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Allotetraploidization event of Coptis chinensis shared by all Ranunculales

Horticultural Plant Journal 2024年第1期10卷 288-303页

作者： Yan Zhang Weina Ge Jia Teng Yanmei Yang Jianyu Wang Zijian Yu Jiaqi Wang Qimeng Xiao Junxin Zhao Shaoqi Shen Yishan Feng Shoutong Bao Yu Li Yuxian Li Tianyu Lei Yuxin Pan Lan Zhang Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China School of Life Sciences North China University of Science and TechnologyTangshanHebei 063000China State Key lab.ratory of systematic and Evolutionary botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Coptis chinensis Franch.,also named Chinese goldthread is a member of Ranunculaceae in the order Ranunculales and represents an important lineage of early eudicots with traditional medicinal *** our study,by using syntenic analysis combined with phylogenomic analysis of *** and four other representative genomes from basal and core eudicots,we confirmed that the WGD event in *** was shared by Aquilegia coerulea and Papaver somniferum *** quickly occurred after Ranunculales diverged from other eudicots,likely a Ranunculales common tetraploidization(RCT).The synonymous nucleotide substitutions at synonymous sites distribution of syntenic blocks across these genomes showed that the evolutionary rate of the *** genome is faster than that of the *** genome by approximately 13.7%,possibly due to Papaveraceaes having an additional special tetraploidization event(PST).After Ks correction,the RCT dated to 115—130 million years ago(MYA),which was close to the divergence of Ranunculaceaes and Papaveraceaes approximately115.45—130.51 ***,we identified homologous genes related to polyploidization and speciation and constructed multiple sequence alignments with different reference ***,the event-related subgenomes in the basal genomes all showed genomic fractionation bias,suggesting a likely allopolyploid nature of the RCT,PST and T-Alpha and T-Beta events in Tetracentron *** addition,we detected that the sixteen P450 subfamilies were markedly expanded in the genomes of Ranunculales,and most of them were related to the RCT and PST *** constructed a new platform for Early Eudicot Comparative Genomic Research(http://***/***)to store more *** summary,our findings support the WGD of *** shared by Ranunculales,which is likely an allotetraploidization *** present effort offered new insights into the evolution of key polyploidization events and the genes related to second

关键词： Coptis chinensis Ranunculales Polyploidization Genomic fractionation P450 genes

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A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

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Horticultural Plant Journal 2024年第3期10卷 911-930页

作者： Yishan Feng Zhenyi Wang Qimeng Xiao Jia Teng Jianyu Wang Zijian Yu Jiaqi Wang Qiang Xu Yan Zhang Shaoqi Shen Shoutong Bao Yu Li Zimo Yan Yue Ding Zihan Liu Yuxian Li Tianyu Lei Min Yuan Xiu-Qing Li Jinpeng Wang Department of Bioinformatics School of Life SciencesNorth China University of Science and TechnologyTangshanHebei 063000China Fredericton Research and Development Centre Agriculture and Agri-Food CanadaFrederictonNew Brunswick E3B 4Z7Canada State Key lab.ratory of systematic and Evolutionary botany Institute of BotanyChinese Academy of ScienceBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global *** investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant *** genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic *** found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor *** genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant *** both its high retention of paleochromosomes and its low mutation rate,*** provides the best case in conservation of the core eudicot paleogenome.

关键词： Nyssaceae Polyploidization Multigenome alignment Evolutionary rate Autotetraploidization Karyotype evolution

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Challenging the term symbiosis in plant-microbe associations to create an understanding across sciences

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Journal of Integrative Plant Biology 2024年第1期66卷 7-11页

作者： Anna Neubauer Daniela Aros‐Mualin Vicente Mariscal Péter Szövényi Department of systematic and Evolutionary botany University of ZurichZurich 8008Switzerland Zurich‐Basel Plant Science Center Zurich 8092Switzerland Instituto de Bioquímica Vegetal y Fotosíntesis CSIC y Universidad de SevillaSevilla 41092Spain

THE IMPORTANCE OF WELL DEFINED TERMINOLOGY,Effective communication across fields and disciplines relies on well defined *** use of accurate definitions has been advocated by scientists across various disciplines(PySek... 详细信息

关键词： terminology definition fields

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(Sm/Eu/Tm)^(3+) doped tantalum semiconductor system for photovoltaic and electrochemical functionality amplification

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Journal of Rare Earths 2024年第8期42卷 1586-1594,I0007页

作者： Shaan Bibi Jaffri Khuram Shahzad Ahmad Isaac Abrahams Ibrahim A.A Materials and Environmental Chemistry lab Lab-E21Department of Environmental SciencesFatima Jinnah Women UniversityRawalpindiPakistan School of Physical and Chemical Sciences Queen Mary University of LondonLondonUnited Kingdom Department of botany and Microbiology College of ScienceKing Saud UniversityP.O.Box 2455Riyadh11451Saudi Arabia

This work reports the synthesis,characterization,and energy focused applications of the novel lanthanides co-doped tantalum pentoxide hetero-system(Sm^(3+)-Eu^(3+)-Tm^(3+):Ta_(2)O_(5)).Ln^(3+)-doped Ta_(2)O_(5) express excellent opto-electronic features reflected by the narrow band gap energy of 3.87 *** vibrations confirm the presence of Ta-O-Ta and Ta-O *** synthesized system possesses orthorhombic geometry with 59.46 nm particle *** the smoother and compact morphology,the synthesized material succeeds in augmenting the performance of different systems aimed at energy *** ambient perovskite solar cell device fabricated with the Ln^(3+)-doped Ta_(2)O_(5) as an electron transport layer excels in achieving an efficiency and fill factor of 14.17% and 76% under artificial *** device was marked by the negligible hysteresis behavior showing profound photovoltaic *** electrochemical activity of the Ln^(3+)-doped Ta_(2)O_(5) decorated electrode was evaluated for electrical charge storage potential with pseudocapacitive behavior,With the highest specific capacitance of 355.39 F/g and quicker ionic diffusion rate,the designed electrode excels conventionally used ***-catalysis of water with Ln^(3+)-doped Ta_(2)O_(5) material indicates its capacity for H_(2) production with the lowest overpotential and Tafel slope values of 148 and 121.2 mV/dec,while the O_(2) generation is comparatively *** the stable electrochemical output,this rare earth modified material has the potential to replace conventionally used environmentally perilous and costly materials.

关键词： Lanthanide doping Rare earth materials Perovskite solar cells Supercapacitors Water splitting

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Flower morphology of Allium(Amaryllidaceae)and its systematic significance

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Plant Diversity 2024年第1期46卷 3-27页

作者： Ju Eun Jang Shukherdorj Baasanmunkh Nudkhuu Nyamgerel Seung-Yoon Oh Jun-Ho Song Ziyoviddin Yusupov Komijlon Tojibaev Hyeok Jae Choi Department of Biology and Chemistry Changwon National UniversityChangwon51140Republic of Korea Department of Forest Biodiversity and Herbarium Korea National ArboretumPocheon11186Republic of Korea Department of Biology Chungbuk National UniversityCheongju28644Republic of Korea International Joint lab.for Molecular Phylogeny and Biogeography Institute of BotanyAcademy of Sciences of UzbekistanTashkent100125Uzbekistan

Allium is a complicated genus that includes approximately 1000 *** its morphology is well studied,the taxonomic importance of many morphological traits,including floral traits,are poorly ***,we examined and measured the floral characteristics of 87 accessions of 74 Allium taxa(belonging to 30 sections and nine subgenera)from Central to Eastern Asian *** then examined the taxonomic relationships between select flower characteristics and a phylogenetic tree based on ITS *** results confirm that floral morphology provides key taxonomic information to assess species delimitation in *** found that perianth color is an important characteristic within the ***,Polyprason,and *** ***,Cepa,and Rhizirideum,significant characteristics include ovary shape,perianth shape,and inner tepal *** species in ***,the key taxonomic character is ovule number(only one ovule in per locule).In the ***,Cepa,Polyprason,and Reticulatobulbosa,which belong to the third evolutionary line of Allium,hood-like appendages occur in the ovary,although these do not occur in *** results also indicated that the flower morphology of several species in some sections are not clearly distinguished,e.g.,***(***)and ***(***).This study provides detailed photographs and descriptions of floral characteristics and information on general distributions,habitats,and phenology of the studied taxa.

关键词： Allium Flower morphology Pistil character Statistical analysis Significant characteristic Species level

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A fossil-calibrated relaxed clock for Ephedra indicates an Oligocene age for the divergence of Asian and New World clades and Miocene dispersal into South America

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Journal of systematics and Evolution 2009年第5期47卷 444-456页

作者： Stefanie M.ICKERT-BOND Catarina RYDIN Susanne S.RENNER University of Alaska UA Museum of the North Herbarium and Institute of Arctic Biology Institute of systematic botany University of Zurich University of Munich Systematic Botany and Mycology

Ephedra comprises approximately 50 species,which are roughly equally distributed between the Old and New World deserts,but not in the intervening regions(amphitropical range).Great heterogeneity in the substitution rates of Gnetales(Ephedra,Gnetum,and Welwitschia) has made it difficult to infer the ages of the major divergence events in Ephedra,such as the timing of the Beringian disjunction in the genus and the entry into South ***,we use data from as many Gnetales species and genes as availab.e from GenBank and from a recent study to investigate the timing of the major divergence *** of the tradeoff between the amount of missing data and taxon/gene sampling,we reduced the initial matrix of 265 accessions and 12 loci to 95 accessions and 10 loci,and further to 42 species(and 7736 aligned nucleotides) to achieve stationary distributions in the Bayesian molecular clock *** from a relaxed clock with an uncorrelated rates model and fossil-based calibration reveal that New World species are monophyletic and diverged from their mostly Asian sister clade some 30 mya,fitting with many other Beringian *** split between the single North American and the single South American clade occurred approximately 25 mya,well before the closure of the Panamanian ***,the biogeographic history of Ephedra appears dominated by long-distance dispersal,but finer-scale studies are needed to test this hypothesis.

关键词： biogeography Ephedra relaxed molecular clock dating uncorrelated rates model.

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Disentangling confusions in inflorescence morphology:Patterns and diversity of reproductive shoot ramification in angiosperms

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Journal of systematics and Evolution 2010年第4期48卷 225-239页

作者： Peter K.ENDRESS Institute of systematic botany University of Zurich

Terminology of inflorescence diversity has often been used in a confusing way in the literature,partly because it was based on uncritical and outdated *** particular,the terms cyme,thyrse,and panicle have been *** a more critical classification worked out by several authors is availab.e,it is unfortunately not in general use because most of the relevant publications are written in *** addition,some terms have not been used in the same way by morphologists and developmental *** present review attempts to remedy the situation with a simple outline of a classification based on:(i)different branching patterns;(ii)differential elongation of axes of different orders;and(iii)repetition of basic ramification patterns in different *** and cymose branching are two extreme patterns;the former with limitation of axial orders to two,the second with limitation of lateral axes of each order to *** a branching system,a sequence of racemose→cymose and,within the cyme,of dichasial→monochasial is common,but the reverse sequence generally does not *** and evolutionary aspects of inflorescences are briefly *** patterns are often stable in larger *** of mutants studied in developmental genetic studies are mainly altered in flower or branch numbers or relative branch length,but not in branching *** is also a contribution towards the goal of a unified terminology for the different fields of biology dealing with inflorescences.

关键词： branching patterns cymose inflorescence panicle racemose reproductive shoot thyrse

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The origin and evolution of carpels and fruits from an evo-devo perspective

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Journal of Integrative Plant Biology 2023年第2期65卷 283-298页

作者： Hongyan Liu Jun Li Pichang Gong Chaoying He State Key lab.ratory of systematic and Evolutionary botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China The Innovative Academy of Seed Design Chinese Academy of SciencesBeijing 100101China

The flower is an evolutionary innovation in angiosperms that drives the evolution of *** carpel is integral to a flower and develops into fruits after fertilization,while the perianth,consisting of the calyx and corolla,is decorative to facilitate pollination and protect the internal organs,including the carpels and ***,the nature of flower origin is carpel and stamen origin,which represents one of the greatest and fundamental unresolved issues in plant evolutionary ***,we briefly summarize the main progress and key genes identified for understanding floral development,focusing on the origin and development of the *** ABC models have played pioneering roles in elucidating flower development,but remain insufficient for resolving flower and carpel *** genetic basis for carpel origin and subsequent diversification leading to fruit diversity also remains *** on current research progress and technological advances,simplified floral models and integrative evolutionary-developmental(evodevo)strategies are proposed for elucidating the genetics of carpel origin and fruit *** birth of a few master regulatory genes and subsequent functional diversification might play a pivotal role in these evolutionary *** the identified transcription factors,AGAMOUS(AG)and CRABS CLAW(CRC)may be the two core regulatory genes for carpel origin as they determine carpel organ identity,determinacy,and ***,a comparative identification of their protein-protein interactions and downstream target genes between flowering and non-flowering plants from an evo-devo perspective may be primary projects for elucidating carpel origin and development.

关键词： AGAMOUS CRABS CLAW carpel origin evo-devo floral development fruit evolution

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A new type of cell related to organ movement for selfing in plants

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National Science Review 2023年第9期10卷 190-203页

作者： Yin-Zheng Wang Yan-Xiang Lin Qi Liu Jing Liu Spencer C.H.Barrett State Key lab.ratory of systematic and Evolutionary botany Institute of BotanyChinese Academy of Sciences China National Botanical Garden College of Life Sciences University of Chinese Academy of Sciences College of Pharmacy Fujian University of Traditional Chinese Medicine Department of Ecology and Evolutionary Biology University of Toronto

Many plants employ osmotic and hydrostatic pressure to generate movement for survival,but little is known about the cellular mechanisms ***,we report a new cell type in angiosperms termed ’contractile cells’ in the stigmas of the flowering plant Chirita pumila with a much-expanded rough endoplasmic reticulum(RER).Cryo-scanning electron microscopy and transmission electron microscopy analyses revealed that the RER is continuously distributed throughout the entirety of cells,confirmed by endoplasmic reticulum(ER)-specific fluorescent lab.ling,and is distinct from the common feature of plant *** RER is water-sensitive and extremely elongated with water *** show that the contractile cells drive circadian stigma closing-bending movements in response to day-to-night moisture ***-seq analyses demonstrated that contractile cells have distinct molecular ***,multiple microstructural changes in stigma movements convert an anti-selfing structure into a device promoting selfing—a unique cellular mechanism of reproductive adaptation for uncertain pollination environments.

关键词： stigma movement rough endoplasmic reticulum contractile cells circadian moisture changes reproductive transition

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WheatCENet:A Database for Comparative Co-expression Network Analysis of Allohexaploid Wheat and Its Progenitors

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Genomics, Proteomics & Bioinformatics 2023年第2期21卷 324-336页

作者： Zhongqiu Li Yiheng Hu Xuelian Ma Lingling Da Jiajie She Yue Liu Xin Yi Yaxin Cao Wenying Xu Yuannian Jiao Zhen Su State Key lab.ratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBejing 100193China StateKey lab.ratory of systematic and Eolutionary botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Bejing 100049China

Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory ***,using large-scale transcriptome data,we constructed co-expression networks for diploid,tetraploid,and hexaploid wheat species,and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors,named *** is a platform for searching and comparing specific functional coexpression networks,as well as identifying the related functions of the genes clustered *** annotations like pathways,gene families,protein-protein interactions,microRNAs(miRNAs),and several lines of epigenome data are integrated into this platform,and Gene Ontology(GO)annotation,gene set enrichment analysis(GSEA),motif identification,and other useful tools are also *** WheatCENet,we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION I(WAPOI)has more co-expressed genes related to spike development in hexaploid wheat than its *** also found a novel motif of CCWWWWWWGG(CArG)specifically in the promoter region of WAPO-Al,suggesting that neofunctionalization of the WAPO-AI gene affects spikelet development in hexaploid *** is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat.

关键词： Co-expression network Species comparison Diploid and polyploid wheat Functional annotation

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