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innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms

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Journal of Integrative plant Biology 2022年第11期64卷 2111-2125页

作者： Yuqi Nie Liangyu Guo Fuqiang Cui Yirong Shen Xiaoxue Ye Deyin Deng Shuo Wang Jianhua Zhu Wenwu Wu State Key Laboratory of Subtropical Silviculture School of Forestry and BiotechnologyZhejiang A&F UniversityHangzhou 311300China Institute of Tropical Biosciences and Biotechnology Chinese Academy of Tropical Agricultural SciencesHaikou 571101China School of Life Sciences Anhui Agricultural UniversityHefei 230036China Department of plant Science and Landscape Architecture University of MarylandCollege ParkMaryland 20742USA

The C-repeat binding factors/dehydrationresponsive element binding protein 1 s(CBFs/DREB1 s)have been identified as major regulators of cold acclimation in many angiosperm ***,their origin and evolutionary process associated to cold responsiveness are still *** integrating multi-omics data of genomes,transcriptomes,and CBFs/DREB1 s genome-wide binding profiles,we unveil the origin and evolution of CBFs/DREB1 s and their regulatory *** collinearity and phylogeny analyses show that CBF/DREB1 is an innovation evolved from tandem duplication-derived DREBⅢgene.A subsequent event of e-whole genome duplication led to two CBF/DREB1 archetypes(CladesⅠandⅡ)in ancient *** contrast to cold-insensitivity of Clade I and their parent DREBⅢgenes,CladeⅡevolved a further innovation in cold-sensitive response and was stepwise expanded in eudicots and monocots by independent *** geological time,the duplication events were mainly enriched around the Cretaceous-Paleogene(K-Pg)boundary and/or in the Late Cenozoic Ice Age,when the global average temperature significantly ***,the duplicated CBF/DREB1 genes contributed to the rewiring of CBFs/DREB1 s-regulatory network for cold ***,our results highlight an origin and convergent evolution of CBFs/DREB1 s and their regulatory network probably for angiosperms adaptation to global cooling.

关键词： CBF/DREB1 cold acclimation global cooling ice age K-Pg boundary paleotemperature tandem duplication(TD) whole genome duplication(WGD)

Phylogenomic Mining of the Mints Reveals Multiple Mechanisms Contributing to the Evolution of Chemical Diversity in Lamiaceae

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Molecular plant 2018年第8期11卷 1084-1096页

作者： Mint Evolutionary Genomics Consortium Department of Biochemistry Purdue University West Lafayette IN 47907-2063 USA Department of plant Biology Michigan State University East Lansing MI 48824 USA Florida Museum of Natural History University of Florida Gainesville FL 32611 USA The John Innes Centre Department of Biological Chemistry Norwich NR4 7UH UK Department of Biology University of Florida Gainesville FL 32611 USA

The evolution of chemical complexity has been a major driver of plant diversification, with novel compounds serving as key innovations. The species-rich mint family （Lamiaceae） produces an enormous variety of compounds that act as attractants and defense molecules in nature and are used widely by humans as flavor additives, fragrances, and anti-herbivory agents. To elucidate the mechanisms by which such diversity evolved, we combined leaf transcriptome data from 48 Lamiaceae species and four outgroups with a robust phylogeny and chemical analyses of three terpenoid classes （monoterpenes, sesquiterpenes, and iridoids） that share and compete for precursors. Our integrated chemical-genomic-phylogenetic approach revealed that：（1） gene family expansion rather than increased enzyme promiscuity of terpene synthases is correlated with mono- and sesquiterpene diversity; （2） differential expression of core genes within the iri- doid biosynthetic pathway is associated with iridoid presence/absence; （3） generally, production of iridoids and canonical monoterpenes appears to be inversely correlated; and （4） iridoid biosynthesis is significantly associated with expression of geraniol synthase, which diverts metabolic flux away from canonical mono- terpenes, suggesting that competition for common precursors can be a central control point in specialized metabolism. These results suggest that multiple mechanisms contributed to the evolution of chemodiversity in this economically important family.

关键词： chemodiversity evolution terpene iridoid

Research Progress of Genomes of Insect Pests in Paddy Field

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Rice science 2023年第5期30卷 369-373页

作者： XU Hongxing ZHAO Xianxin LÜZhongxian LI Fei State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts Institute of Plant Protection and MicrobiologyZhejiang Academy of Agricultural SciencesHangzhou 310021China State Key Laboratory of Rice Biology and Breeding/Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests Institute of Insect SciencesZhejiang UniversityHangzhou 310058China

innovations in sequencing technology and the development of bioinformatics have allowed for studies of the genomics of many rice *** present,draft genomes of rice pests including Nilaparvata lugens,Sogatella furcifera... 详细信息

关键词： pests Chilo allowed

A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales

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Horticulture Research 2023年第8期10卷 85-96页

作者： Lan Lan Huiqi Zhao Suxia Xu Shenglong Kan Xiaoni Zhang Weichao Liu Xuezhu Liao Luke RTembrock Yonglin Ren Wayne Reeve Jun Yang Zhiqiang Wu 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 SciencesShenzhen518120China School of Medical Molecularand Forensic SciencesMurdoch University6150Western Australia90 South StreetMurdochAustralia Kunpeng Institute of Modern Agriculture at Foshan Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China Sanya Institute Hainan Academy of Agricultural SciencesSanya572025China Institute of Tropical Horticulture Research Hainan Academy of Agricultural SciencesHaikou571100China Fujian Key Laboratory of Subtropical plant Physiology&Biochemistry Fujian Institute of Subtropical BotanyXiamen361006China Key Laboratory of Horticultural plant Biology College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan430070China Department of Agricultural Biology Colorado State UniversityFort CollinsCO80523USA

Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the ***,the absence of genome data limits our understanding of the pathways involved in bract coloration and ***,we report a chromosome-level assembly of the giga-genome of Bougainvillea×buttiana‘Mrs Butt’,a cultivar thought to be the origin of many other Bougainvillea *** assembled genome is∼5 Gb with a scaffold N50 of 151756278 bp and contains 86572 genes which have undergone recent whole-genome *** confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales,reconstructed the relationship in the Caryophyllales at whole genome level,and found discordance between species and gene trees as the result of complex introgression *** investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales *** explore the potential formation mechanism of diverse bract colors in Bougainvillea,we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars,which may limit anthocyanin *** findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color,and a higher expression level in the betalain biosynthetic pathway is required for colored *** improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.

关键词： evolutionary insight breeding

Deciphering Starch Quality of Rice Kernels Using Metabolite Profiling and Pedigree Network Analysis

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Molecular plant 2012年第2期5卷 442-451页

作者： Miyako Kusano Atsushi Fukushima Naoko Fujita Yozo Okazaki Makoto Kobayashi Naoko Fujita Oitome Kaworu Ebana Kazuki Saito RIKEN plant Science Center Tsurumi Yokohama 230-0045 Japan KIHARA Institute for Biological Research Yokohama City University Totsuka Yokohama 244-0813 Japan Department of Biological Production Akita Prefectural University Akita 010-0195 Japan National Institute of Agrobiological Sciences 2-1-2 Kannondai Tsukuba Ibaraki 305-8602 Japan Graduate School of Pharmaceutical Sciences Chiba University Chiba 260-8675 Japan

The physiological properties of rice grains are immediately obvious to consumers. High-coverage metabolomic characterization of the rice diversity research set predicted a negative correlation between fatty acid and lipid levels and amylose/total starch ratio （amylose ratio）, but the reason for this is unclear. To obtain new insight into the relationships among the visual phenotypes of rice kernels, starch granule structures, amylose ratios, and metabolite changes, we investigated the metabolite changes of five Japonica cultivars with various amylose ratios and two knockout mutants （e 1, a Starch synthase Ilia （SSIIla）-deficient mutant and the SSIIla/starch branching enzyme （BE） double-knockout mutant 4019） by using mass spectrometry-based metabolomics techniques. Scanning electron microscopy clearly showed that the two mutants had unusual starch granule structures. The metabolomic compositions of two cultivars with high amylose ratios （Hoshiyutaka and Yumetoiro） exhibited similar patterns, while that of the double-knockout mutant, which has an extremely high amylose ratio, differed. Rice pedigree network analysis of the cultivars and the mutants provided insight into the association between metabolic-trait properties and their underlying genetic basis in rice breeding in Japan. Multidimensional scaling analysis revealed that the Hoshiyutaka and Yumetoiro cultivars were Indica-like, yet they are classified as Japonica subpopulations. Exploring metabolomic traits is a powerful way to follow rice genetic traces and breeding history.

关键词： starch quality traits amylose ratio metabolite profiling pedigree networks rice.

Reservoir formation conditions and key technologies for exploration and development in Qingcheng large oilfield

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Petroleum Research 2020年第3期5卷 181-201页

作者： Suotang Fu Jinhua Fu Xiaobing Niu Shixiang Li Zhiyu Wu Xinping Zhou Jiangyan Liu National Engineering Laboratory for Exploration and Development of Low-Permeability Oil&Gas Fields Xi’an City710018China PetroChina Changqing Oilfield Company Xi’an City710018China No.11 Oil Production plant PetroChina Changqing Oilfield CompanyXifeng745000China China University of Petroleum(East China) Qingdao266580China Exploration and Development Research Institute PetroChina Changqing Oilfield CompanyXi’an710018China

The Qingcheng oilfield,the largest shale oil field in China,was discovered in 2019 in source rock of Chang 7 Member of Mesozoic Yanchang Formation,Changqing Oilfield in Ordos Basin,with newly increased proven geological reserves of 358 million tons,predicted geological reserves of 693 million tons,and a total of 1.051 billion tons of shale oil *** achieves a historic breakthrough in exploration of shale oil in Chang 7 *** recent years,focusing on key issues,such as whether there develop sweet spots in source rock,whether commercial oil production capacity can be formed,and whether scale-effective development can be achieved,studies about geological conditions for shale oil accumulation have been continuously carried out,key supporting technologies have been developed,and a series of theoretical innovations and technological breakthroughs have been achieved in oil exploration in source *** results indicate that shale oil accumulation in Chang 7 Member is controlled by following ***,lacustrine black shale,dark mudstone and other high-quality source rocks lay a material foundation for shale oil ***,sandy deposits intercalated within black shale and dark mudstones are exploration sweet spots,and sandbody combination types are controlled by morphology of bottom of the lacustrine ***,reservoir properties are good due to development of micro-nano pore ***,reservoirs with high oil saturation and high gas-oil ratio are formed due to high-intensity oil charging in source *** matching of multiple factors is a key for shale oil accumulation in Chang 7 Member in Ordos *** innovation of key supporting technologies,exploration and development technologies for shale oil are developed,and substantial breakthrough on exploration and development of shale oil is *** first application of logging-seismic combination technology in loess plateau improves significantly quality of 3D seismic

关键词： Chang 7 member of Yanchang formation Shale oil Geological conditions for oil accumulation Supporting technologies for exploration and development Qingcheng oilfield Ordos basin

innovations of phosphorus sustainability:implications for the whole chain

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Frontiers of Agricultural Science and Engineering 2019年第4期6卷 321-331页

作者： Jianbo SHEN Liyang WANG Xiaoqiang JIAO Fanlei MENG Lin ZHANG Gu FENG Junling ZHANG Lixing YUAN Lin MA Yong HOU Tao ZHANG Weifeng ZHANG Guohua LI Kai ZHANG Fusuo ZHANG National Academy of Agriculture Green Development Key Laboratory of Plant-Soil InteractionsMinistry of EducationCollege of Resources and Environmental SciencesChina Agricultural UniversityBeijing 100193China Key Laboratory of Agricultural Water Resources Center for Agricultural Resources ResearchInstitute of Genetic and Developmental BiologyChinese Academy of SciencesShijiazhuang 050021China Department of Environmental Science and Engineering College of Resources and Environmental SciencesChina Agricultural UniversityBeijing 100193China

Phosphorus(P)is a non-renewable resource,therefore ensuring global food and environmental security depends upon sustainable P *** achieve this goal,sustainable P management in the upstream and downstream sectors of agriculture from mineral extraction to food consumption must be addressed *** innovation and feasibility of P sustainability are highlighted from the perspective of the whole P-based chain,including the mining and processing of P rock,production of P fertilizers,soil and rhizosphere processes involving P,absorption and utilization of P by plants,P in livestock production,as well as flow and management of P at the catchment *** paper also emphasizes the importance of recycling P and the current challenges of P ***,sustainable solutions of holistic P management are proposed from the perspective of technology improvement with policy support.

关键词： P-use efficiency recycling sustainable management the whole Pchain

Hypercompact CRISPR–Cas12j2 (CasF) enables genome editing, gene activation, and epigenome editing in plants

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plant Communications 2022年第6期3卷 131-134页

作者： Shishi Liu Simon Sretenovic Tingting Fan Yanhao Cheng Gen Li Aileen Qi Xu Tang Yang Xu Weijun Guo Zhaohui Zhong Yao He Yanling Liang Qinqin Han Xuelian Zheng Xiaofeng Gu Yiping Qi Yong Zhang Department of Biotechnology School of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaRoom 216Main BuildingNo.4Section 2North Jianshe RoadChengdu 610054China Department of plant Science and Landscape Architecture University of MarylandCollege ParkMD 20742USA Biotechnology Research Institute Chinese Academy of Agricultural SciencesBeijing 100081China Institute for Bioscience and Biotechnology Research University of MarylandRockvilleMD 20850USA

CRISPR-Cas9,-Cas12a,-Cas12b,and-Cas13 have been harnessed for genome engineering in human and plant cells(Liu et al.,2022).However,the large size of these Cas proteins(e.g.190 kDa for SpCas9)makes them difficult to deliver into cells via a viral *** development of smaller Cas proteins will lead to reduced viral vector sizes that can be more widely adopted in versatile genome engineering ***,a CRISPR-Cas12j2(CasF)system was discovered in huge phages and developed into a hypercompact genome editor due to the small size of Cas12j2(80 kDa)(Pausch et al.,2020).Unfortunately,the gene editing efficiency of Cas12j2 in Arabidopsis protoplasts using ribonucleoprotein delivery was less than one percent(Pausch et al.,2020).Further optimization of this system is clearly required if CRISPR-Cas12j2-mediated editing in plant genomes is to be adopted by the plant sciences community.

关键词： CRISPR activation system

Effects of different inputs of organic matter on the response of plant production to a soil water stress in Sahelian region

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Natural Science 2012年第12期4卷 969-975页

作者： Abdoulaye Badiane Ndeye Yacine Badiane Ndour Fatou Guèye Saliou Faye Ibrahima Ndoye Dominique Masse Research Center IRD-ISRA-UCAD of Bel-Air Laboratory of Soil Microbial Ecology and Tropical Agrosystems Dakar Senegal Research Centre IRD-ISRA Bel-Air National Laboratory for Research on Crop Production Dakar Senegal University Cheikh Anta Diop Department of Plant Biology Dakar Senegal

The aim was to study the effects of organic management like the application of organic matters on crop production. This research is placed in the context of climate change impact mitigation. A field experiment was conducted during the dry season. Rainfall inputs were simulated by irrigation to study the effects of water stress during the flowering period of a grain on the agronomic and the physiological behavior of the plant. The measurements were made on the volumetric soil moisture, stomatal conductance, and leaf area index (LAI), grain yield, straw and weight of 100 grains. The water use efficiency (WUE) and yield losses were evaluated. The results of the volumetric soil moisture showed that the use of localized input under water stress (STR-T1) recorded the lowest moisture in the surface horizons. Treatment with localized input under water stress with or without fertilization (STR-T1, STR-T1 + N) showed an ability of stomatal regulation compared to the control (STR- T0) and the input application by spreading (STR- T2). (STR-T1 + N) has initiated an early stomatal closure of the plant because of the effect of nitrogen. However, despite a more pronounced water stress with stomatal closure, the LAI and the grain yield were greater with (STR-T1) and (STR-T1 + N). The results showed that the inputs of localized organic fertilization with or without nitrogen grain yields were the highest regardless of the hydric regime applied. However the losses of grain yield were higher in treatments with organic inputs in spreading and localized under water stress. The WUE by the crop was reduced compared to the control with organic inputs under STR. In this study we show that the use of organic matter increases de farmers risk and this notion of risk is high and it is necessary to consider this risk in the proposals of technical innovations.

关键词： Organic Matter Water Stress Volumetric Soil Moisture Stomatal Conductance Leaf Area Index