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Journal of Integrative Agriculture 2024年第3期23卷 876-887页

作者： Liyao Su Min Wu Tian Zhang Yan Zhong Zongming(Max) Cheng State Key laboratory of Crop genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing210095China

Rosa roxburghii fruit is rich in flavonoids, but little is known about their biosynthetic pathways. In this study, we employed transcriptomics and metabolomics to study changes related to the flavonoids at five different stages of R. roxburghii fruit development. Flavonoids and the genes related to their biosynthesis were found to undergo significant changes in abundance across different developmental stages, and numerous quercetin derivatives were identified. We found three gene expression modules that were significantly associated with the abundances of the different flavonoids in R. roxburghii and identified three structural UDP-glycosyltransferase genes directly involved in the synthesis of quercetin derivatives within these modules. In addition, we found that RrBEH4, RrLBD1 and RrPIF8could significantly increase the expression of downstream quercetin derivative biosynthesis genes. Taken together,these results provide new insights into the metabolism of flavonoids and the accumulation of quercetin derivatives in R. roxburghii.

关键词： Rosa roxburghii quercetin derivatives weighted gene co-expression network analysis transcription factor transcriptome metabolome

E3 ubiquitin ligase PbrATL18 is a positive factor in pear resistance to drought and Colletotrichum fructicola infection

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Horticultural Plant Journal 2024年第3期10卷 698-712页

作者： Likun Lin Qiming Chen Kaili Yuan Caihua Xing Qinghai Qiao Xiaosan Huang Shaoling Zhang State Key laboratory of Crop genetics and Germplasm Enhancement/College of Horticulture Nanjing Agricultural UniversityNanjingJiangsu210095China

The Arabidopsis Toxicos en Levadura(ATL)protein is a subfamily of the E3 ubiquitin ligases,which exists widely in plants and is extensively involved in plant growth and *** the ATL family has been identified in other species,such as Arabidopsis,Oryza sativa,and grapevine,few reports on pear ATL gene families have been *** this study,92 PbrATL genes were identified and analyzed from the Pyrus breschneideri *** analysis and phylogenetic tree generation divided them into nine subgroups,and chromosome localization analysis showed that the 92 PbrATL genes were distributed in 16 of 17 pear *** data and quantitative real-time polymerase chain reaction(qRT-PCR)experiments demonstrated that PbrATL18,PbrATL41,and PbrATL88 were involved in both pear drought resistance and Colletotrichum fructicola *** addition,Arabidopsis thaliana overexpressing PbrATL18 showed greater resistance to drought stress than the wild type(WT),and PbrATL18-silenced pear seedlings showed greater sensitivity to drought and *** infection than the ***18 regulated plant resistance by regulating chitinase(CHI),phenylalanine ammonia-lyase(PAL),polyphenol oxidase(PPO),catalase(CAT),peroxidase(POD),and superoxide dismutase(SOD)*** study provided a reference for further exploring the functions of the PbrATL gene in drought resistance and *** infection.

关键词： Pear Colletotrichum fructicola Arabidopsis Toxicos en Levadura(ATL) Drought stress

CmMYB3-like negatively regulates anthocyanin biosynthesis and flower color formation during the post-flowering stage in Chrysanthemum morifolium

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Horticultural Plant Journal 2024年第1期10卷 194-204页

作者： Lijie Zhou Shenhui Liu Yiguang Wang Yuxi Wang Aiping Song Jiafu Jiang Sumei Chen Zhiyong Guan Fadi Chen State Key laboratory of Crop genetics and Germplasm Enhancement The Key Laboratory of LandscapingMinistry of Agriculture and Rural AffairsCollege of HorticultureNanjing Agricultural UniversityNanjingJiangsu 210095China

Color fading caused by a decrease in anthocyanin accumulation during the post-flowering stage significantly affects postharvest quality of ***,the underlying mechanism by which anthocyanin accumulation decreases during the post-flowering stage still unclear,which greatly restricts design of molecular breeding in ***,a chrysanthemum SG7 R2R3 MYB transcription factor(TF),CmMYB3-like,was identified to have a function in regulating anthocyanin biosynthesis during the post-flowering *** real time PCR(qRT-PCR)assays showed that the expression of CmMYB3-like was gradually downregulated when anthocyanin content increased during the flowering stage and was significantly upregulated during the post-flowering *** transformation of chrysanthemum and dual-luciferase assays in *** leaves showed that CmMYB3-like suppressed anthocyanin accumulation by inhibiting the transcription of CmCHS and CmANS directly and that of CmF3H ***,overexpression or suppression of CmMYB3-like did not affect the biosynthesis of flavones or *** transformation of chrysanthemum revealed that the overexpression of CmMYB3-like inhibited anthocyanin accumulation,but its suppression prevented the decrease in anthocyanin accumulation during the post-flowering *** results revealed a crucial role of CmMYB3-like in regulating the color of petals during the post-flowering stage and provided a target gene for molecular design breeding to improve the postharvest quality of chrysanthemum.

关键词： Post-flowering stage Color fading Anthocyanins CmMYB3-like Chrysanthemum Molecular breeding

From molecule to cell:the expanding frontiers of plant immunity

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Journal of genetics and Genomics 2024年第7期51卷 680-690页

作者： Lei Li Jing Liu Jian-Min Zhou Key laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Hainan Yazhou Bay Seed laboratory SanyaHainan 572025China

In recent years,the field of plant immunity has witnessed remarkable *** the co-evolution between plants and pathogens,plants have developed a wealth of intricate defense mechanisms to safeguard their *** identified immune receptors have added unexpected complexity to the surface and intracellular sensor networks,enriching our understanding of the ongoing plant–pathogen *** the molecular mechanisms of resistosome shapes our understanding of these mysterious molecules in plant ***,technological innovations are expanding the horizon of the plant–pathogen battlefield into spatial and temporal *** the development provides new opportunities for untangling the complex realm of plant immunity,challenges remain in uncovering plant immunity across spatiotemporal dimensions from both molecular and cellular levels.

关键词： Plant immunity Calcium Spatiotemporal Biomolecular condensate Immune receptor Resistosome

Pollen-expressed RLCKs control pollen tube burst

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Plant Communications 2024年第8期5卷 147-156页

作者： Yin-Jiao Xu Ting Luo Peng-Min Zhou Wei-Qi Wang Wei-Cai Yang Hong-Ju Li Center for Developmental Biology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Center for Molecular Agrobiology Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina Key laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina

In angiosperms,the pollen tube enters the receptive synergid cell,where it ruptures to release its cytoplasm along with two sperm *** interaction is complex,and the exact signal transducers that trigger the bursting of pollen tubes are not well *** this study,we identify three homologous receptor-like cytoplasmic kinases(RLCKs)expressed in pollen tubes of Arabidopsis,Delayed Burst 1/2/3(DEB1/2/3),which play a crucial role in this *** genes produce proteins localized on the plasma membrane,and their knockout causes delayed pollen tube burst and entrance of additional pollen tubes into the embryo sac due to fertilization *** show that DEBs interact with the Ca^(2+)pump ACA9,influencing the dynamics of cytoplasmic Ca^(2+)in pollen tubes through *** results highlight the importance of DEBs as key signal transducers and the critical function of the DEB-ACA9 axis in timely pollen tube burst in synergids.

关键词： Pollen tube burst RLCKs Calcium signaling/transport Double fertilization

shinyTempSignal:an R shiny application for exploring temporal and other phylogenetic signals

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Journal of genetics and Genomics 2024年第7期51卷 762-768页

作者： Li Zhan Xiao Luo Wenqin Xie Xuan-An Zhu Zijing Xie Jianfeng Lin Lin Li Wenli Tang Rui Wang Lin Deng Yufan Liao Bingdong Liu Yantong Cai Qianwen Wang Shuangbin Xu Guangchuang Yu Department of Bioinformatics School of Basic Medical SciencesSouthern Medical UniversityGuangzhouGuangdong 510515China Faculty of Computers Guangdong University of TechnologyGuangzhouGuangdong 510006China Ubigene Biosciences Co. Ltd.GuangzhouGuangdong 510530China State Key laboratory of Applied microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangdong Academy of SciencesGuangzhouGuangdong 510070China

The molecular clock model is fundamental for inferring species divergence times from molecular ***,its direct application may introduce significant biases due to sequencing errors,recombination events,and inaccurately labeled sampling *** accuracy necessitates rigorous quality control measures to identify and remove potentially erroneous ***,while not all branches of a phylogenetic tree may exhibit a clear temporal signal,specific branches may still adhere to the assumptions,with varying evolutionary *** a relaxed molecular clock model better aligns with the complexities of *** root-to-tip regression method has been widely used to analyze the temporal signal in phylogenetic studies and can be generalized for detecting other phylogenetic *** its utility,there remains a lack of corresponding software implementations for broader *** address this gap,we present shinyTempSignal,an interactive web application implemented with the shiny framework,available as an R package and publicly accessible at https://***/YuLab-SMU/*** tool facilitates the analysis of temporal and other phylogenetic signals under both strict and relaxed *** extending the root-to-tip regression method to diverse signals,shinyTempSignal helps in the detection of evolving features or traits,thereby laying the foundation for deeper insights and subsequent analyses.

关键词： Molecular clock Root-to-tip regression Temporal signal Phylogenetic signal

Searching for plant NLR immune receptors conferring resistance to potyviruses

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The Crop Journal 2024年第1期12卷 28-44页

作者： Xin Hong Shufen Li Xiaofei Cheng Haijian Zhi Jinlong Yin Kai Xu Jiangsu Key laboratory for Microbes and Functional Genomics Jiangsu Engineering and Technology Research Center for MicrobiologyCollege of Life SciencesNanjing Normal UniversityNanjing 210023JiangsuChina College of Plant Protection Northeast Agricultural UniversityHarbin 150030HeilongjiangChina National Center for Soybean Improvement National Key Laboratory for Crop Genetics and Germplasm EnhancementKey Laboratory of Biology and Genetic Improvement of Soybean-Ministry of AgricultureNanjing Agricultural UniversityNanjing 210095JiangsuChina

To fight against invasion by pathogens,plants have evolved an elaborate innate immune system,of which the nucleotide-binding domain leucine-rich repeat-containing receptor(NLR)acts as the sensor and immune ***,comprising one of the largest genera of plant viruses,cause severe crop yield losses *** crop resistance to potyviruses can be used in breeding and plant transgenesis to control disease *** review summarizes achievements in mapping and cloning NLR genes conferring dominant resistance against potyvirus in the families Fabaceae,Solanaceae,Brassicaceae,and *** compares mechanisms of potyviral protein recognition and downstream signaling employed by NLRs and discusses strategies for exploiting NLRs to better control diseases caused by potyviruses.

关键词： NLR Potyvirus resistance Genetic diversity Mapping Engineer

Dynamics design of a non-natural transcription factor responding to androst-4-ene-3,17-dione

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Synthetic and Systems Biotechnology 2024年第3期9卷 436-444页

作者： Ming Zhao Mengkai Hu Rumeng Han Chao Ye Xiangfei Li Tianwen Wang Yan Liu Zhenglian Xue Kun Liu Anhui Engineering laboratory for Industrial microbiology Molecular Breeding College of Biology and Food EngineeringAnhui Polytechnic UniversityWuhu 241000China

The production of androst-4-ene-3,17-dione(AD)by the steroidal microbial cell factory requires transcription factors(TFs)to participate in metabolic ***,microbial cell factory lacks effective TFs that can respond to AD in its metabolic ***,finding and obtaining natural TFs that specifically respond to AD is a complex and onerous *** this study,we devised an artificial TF that responds to AD,termed AdT,based on structure-guided molecular dynamics(MD)*** to MD analysis of the conformational changes of AdT after binding to AD,an LBD in which the N-and C-termini exhibited convergence tendencies was used as a microswitch to guide the assembly of a DNA-binding domain lexA,a linker(GGGGS)2,and a transcription activation domain B42 into an artificial *** a proof of design,a AD biosensor was designed and constructed in yeast on the basis of the ligand-binding domain(LBD)of hormone *** addition,the transcription factor activity of AdT was increased by 1.44-fold for its variant ***,we created non-natural TF elements for AD microbial cell factory,and expected that the design TF strategy will be applied to running in parallel to the signaling machinery of the host cell.

关键词： Protein design Artificial transcription factor Molecular dynamics Steriods Site-mutations

Identification and Transcriptional Regulation of CAMTA Genes in Liriodendron chinense

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Phyton-International Journal of Experimental Botany 2024年第3期93卷 413-425页

作者： Kaiyue Hong Yasmina Radani Teja Manda Jinhui Chen Liming Yang State Key laboratory of Tree genetics and Breeding College of Life SciencesNanjing Forestry UniversityNanjing210037China

This study explores CAMTA genes in the rare and endangered Chinese plant species,Liriodendron *** the completion of whole-genome sequencing,the roles of CAMTA genes in calcium regulation and stress responses in this species remain largely *** the *** genome,we identiﬁed two CAMTA genes,Lchi09764 and Lchi222536,characterized by four functional domains:CG-1,TIG,ANK repeats,and IQ *** analyses,including phylogenetic investigations,cis-regulatory element analyses,and chromosomal location studies,aim to elucidate the deﬁning features of CAMTA genes in *** Weighted Gene Co-Expression Network Analysis(WGCNA),we explored the impact of CAMTA genes on different organs and their regulation under abiotic stress *** identiﬁcation of signiﬁcant gene modules and the prediction of promoter binding sites revealed co-expressed genes associated with CAMTA transcription *** summary,this study provides initial insights into CAMTA genes in ***,laying the groundwork for future research on their evolution and biological *** knowledge enhancement contributes to a better understanding of plant responses to environmental stress—an essential aspect of plant biology.

关键词： Liriodendron chinense CAMTA genes abiotic stress WGCNA different organs

Enhancing growth, liver health, and bile acid metabolism of tilapia(Oreochromis niloticus) through combined cholesterol and bile acid supplementation in plant-based diets

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Animal Nutrition 2024年第2期17卷 335-346页

作者： Jiayuan Jiang Xing Lu Lixue Dong Juan Tian Jianmin Zhang Zhongbao Guo Yongju Luo Zongbin Cui Hua Wen Ming Jiang College of Fisheries and Life Science Shanghai Ocean University Yangtze River Fisheries Research Institute Chinese Academy of Fishery Sciences Guangdong Provincial Key laboratory of Microbial Culture Collection and Application State Key Laboratory of Applied Microbiology Southern ChinaInstitute of MicrobiologyGuangdong Academy of Sciences Guangxi Institute of Fisheries

The present study aimed to compare the nutritional effects of cholesterol, bile acids, and combination of cholesterol with bile acids in plant-based diets on juvenile genetically improved farmed tilapia(GIFT;Oreochromis niloticus). The isonitrogenous(321 g/kg crude protein) and isolipidic(76 g/kg crude fat) diets(Con diet) were based on plant protein sources, which included corn gluten meal, soybean meal, cottonseed meal and rapeseed meal. The Con diet was supplemented with 12 g/kg cholesterol(CHO diet), 0.2 g/kg bile acids(BAs diet), a combination of 12 g/kg cholesterol and 0.2 g/kg bile acids(CHO-BAs diet),respectively. Each diet was fed to three tanks in an indoor recirculating aquaculture system for 9 *** showed that compared to the Con group, fish had a higher weight gain rate, hepatosomatic index,and a lower feed conversion ratio in the CHO-BAs group. The highest levels of whole-fish fat and ash were found in the Con group. Serum parameters, including activities of alanine aminotransferase(ALT) and aspartate transaminase(AST), along with levels of glucose(GLU) and triglyceride(TG) except for total cholesterol(TCHO), were lower in the CHO, BAs, and CHO-BAs groups than those in the Con group(P <0.001). Histological examination revealed that fish in the Con group exhibited severe hepatocyte vacuolization and diminished hepatocyte proliferation. Gene expression analysis indicated that the transcriptional levels of bile acid metabolism-related genes(including fxr, fgf19, bsep) were up-regulated in the CHO-BAs group(P < 0.05), whereas cholesterol metabolism-related genes(acly and hmgcr) were downregulated in both CHO and CHO-BAs groups(P < 0.001). Moreover, UPLC-MS/MS analysis revealed that the higher taurine-conjugated bile acids(T-BAs), followed by free bile acids(Free-BAs) and glycine(G-BAs)were determined in tilapia bile. Among these, taurochenodeoxycholic bile acid was the predominant bile acid. Dietary bile acids supplementation also increased the pr

关键词： Bile acid metabolism Tilapia Plant-based feed Cholesterol Liver health