. Additionally, mutational examination using the cBioPortal stage revealed that no critical change was found in COAD. Overall, these findings revealed the complex contribution of GINS1.in COAD pathogenesis, underlining its actual limit as a prognostic biomarker and supportive therapeutic agent in COAD management.

关键词： Colon adenocarcinoma Diagnosis Treatment

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Characterization and screening of cotton(Gossypium hirsutum L.)germplasm for leafhopper(Amrasca biguttula biguttula(Ishida))resistance

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Journal of Cotton Research 2024年第2期7卷 188-195页

作者： Mawblei Chossterfield Premalatha Nallathambi Manivannan Alagarsamy Senguttuvan Kannan department of {1. and Plant breeding Tamil Nadu Agricultural UniversityCoimbatore 641003India department of Cotton Tamil Nadu Agricultural UniversityCoimbatore 641003India Indian Council of Agricultural Research‑Centre Institute for Cotton Research Regional StationCoimbatore 641003India

Background Cotton(Gossypium hirsutum L.)is one of the most significant fibre and cash crops and plays an important role in Indian industrial and agricultural ***,over the years quantity and quality have been hampered by the pest *** alone has been shown to cause yield losses of up to 40%.In this study,screening and evaluation were performed to identify and categorize 1.0 cotton genotypes along with 5 checks as resistant,moderately resistant,sensitive and highly sensitive to *** A total of hundred genotypes were evaluated along with five checks for leafhopper *** on the screening results,a total of 1. genotypes were resistant to leafhoppers,which was on par with the findings of the check KC *** contents of total soluble sugar,total soluble protein,and total free amino acids were significantly positively correlated with the mean grade,whereas total phenols content and trichome density were significantly negatively correlated with the susceptibility ***,based on screening and biochemical analysis,the genotypes KC 2,JR-23,Samaru-26-T,D 4,TCH 1.28,RS 253,and B-61.1.62 exhibited high resistance to *** According to the findings of this study,choosing genotypes with high total phenolics content together with high trichome density and low contents of total soluble sugar,total soluble protein,and free amino acids may aid in the development of resistant genotypes.

关键词： Gossypium Amrasca biguttula biguttula Field screening Host plant resistance Biochemical parameters

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The first mitogenome of Lauraceae(Cinnamomum chekiangense)

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Plant Diversity 2024年第1期46卷 144-148页

作者： Changwei Bi Ning Sun Fuchuan Han Kewang Xu Yong Yang David K.Ferguson State Key Laboratory of Tree genetics and {1. Co-Innovation Center for Sustainable Forestry in Southern ChinaKey Laboratory of Tree Genetics and Biotechnology of Educational Department of ChinaKey Laboratory of Tree Genetics and Silvicultural Sciences of Jiangsu ProvinceNanjing Forestry UniversityNanjing 210037China College of Information Science and Technology Nanjing Forestry UniversityNanjing 210037China Research Institute of Subtropical Forestry Chinese Academy of ForestryHangzhou 311400China Co-Innovation Center for Sustainable Forestry in Southern China College of Life SciencesNanjing Forestry UniversityNanjing 210037China department of Paleontology University of ViennaViennaAustria

There are three distinct genetic systems in higher plants,the dominant nuclear genome and the semi-autonomous organelle genomes(plastids and mitochondria).In contrast to the conserved plastid genome(plastome),the plant mitochondrial genome(mitogenome)is characterized by an intriguing“evolutionary paradox”distinguished by a remarkably low mutation rate but with a significantly high rearrangement rate(Palmer and Herbon,1.88;Lai et al.,2022).

关键词： autonomous distinguished Palmer

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