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| 1 | Karyotype Stability and Unbiased Fractionation in the Paleo-Allotetraploid Cucurbita Genomes显示文摘 | Honghe Sun Shan WU Guoyu Zhang Chen Jiao Shaogui Guo Yi Ren Jie Zhang Haiying Zhang Guoyi Gong Zhangcai Jia Fan Zhang Jiaxing Tian William J. Lucas Jeff J. Doyle Haizhen Li Zhangjun Fei Yong Xu | 2017 | Molecular Plant2017，10，10： | 33 |
| 2 | A Genomic Variation Map Provides Insights into the Genetic Basis of Spring Chinese Cabbage (Brassica rapa ssp.pekinensis)Selection显示文摘Chinese cabbage is the most consumed leafy crop in East Asian countries.However,premature bolting induced by continuous low temperatures severely decreases the yield and quality of the Chinese cabbage, and therefore restricts its planting season and geographic distribution.In the past 40years,spring Chinese cabbage with strong winterness has been selected to meet the market demand.Here,we report a genome variation map of Chinese cabbage generated from the resequencing data of 194 geographically diverse accessions of three ecotypes.In-depth analyses of the selection sweeps and genome-wide patterns revealed that spring Chinese cabbage was selected from a specific population of autumn Chinese cabbage around the area of Shandong peninsula in northern China.We identified 23 genomic loci that underwent intensive selection,and further demonstrated by gene expression and haplotype analyses that the incorporation of elite alleles of VERNALISATION INSENTIVE 3.1(BrVIN3.1)and FLOWER LOCUS C 1(BrFLC1)is a determinant genetic source of variation during selection.Moreover,we showed that the quantitative response of BrVIN3.1 to cold due to the sequence variations in the cis elements of the BrVlN3.1 promoter significantly contributes to bolting-time variation in Chinese cabbage.Collectively, our study provides valuable insights into the genetic basis of spring Chinese cabbage selection and will facilitate the breeding of bolting-resistant Varieties by molecular-marker-assisted selection,transgenic or gene editingapproaches. | Tongbing Su Weihong Wang Peirong Li Bin Zhang Pan Li Xiaoyun Xin Honghe Sun Yangjun Yu Deshuang Zhang Xiuyun Zhao Changlong Wen Gang Zhou Yuntong Wang Hongkun Zheng Shuancang Yu Fenglan Zhang | 2018 | Molecular Plant2018，11，11： | 6 |
| 3 | A key‘foxy’aroma gene is regulated by homologyinduced promoter indels in the iconic juice grape‘Concord’显示文摘‘Concord’,the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L.,possesses a special‘foxy’aroma predominantly resulted from the accumulation of methyl anthranilate(MA)in berries.This aroma,however,is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V.vinifera.Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key‘foxy’aroma gene,anthraniloyl-CoA:methanol acyltransferase(AMAT),that is responsible for MA biosynthesis.We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in‘Concord’and other V.labrusca-derived grapes.These promoter variants,all with direct and inverted repeats,were further confirmed in more than 1,300 Vitis germplasm.Moreover,functional impact of these indels was validated in transgenic Arabidopsis.Superimposed on the promoter regulation,large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V.vinifera grapes.Elucidation of the AMAT genetic regulation advances our understanding of the‘foxy’aroma trait and makes it genetically trackable and amenable in grapevine breeding. | Yingzhen Yang JoséCuenca Nian Wang Zhenchang Liang Honghe Sun Benjamin Gutierrez Xiaojun Xi Jie Arro YiWang Peige Fan Jason Londo Peter Cousins Shaohua Li Zhangjun Fei Gan-Yuan Zhong | 2020 | Horticulture Research2020，7，1： | 3 |
| 4 | Mutation in the gene encoding 1-aminocyclopropane-1-carboxylate synthase 4 (CitACS4) led to andromonoecy in watermelon显示文摘Although it has been reported previously that ethylene plays a critical role in sex determination in cucurbit species, how the andromonoecy that carries both the male and hermaphroditic flowers is determined in watermelon is still unknown. Here we showed that the watermelon gene 1-aminocyclopropane-1-carboxylate synthase 4(Cit ACS4), expressed specifically in carpel primordia, determines the andromonoecy in watermelon. Among four single nucleotide polymorphism(SNPs) and one InDel identified in the coding region of Cit ACS4, the C364 W mutation located in the conserved box 6 was cosegregated with andromonoecy. Enzymatic analyses showed that the C364 W mutation caused a reduced activity in Cit ACS4. We believe that the reduced Cit ACS4 activity may hamper the programmed cell death in stamen primordia, leading to the formation of hermaphroditic flowers. | Gaojie Ji Jie Zhang Haiying Zhang Honghe Sun Guoyi Gong Jianting Shi Shouwei Tian Shaogui Guo Yi Ren Huolin Shen Junping Gao Yong Xu | 2016 | Journal of Integrative Plant Biology2016，58，9： | 1 |
| 5 | An in-situ spectroscopy investigation of alkali metal interaction mechanism with the imide functional group显示文摘Organic anode materials have attracted considerable interest owing to their high tunability by adopting various active functional groups.However,the interaction mechanisms between the alkali metals and the active functional groups in host materials have been rarely studied systematically.Here,a widely used organic semiconductor of perylene-3,4,9,10-tetracarboxylic diimide(PTCDI)was selected as a model system to investigate how alkali metals interact with imide functional groups and induce changes in chemical and electronic structures of PTCDI.The interaction at the alkali/PTCDI interface was probed by in-situ X-ray photoelectron spectroscopy(XPS),ultraviolet photoelectron spectroscopy(UPS),synchrotron-based near edge X-ray absorption fine structure(NEXAFS),and corroborated by density functional theory(DFT)calculations.Our results indicate that the alkali metal replaces the hydrogen atoms in the imide group and interact with the imide nitrogen of PTCDI.Electron transfer induced gap states and downward band-bending like effects are identified on the alkali-deposited PTCDI surface.It was found that Na shows a stronger electron transfer effect than Li.Such a model study of alkali insertion/intercalation in PTCDI gives insights for the exploration of the potential host materials for alkali storage applications. | Xu Lian Zhirui Ma Zhonghan Zhang Jinlin Yang Shuo Sun Chengding Gu Yuan Liu Honghe Ding Jun Hu Xu Cao Junfa Zhu Shuzhou Li Wei Chen | 2020 | Nano Research2020，13，12： | 0 |
| 6 | The monkey microbial biobank brings previously uncultivated bioresources for nonhuman primate and human gut microbiomes显示文摘Impact statement Nonhuman primates(NHPs)such as monkeys are the closest living relatives to humans and are the best available models for causative studies of human health and diseases.Gut microbiomes are intensively involved in host health.In this study,by large-scale cultivation of microbes from fecal samples of monkeys,we obtained previously uncultured bacterial species and constructed a Macaca fascicularis Gut Microbial Biobank(MfGMB).The MfGMB consisted of 250 strains that represent 97 species of 63 genera,25 families,and 4 phyla.The information of the 250 strains and the genomes of 97 cultured species are publicly accessible.The MfGMB represented nearly 50% of core gut microbial compositions at the genus level and covered over 80% of the KO-based known gut microbiome functions of M.fascicularis.Data mining showed that the bacterial species in the MfGMB were prevalent not only in NHPs gut microbiomes but also in human gut microbiomes.This study will help the understanding and future investigations on how gut microbiomes interact with their mammalian hosts. | Danhua Li Chang Liu Rexiding Abuduaini Mengxuan Du Yujing Wang Haizhen Zhu Honghe Chen Nan Zhou Yuhua Xin Linhuan Wu Juncai Ma Yuguang Zhou Yong Lu Chengying Jiang Qiang Sun Shuang-Jiang Liu | 2022 | mLife2022，1，2： | 0 |
| 7 | The role of machine learning in carbon neutrality:Catalyst property prediction,design,and synthesis for carbon dioxide reduction显示文摘Achieving carbon neutrality is an essential part of responding to climate change caused by the deforestation and over-exploitation of natural resources that have accompanied the development of human society.The carbon dioxide reduction reaction(CO_(2)RR)is a promising strategy to capture and convert carbon dioxide(CO_(2))into value-added chemical products.However,the traditional trial-and-error method makes it expensive and time-consuming to understand the deeper mechanism behind the reaction,discover novel catalysts with superior performance and lower cost,and determine optimal support structures and electrolytes for the CO_(2)RR.Emerging machine learning(ML)techniques provide an opportunity to integrate material science and artificial intelligence,which would enable chemists to extract the implicit knowledge behind data,be guided by the insights thereby gained,and be freed from performing repetitive experiments.In this perspective article,we focus on recent ad-vancements in ML-participated CO_(2)RR applications.After a brief introduction to ML techniques and the CO_(2)RR,we first focus on ML-accelerated property prediction for potential CO_(2)RR catalysts.Then we explore ML-aided prediction of catalytic activity and selectivity.This is followed by a discussion about ML-guided catalyst and electrode design.Next,the potential application of ML-assisted experimental synthesis for the CO_(2)RR is discussed. | Zhuo Wang Zhehao Sun Hang Yin Honghe Wei Zicong Peng Yoong Xin Pang Guohua Jia Haitao Zhao Cheng Heng Pang Zongyou Yin | 2023 | eScience2023，3，4： | 0 |
| 8 | Devonian integrative stratigraphy,biotas,and paleogeographical evolution of the Qinghai-Tibetan Plateau and its surrounding areas显示文摘The Devonian System in the Qinghai-Tibetan Plateau and its surrounding areas is widely distributed,diverse in lithotypes and rich in fossils.It records the crucial processes of continuous subduction and reduction of the Paleo-Asian Ocean in the northern hemisphere and the transformation of the Proto-Tethys Ocean into the Paleo-Tethys Ocean in the southern hemisphere.Thus,it is of great significance for explaining the global paleogeographic evolution,tectonic activities and biodiversity changes during this critical period.The blocks on both sides of the southern Tienshan suture zone and the Longmu Co-ShuanghuChangning-Menglian suture zone belong to different sedimentary systems and paleobiogeographic realms and regions,showing important tectonic paleogeographic partitioning significance.The two suture zones represent the main branches of the PaleoAsian Ocean and the Paleo-Tethys Ocean,respectively,and on this basis the Devonian System can be subdivided into three types:the Tienshan type,the Tethys type and the Gondwana type.Based on recent research progress on the Devonian stratigraphy and paleontology in combining provenance analysis and biotic characteristics in the Qinghai-Tibetan Plateau and surrounding areas,this paper aims to establish the latest integrative stratigraphic framework and conduct paleogeographic reconstruction,providing foundation for exploring the geological evolution and dynamic mechanisms of various terranes and blocks in the northern margin of Gondwana.The results indicate that the North Qiangtang,South Qiangtang,Simao,Baoshan and Tengchong terranes,as well as the Himalaya Tethys Zone and the South China Block have affinities with the Indian Block,while the Lhasa Terrane has affinities with the Australian Block,and may be located between the South China and Australian blocks.In the Emsian(Early Devonian),the South China Block separated from the northern margin of Gondwana,a process that was accompanied by the opening of the Jinshajiang-Ailaoshan Ocean.In the Middle Devonian,the mid-oceanic ridge of the Paleo-Tethys Ocean expanded rapidly,corresponding with a global sea-level rise,the widespread development of carbonate platforms and nadir values of Devonian seawater strontium isotopes.By the Late Devonian,the Paleo-Tethys Ocean had reached a considerable size,leading to abundant occurrences of Upper Devonian radiolarian cherts in the Paleo-Tethys suture zones. | Wenkun QIE Kun LIANG Wen GUO Biao GAO Junjun SONG Bo CHEN Pu HUANG Li QIAO Honghe XU Jitao CHEN Yucong SUN Yichun ZHANG | 2024 | Science China Earth Sciences2024，67，4： | 0 |
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