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Cryptic divergences and repeated hybridizations within the endangered “living fossil” dove tree(Davidia involucrata) revealed by whole genome resequencing

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Plant Diversity 2024年第2期46卷 169-180页

作者： Yumeng Ren Lushui Zhang Xuchen Yang Hao Lin Yupeng Sang Landi Feng jianquan liu Minghui Kang Key Laboratory of Bio-resource and Eco-environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystem College of EcologyLanzhou UniversityLanzhou 730000China Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China

The identification and understanding of cryptic intraspecific evolutionary units(lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered ***, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional ***, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

关键词： Davidia involucrata Cryptic lineage Hybridization Population genomics Positive evolution

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ACBP4-WRKY70-RAP2.12 module positively regulates submergence-induced hypoxia response in Arabidopsis thaliana

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Journal of Integrative Plant Biology 2024年第6期66卷 1052-1067页

作者： Mengyun Guo Yingjun Yao Kangqun Yin† Luna Tan Meng liu Jing Hou Han Zhang Ruyun Liang Xinran Zhang Heng Yang Xiaoxiao Chen Jinrui Tan Yan Song Shangling Lou Liyang Chen Xuejing liu Si Tang Yongqi Hu Jin Yan Wensen Fu Kai Yang Ruijia Zhang Xuerui Li Yao liu Zhen Yan Wei liu Yu Han jianquan liu Kangshan Mao Huanhuan liu Key Laboratory for Bio‐resources and Eco‐environment&State Key Lab of Hydraulics&Mountain River Engineering Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research StationKey Laboratory for Bio‐resource and Eco‐environment of Ministry of EducationCollege of Life SciencesSichuan UniversityChengdu 610065China

ACYL-CoA-BINDING PROTEINs(ACBPs)play crucial regulatory roles during plant response to hypoxia,but their molecular mechanisms remain poorly *** study reveals that ACBP4 serves as a positive regulator of the plant hypoxia response by interacting with WRKY70,influencing its nucleocytoplasmic shuttling in Arabidopsis ***,we demonstrate the direct binding of WRKY70 to the ACBP4 promoter,resulting in its upregulation and suggesting a positive feedback ***,we pinpointed a phosphorylation site at Ser638 of ACBP4,which enhances submergence tolerance,potentially by facilitating WRKY70's nuclear ***,a natural variation in this phosphorylation site of ACBP4 allowed *** to adapt to humid conditions during its historical demographic *** further observed that both phosphorylated ACBP4 and oleoyl-Co A can impede the interaction between ACBP4 and WRKY70,thus promoting WRKY70's nuclear ***,we found that the overexpression of orthologous Bna ***4and Bna ***70 in Brassica napus increases submergence tolerance,indicating their functional similarity across *** summary,our research not only sheds light on the functional significance of the ACBP4 gene in hypoxia response,but also underscores its potential utility in breeding flooding-tolerant oilseed rape varieties.

关键词： ACBP4 Arabidopsis thaliana humid adaptation natural variation RAP2.12 WRKY70

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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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Molecular Plant 2024年第5期17卷 725-746页

作者： Tingting Shi Xinxin Zhang Yukang Hou Changfu Jia Xuming Dan Yulin Zhang Yuanzhong Jiang Qiang Lai Jiajun Feng Jianju Feng Tao Ma Jiali Wu Shuyu liu Lei Zhang Zhiqin Long Liyang Chen Nathaniel R.Street Par K.Ingvarsson jianquan liu Tongming Yin Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuanChina College of Horticulture and Forestry Tarim UniversityAlar 843300China Umea Plant Science Centre Department of Plant PhysiologyUmea UniversityUmeaVasterbottenSweden Linnean Centre for Plant Biology Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China Nanjing Forestry UniversityNanjingJiangsuChina

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary ***,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental *** this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate *** the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body *** comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive *** have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration ***,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://***).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

关键词： Populus pangenomes whole-genome duplication structural variation genome evolution

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面向个性化需求的自动驾驶微公交动态调度方法

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同济大学学报（自然科学版） 2024年第11期52卷 1731-1741页

作者：涂辉招刘建泉郑叶明李浩同济大学道路与交通工程教育部重点实验室上海201804

根据个性化出行需求调查,梳理出乘坐资源、合乘意愿以及出行效率3类个性化需求。在此基础上,提出了面向个性化需求的“预约乘车+实时乘车+非固定站点”自动驾驶微公交服务模式,并构建了动态调度模型及求解算法。基于真实路网与随机订单... 详细信息

根据个性化出行需求调查,梳理出乘坐资源、合乘意愿以及出行效率3类个性化需求。在此基础上,提出了面向个性化需求的“预约乘车+实时乘车+非固定站点”自动驾驶微公交服务模式,并构建了动态调度模型及求解算法。基于真实路网与随机订单测试集开展的典型案例分析结果表明,在同样的订单需求下,提供轮椅空间和非合乘服务可显著提高订单服务率和社会公平性,但系统成本会增加。

关键词：个性化需求自动驾驶微公交动态调度

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“五育融合”视域下洛阳市民族健身操发展研究

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洛阳师范学院学报 2024年第2期43卷 38-44页

作者：刘健权洛阳师范学院公共体育教研部河南洛阳471934

从“体教结合”到“体教融合”再到“五育融合”,体育与健康课程之于国家、社会、教育与个人的重要意义不言而喻.民族健身操是一种以健美操为原型,吸收并借鉴我国少数民族舞蹈动作元素,在其基础上与健身操的编创理念、风格特征、动作技... 详细信息

从“体教结合”到“体教融合”再到“五育融合”,体育与健康课程之于国家、社会、教育与个人的重要意义不言而喻.民族健身操是一种以健美操为原型,吸收并借鉴我国少数民族舞蹈动作元素,在其基础上与健身操的编创理念、风格特征、动作技巧、创编技巧有机融合所形成的新型体育健身项目.从体育教育层面来说,民族健身操有利于激发学生的参与兴趣,能够在提高学生身体素质的同时,有效传播并推广我国民族民间舞蹈艺术和少数民族的传统文化;有利于将中华优秀传统文化融入课程,体现舞蹈与体育跨学科融合的特征,强化体育课程的综合性和实践性.为解决当前洛阳市民族健身操发展较为滞后的现实问题,要将功夫下在平时,重塑对民族健身操的价值认识,重视民族健身操项目发展,加强民族健身操教练员队伍建设,打造跨学科的师资团队,提倡“走出去”,做到多沟通、多交流、多学习.

关键词：五育融合体教融合洛阳市民族健身操

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银催化邻羟基苯基炔丙醇5-exo-dig环化反应构筑2-亚甲基-2,3-二氢苯并呋喃-3-醇

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有机化学 2024年第4期44卷 1218-1225页

作者：冯淼吕兰兰郭一佳刘建全王香善江苏师范大学化学与材料科学学院江苏徐州221116

2-亚甲基-2,3-二氢苯并呋喃衍生物作为多种天然产物及药物的核心骨架之一,寻找由简便易得原料有效合成2-亚甲基-2,3-二氢苯并呋喃的新方法具有重要的意义.开发了一种新的银催化邻羟基苯基炔丙醇的5-exo-dig环化反应,为2-亚甲基-2,3-二... 详细信息

2-亚甲基-2,3-二氢苯并呋喃衍生物作为多种天然产物及药物的核心骨架之一,寻找由简便易得原料有效合成2-亚甲基-2,3-二氢苯并呋喃的新方法具有重要的意义.开发了一种新的银催化邻羟基苯基炔丙醇的5-exo-dig环化反应,为2-亚甲基-2,3-二氢苯并呋喃的构筑提供了一种高效、模块化的方法.在室温条件下,反应仅需使用2 mol%量的银催化剂和5 mol%的异腈为配体,具有条件温和、操作简单和高效等优点.

关键词：银异腈环化炔丙醇苯并呋喃

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Genomic signature of the mangrove adaptation and demography

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National Science Review 2017年第5期4卷 737-738页

作者： jianquan liu Ministry of Education Key Laboratory for Bio-resources and Eco-environment College of Life Science Sichuan University

As the most spectacular landscape,mangroves not only attract everyone before the sea,but also maintain a unique intertidal ecosystem with diverse biodiversity as the dominant ***,these trees have to tolerate the highl... 详细信息

关键词： Genomic signature of the mangrove adaptation and demography

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Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau

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Plant Diversity 2021年第3期43卷 198-205页

作者： Bibo Yang Liangda Li jianquan liu Lushui Zhang Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu610065China

The phylogenetic position of the monotypic woody Parapteropyrum(Polygonaceae)remains *** has been thought to be closely related to the woody genera of the tribe Atraphaxideae,although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe *** this study,we used plastome data to determine the phylogenetic position of Parapteropyrum(Fagopyrum)*** reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae:Parapteropyrum(Fagopyrum)tibeticum,Atraphaxis bracteata and Calligonum *** assembled,plastomes were characterized and compared to plastomes of 12 species across the family *** analyses of Polygonaceae were performed using whole plastome,all plastome genes,and single-copy *** assembled using different reference plastomes did not differ;however,annotations showed small *** of Parapteropyrum(Fagopyrum)tibeticum,*** and *** have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp,and a total number of plastome genes of about *** microsatellites(SSR)ranged in number from 48 to *** Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus ***,our analyses indicated that sampled woody genera of the family Polygonaceae are *** study provides strong evidence that the woody Parapteropyrum tibeticum,which is distantly related to woody genera sampled here,should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum.

关键词： Woody buckwheat Atraphaxideae Plastome Phylogeny Woodiness

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Genome-scale angiosperm phylogenies based on nuclear,plastome,and mitochondrial datasets

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Journal of Integrative Plant Biology 2023年第6期65卷 1479-1489页

作者： Hongyin Hu Pengchuan Sun Yongzhi Yang Jianxiang Ma jianquan liu State Key Laboratory of Grassland Agro-Ecosystems College of EcologyLanzhou UniversityLanzhou 730000China Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China

Angiosperms dominate the Earth’s ecosystems and provide most of the basic necessities for human *** major angiosperm clades comprise 64 orders,as recognized by the APGⅣ***,the phylogenetic relationships of angiosperms remain unclear,as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized,from targeted genes to ***,we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear,plastid,and mitochondrial genomes of the same species with compatible *** phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome ***,there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were *** discuss ways to address these inconsistencies,which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of *** angiosperm phylogenies presented here provide a basic framework for further updates and *** phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

关键词： angiosperms divergence times genomic phylogenomics

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Co-occurrence prediction in a large location-based social network

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Frontiers of Computer Science 2013年第2期7卷 185-194页

作者： Rong-Hua LI jianquan liu Jeffrey Xu YU Hanxiong CHEN Hiroyuki KITAGAWA Department of System Engineering and Engineering Management The Chinese University of Hong Kong Hong Kong China Faculty of Engineering Information and systems University of TsukubaJapan Ibaraki 305-8577 Cloud System Research Laboratories NEC CorporationJapan Tokyo 108-8001

Location-based social network （LBSN） is at the forefront of emerging trends in social network services （SNS） since the users in LBSN are allowed to ＂check-in＂ the places （locations） when they visit them. The accurate geographi- cal and temporal information of these check-in actions are provided by the end-user GPS-enabled mobile devices, and recorded by the LBSN system. In this paper, we analyze and mine a big LBSN data, Gowalla, collected by us. First, we investigate the relationship between the spatio-temporal co- occurrences and social ties, and the results show that the co- occurrences are strongly correlative with the social ties. Sec- ond, we present a study of predicting two users whether or not they will meet （co-occur） at a place in a given future time, by exploring their check-in habits. In particular, we first intro- duce two new concepts, bag-of-location and bag-of-time-lag, to characterize user＇s check-in habits. Based on such bag rep- resentations, we define a similarity metric called habits sim- ilarity to measure the similarity between two users＇ check-in habits. Then we propose a machine !earning formula for pre- dicting co-occurrence based on the social ties and habits sim- ilarities. Finally, we conduct extensive experiments on our dataset, and the results demonstrate the effectiveness of the proposed method.

关键词： location-based social networks Gowalla co-occurrence

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