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Genomic mosaicism due to homoeologous exchange generates extensive phenotypic diversity in nascent allopolyploids

National Science Review 2021年第5期8卷 23-37页

作者： Ying Wu Fan Lin Yao Zhou Jie Wang Shuai Sun Bin Wang Zhibin Zhang Guo Li Xiuyun Lin Xutong Wang Yue Sun Qianli Dong Chunming Xu Lei Gong Jonathan F.Wendel Zhiwu Zhang Bao Liu Key Laboratory of Molecular Epigenetics of the Ministry of Education Northeast Normal University Department of Crop & Soil Sciences Washington State University Brightseed Inc. Department of Ecology Evolution& Organismal BiologyIowa State University

Allopolyploidy is an important process in plant speciation, yet newly formed allopolyploid species typically suffer from extreme genetic bottlenecks. One escape from this impasse might be homoeologous meiotic pairing, during which homoeologous exchanges(HEs) generate phenotypically variable progeny. However,the immediate genome-wide patterns and resulting phenotypic diversity generated by HEs remain largely unknown. Here, we analyzed the genome composition of 202 phenotyped euploid segmental allopolyploid individuals from the fourth selfed generation following chromosomal doubling of reciprocal F1 hybrids of crosses between rice subspecies, using whole-genome sequencing. We describe rampant occurrence of HEs that, by overcoming incompatibility or conferring superiority of hetero-cytonuclear interactions, generate extensive and individualized genomic mosaicism across the analyzed tetraploids. We show that the resulting homoeolog copy number alteration in tetraploids affects known-function genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level following a single initial hybridization. Our results illuminate the immediate genomic landscapes possible in a tetraploid genomic environment, and underscore HE as an important mechanism that fuels rapid phenotypic diversification accompanying the initial stages of allopolyploid evolution.

关键词： nascent allopolyploidy homoeologous recombination phenotypic diversity plant evolution GWAS dosage effects epistasis

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The origin and evolution of salicylic acid signaling and biosynthesis in plants

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Molecular plant 2023年第1期16卷 245-259页

作者： Xianqing Jia Long Wang Hongyu Zhao Yibo Zhang Zhixiang Chen Lei Xu Keke Yi Key Laboratory of plant Nutrition and Fertilizer Ministry of Agriculture and Rural AffairsInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081China Department of Botany and plant Pathology Center for Plant BiologyPurdue UniversityWest LafayetteIN 47907-2054USA

Salicylic acid(SA)plays a pivotal role in plant response to biotic and abiotic *** core SA signaling regulators and key proteins in SA biosynthesis have been well ***,much remains unknown about the origin,evolution,and early diversification of core elements in plant SA signaling and *** this study,we identified 10 core protein families in SA signaling and biosynthesis across green plant *** found that the key SA signaling receptors,the nonexpresser of pathogenesis-related(NPR)proteins,originated in the most recent common ancestor(MRCA)of land plants and formed divergent groups in the ancestor of seed ***,key transcription factors for SA signaling,TGACG motif-binding proteins(TGAs),originated in the MRCA of streptophytes,arguing for the stepwise evolution of core SA signaling in *** from the assembly of the core SA signaling pathway in the ancestor of seed plants,SA exists extensively in green plants,including chlorophytes and streptophyte ***,the full isochorismate synthase(ICS)-based SA synthesis pathway was first assembled in the MRCA of land *** further revealed that the ancient abnormal inflorescence meristem 1(AIM1)-basedβ-oxidation pathway is crucial for the biosynthesis of SA in chlorophyte algae,and this biosynthesis pathway may have facilitated the adaptation of early-diverging green algae to the high-light-intensity environment on *** together,our findings provide significant insights into the early evolution and diversification of plant SA signaling and biosynthesis pathways,highlighting a crucial role of SA in stress tolerance during plant terrestrialization.

关键词： salicylic acid SA signaling SA biosynthesis plant evolution high irradiance

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Loss of two families of SPX domain-containing proteins required for vacuolar polyphosphate accumulation coincides with the transition to phosphate storage in green plants

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Molecular plant 2021年第5期14卷 838-846页

作者： Long Wang Xianqing Jia Yuxin Zhang Lei Xu Benoit Menand Hongyu Zhao Houqing Zeng Liam Dolan Yiyong Zhu Keke Yi Key Laboratory of plant Nutrition and Fertilizers Ministry of Agriculture and Rural AffairsInstitute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijing 100081China Jiangsu Provincial Key Lab for Organic Solid Waste Utilization National Engineering Research Center for Organic-based FertilizersJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNanjing Agricultural UniversityNanjing 210095China Aix Marseille Univ CEACNRSBIAMLuminy Plant Genetics and Biophysics TeamMarseille 13009France College of Life and Environmental Sciences Hangzhou Normal UniversityHangzhou 311121China Gregor Mendel Institute of Molecular plant Biology GmbH Dr.Bohr-Gasse 31030 ViennaAustria

Phosphorus is an essential nutrient for *** is stored as inorganic phosphate(Pi)in the vacuoles of land plants but as inorganic polyphosphate(polyP)in chlorophyte *** it is recognized that the SPX-Major Facilitator Superfamily(MFS)and VPE proteins are responsible for Pi influx and efflux,respectively,across the tonoplast in land plants,the mechanisms that underlie polyP homeostasis and the transition of phosphorus storage forms during the evolution of green plants remain *** this study,we showed that CrPTCI,encoding a protein with both SPX and SLC(permease solute carrier 13)domains for Pi transport,and CrVTC4,encoding a protein with both SPX and vacuolar transporter chaperone(VTC)domains for polyP synthesis,are required for vacuolar polyP accumulation in the chlorophyte Chlamydomonas *** analysis showed that the SPX-SLC,SPX-VTC,and SPX-MFS proteins were present in the common ancestor of green plants(Viridiplantae).The SPX-SLC and SPX-VTC proteins are conserved among species that store phosphorus as vacuolar polyP and absent from genomes of plants that store phosphorus as vacuolar *** contrast,SPX-MFS genes are present in the genomes of streptophytes that store phosphorus as Pi in the *** results suggest that loss of SPX-SLC and SPX-VTC genes and functional conservation of SPX-MFS proteins during the evolution of streptophytes accompanied the change from ancestral polyP storage to Pi storage.

关键词： Chlamydomonas polyphosphate SPX-SLC SPX-VTC vacuolar phosphate plant evolution

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Major episodes of horizontal gene transfer drove the evolution of land plants

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Molecular plant 2022年第5期15卷 857-871页

作者： Jianchao Ma Shuanghua Wang Xiaojing Zhu Guiling Sun Guanxiao Chang Linhong Li Xiangyang Hu Shouzhou Zhang Yun Zhou Chun-Peng Song Jinling Huang State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Key Laboratory for plant Diversity and Biogeography of East Asia Yunnan Key Laboratory for Fungal Diversity and Green DevelopmentKunming Institute of BotanyChinese Academy of SciencesKunming 650201China Department of Entomology China Agricultural UniversityBeijing 100193China Shanghai Key Laboratory of Bio-Energy Crops School of Life SciencesShanghai UniversityShanghai 200444China Fairy Lake Botanical Garden Shenzhen&Chinese Academy of SciencesShenzhen 518004China Department of Biology East Carolina UniversityGreenvilleNC 27858USA

How horizontal gene transfer(HGT)has contributed to the evolution of animals and plants remains a major *** recent progress,defining the overall scale and pattern of HGT events in land plants has been largely *** this study,we performed systematic analyses for acquired genes in different plant groups and throughout land plant *** found that relatively recent HGT events occurred in char-ophytes and all major land plant groups,but their frequency declined rapidly in seed *** major ep-isodes of HGT events occurred in land plant evolution,corresponding to the early evolution of strepto-phytes and the origin of land plants,***,a vast majority of the genes acquired in the two episodes have been retained in descendant groups,affecting numerous activities and processes of land *** analyzed some of the acquired genes involved in stress responses,ion and metabolite transport,growth and development,and specialized metabolism,and further assessed the cumulative ef-fects of HGT in land plants.

关键词： plant evolution adaptation streptophytes cumulative effect stress response growth and development

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Viroids:Small Probes for Exploring the Vast Universe of RNA Trafficking in plants

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Journal of Integrative plant Biology 2010年第1期52卷 28-39页

作者： Ying Wang Biao Ding Department of plant Cellular and Molecular Biology and plant Biotechnology Center The Ohio State University The Center for RNA Biology The Ohio State University Molecular Cellular and DeVelopmental Biology Program The Ohio State University Columbus OH 43210 USA

Cell-to-cell and long-distance trafficking of RNA is a rapidly evolving frontier of integrative plant biology that broadly impacts studies on plant growth and development, spread of infectious agents and plant defense responses. The fundamental questions being pursued at the forefronts revolve around function, mechanism and evolution. In the present review, we will first use specific examples to illustrate the biological importance of cell-to-cell and long-distance trafficking of RNA. We then focus our discussion on research findings obtained using viroids that have advanced our understanding of the underlying mechanisms involved in RNA trafficking. We further use viroid examples to illustrate the great diversity of trafficking machinery evolved by plants, as well as the promise for new insights in the years ahead. Finally, we discuss the prospect of integrating findings from different experimental systems to achieve a systems-based understanding of RNA trafficking function, mechanism and evolution.

关键词： VIROIDS plant defenses RNA plant evolution plant cells & tissues

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Early Cretaceous Archaefructus eoflora sp. nov. with Bisexual Flowers from Beipiao, Western Liaoning, China

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Acta Geologica Sinica(English Edition) 2004年第4期78卷 883-896页

作者： JIQiang LIHongqi L.MichelleBOWE LIUYusheng DavidWinshipTAYLOR InstituteofGeology ChineseAcademyofGeologicalSciences26BaiwangzhuangRoadBeijing100037China／／DepartmentofEarthSciencesNanjingUniversity29HankouRoadNanjingJiangsu210008China DepartmentofBiology FrostburgStateUniversity101BraddockRoadFrostburgMD21532USA DepartmentofBiology SouthwestMissouriStateUniversity901SouthNationalAvenueSpringfieldMO65804USA DepartmentofBiology UniversityofWisconsin-StevensPointStevensPointWI54481USA DepartmentofBiology IndianaUniversitySoutheast4201GrantLineRoadNewAlbanyIN47150USA

Recently, whether Archaefructus has bisexual multi-parted flowers or just inflorescences of unisexual flowers, and whether it is ancestral to all angiosperms or a derived eudicot have been debated. Here, from the same Yixian Formation, NE China, we report a new Archaefructus species, A. eoflora sp. nov., with the generic characteristics of dissected leaves and bisexual reproductive axes. It is entirely preserved with roots, rhizome, shoots and protogynous reproductive organs at different developmental stages. Its lateral and main fertile shoots form a pseudo-indeterminate pattern, while the reproductive branches on the main shoot form a cymose inflorescence. Subtended by 1-2 bract-like leaves, the section of stamen clusters changes into a much shorter section of carpels that have one row of orthotropous ovules. Significantly, one cluster bearing two carpels and one stamen between the two sections demonstrates a true bisexual flower, an important step of the origin of floral bisexuality, and the homology between the stamen and carpel. The complex reproductive axes represent a mix between flowers and inflorescences, and suggest that A. eoflora sp. nov. possesses the potential to evolve into a variety of diverse flower types as found in modern basal and early fossil angiosperms. A comparison with other two species also leads to a revision of the generic diagnosis.

关键词： Archaefructus eoflora bisexual flower fossil angiosperm orthotropous ovules plant evolution protogynous development Lower Cretaceous Yixian Formation

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Selection in monoculture vs. mixture alters plant metabolic fingerprints

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Journal of plant Ecology 2015年第5期8卷 549-557页

作者： Debra Zuppinger-Dingley Dan F.B.Flynn Helmut Brandl Bernhard Schmid Institute of evolutionary Biology and Environmental Studies University of ZurichWinterthurerstrasse 190CH-8057 ZurichSwitzerland The Arnold Arboretum of Harvard University 1300 Centre StreetBostonMA 02131USA

Aims In grassland biodiversity experiments,positive biodiversity effects on primary productivity increase over *** research has shown that differential selection in monoculture and mixed-species communities leads to the rapid emergence of monoculture and mix-ture types,adapted to their own biotic *** used eight plant species selected for 8 years in such a biodiversity experiment to test if monoculture and mixture types differed in metabolic pro-files using infrared *** Fourier transform infrared spectroscopy(FTIr)was used to assess metabolic fingerprints of leaf samples of 10 individuals of each species from either monocultures or *** FTIr spectra were analyzed using multivariate procedures to assess(i)whether indi-viduals within species could be correctly assigned to monoculture or mixture history based on the spectra alone and(ii)which parts of the spectra drive the group assignment,*** metabolic groups were subject to differential selection in monocultures *** Findings plant individuals within each of the eight species could be classified as either from monoculture or mixture selection history based on their FTIr *** metabolic groups were differentially selected in the different species;some of them may be related to defense of patho-gens accumulating more strongly in monocultures than in *** rapid selection of the monoculture and mixture types within the eight study species could have been due to a sorting-out process based on large initial genetic or epigenetic variation within the species.

关键词： biodiversity plant evolution selection FTIr spectroscopy metabolic fingerprint

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evolution of Abscisic Acid Signaling for Stress Responses to Toxic Metals and Metalloids

Evolution of Abscisic Acid Signaling for Stress Responses to...

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第十九届中国作物学会学术年会

作者：胡蓓蓓邓锋林陈光陈萱高巍龙璐夏继星陈仲华长江大学农学院作物逆境适应与改良国家重点实验室/河南大学亚热带农业生物资源保护与利用国家重点实验室/广西大学 School of Science Western Sydney University

Toxic heavy metals and metalloids in agricultural ecosystems are crucial factors that limit global crop productivity and food safety. Industrial toxic heavy metals and metalloids such as cadmium, lead, and arsenic have contaminated large areas of arable land in the world and their accumulation in the edible parts of crops is causing serious health risks to humans and animals. plants have co-evolved with various concentrations of these toxic metals and metalloids in soil and water. Some green plant species have significant innovations in key genes for the adaptation of abiotic stress tolerance pathways that are able to tolerate heavy metals and metalloids. Increasing evidence has demonstrated that phytohormone abscisic acid(ABA) plays a vital role in the alleviation of heavy metal and metalloid stresses in plants. Here, we trace the evolutionary origins of the key gene families connecting ABA signaling with tolerance to heavy metals and metalloids in green plants. We also summarize the molecular and physiological aspects of ABA in the uptake, root-to-shoot translocation, chelation, sequestration, reutilization, and accumulation of key heavy metals and metalloids in plants. The molecular evolution and interaction between the ABA signaling pathway and mechanisms for heavy metal and metalloid tolerance are highlighted in this review. Therefore, we propose that it is promising to manipulate ABA signaling in plant tissues to reduce the uptake and accumulation of toxic heavy metals and metalloids in crops through the application of ABA-producing bacteria or ABA analogues. This may lead to improvements in tolerance of major crops to heavy metals and metalloids.

关键词： plant evolution comparative genomics cadmium arsenic lead detoxification

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