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Genome architecture and tetrasomic inheritance of autotetraploid potato

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Molecular Plant 2022年第7期15卷 1211-1226页

作者： Zhigui bao Canhui Li Guangcun Li Pei wang Zhen Peng Lin Cheng Hongbo Li Zhiyang Zhang Yuying Li wu Huang Mingwang Ye Daofeng Dong Zhukuan Cheng Peter VanderZaag Evert Jacobsen christian w.b.bachem Suomeng Dong Chunzhi Zhang Sanwen Huang Qian Zhou 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 SciencesShenzhen 518120China Key Laboratory for Potato biology of Yunnan Province The CAAS-YNNU-YINMORE Joint Academy of Potato ScienceYunnan Normal UniversityKunming 650500China Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Tuber and Root CropMinistry of Agriculture and Rural AffairsBeijing100081.China Plant breeding Wageningen University and ResearchDroevendaalsesteeg 16708 PB Wageningenthe Netherlands Vegetable Research Institute Shandong Academy of Agricultural SciencesJinan 250100China State Key Lab of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China Sunrise Potato Storage Ltd. AllistonON L9R1V3Canada Department of Plant Pathology and Key Laboratory of Plant Immunity Nanjing Agricultural UniversityNanjing 210095China Peng Cheng Laboratory Shenzhen 518055China

Potato(Solanum tuberosum)is the most consumed non-cereal food *** commercial potato cultivars are autotetraploids with highly heterozygous genomes,severely hampering genetic analyses and *** leveraging the state-of-the-art sequencing technologies and polyploid graph binning,we achieved a chromosome-scale,haplotype-resolved genome assembly of a cultivated potato,Cooperation-88(C88).lntra-haplotype comparative analyses revealed extensive sequence and expression differences in this tetraploid *** identified haplotype-specific pericentromeres on chromosomes,suggesting a distinct evolutionary trajectory of potato homologous ***,we detected double reduction events that are unevenly distributed on haplotypes in 1021 of 1034 selfing progeny,a feature of autopolyploid *** distinguishing maternal and paternal haplotype sets in C88,we simulated the origin of heterosis in cultivated tetraploid with a survey of 3110 tetra-allelic loci with deleterious mutations,which were masked in the heterozygous condition bytwo *** study provides insights into the genomic architecture of autopolyploids and will guide their breeding.

关键词： potato genome polyploid genome haplotype-resolved assembly haplotype diversity potato centromere

Phased,chromosome-scale genome assemblies of tetraploid potato reveal a complex genome,transcriptome,and predicted proteome landscape underpinning genetic diversity

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Molecular Plant 2022年第3期15卷 520-536页

作者： Genevieve Hoopes Xiaoxi Meng John P.Hamilton Sai Reddy Achakkagari Fernanda de Alves Freitas Guesdes Marie E.bolger Joseph J.Coombs Danny Esselink Natalie R.Kaiser Linda Kodde Maria Kyriakidou brian Lavrijssen Natascha van Lieshout Rachel Shereda Heather K.Tuttle brieanne Vaillancourt Joshua C.wood Jan Mde boer Nolan bornowski Peter bourke David Douches Herman Jvan Eck Dave Ellis Max J.Feldman Kyle M.Gardner Johannes C.P.Hopman Jiming Jiang walter S.De Jong Joseph C.Kuhl Richard G.Novy Stan Oome Vidyasagar Sathuvalli Ek Han Tan Remco A.Ursum M.Isabel Vales Kelly Vining Richard G.F.Visser Jack Vossen G.Craig Yencho Noelle L.Anglin christian w.b.bachem Jeffrey b.Endelman Laura M.Shannon Martina V.Stromvik Helen H.Tai bjorn Usadel C.Robin buell Richard Finkers Department of Plant biology Michigan State UniversityEast LansingMI 48824USA Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Department of Plant Science McGill UniversitySainte-Anne-de-BellevueQC H9X 3V9Canada Plant breeding Wageningen University&ResearchPlant Breeding6708 PB Wageningenthe Netherlands IbG-4 bioinformatics Forschungszentrum JülichWilhelm Johnen Str52428 JülichGermany Department of Plant Soiland Microbial SciencesMichigan State UniversityEast LansingMI 48824USA bayer Crop Science WoodlandCA 95695USA Averis Seeds b.V. 9640 AA Veendamthe Netherlands International Potato Center 1895 Avenida La MolinaLimaPeru USDA-ARS ProsserWA 99350USA Agriculture and Agri-Food Canada Fredericton Research and Development Centre FrederictonNB E3B 4Z7Canada School of Integrative Plant Science Cornell UniversityIthacaNY 14853-1901USA Department of Plant Sciences University of IdahoMoscowID 83844USA USDA-ARS Small Grains and Potato Germplasm ResearchAberdeenID 83210USA HZPC Research b.V. Edisonweg 58501 XG Jourethe Netherlands Department of Crop and Soil Science Oregon State UniversityHermistonOR 97838USA School of biology and Ecology University of Maine5735 Hitchner Hall OronoME 04469USA Department of Horticultural Sciences Texas A&M UniversityCollege StationTX 77843-2133USA Department of Horticulture Oregon State UniversityCorvallisOR 97331USA Department of Horticultural Science North Carolina State UniversityRaleighNC 27695-7609USA Department of Horticulture University of Wisconsin-MadisonMadisonWI 53706USA Department of Horticulture Michigan State UniversityEast LansingMI 48824USA Institute for biological Data Science Heinrich Heine UniversityDusseldorf40225 DusseldorfGermany Plant Resilience Institute Michigan State UniversityEast LansingMI 48824USA Present address:GenNovation b.V. Wageningenthe Netherlands

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous *** assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity,including altered coding and transcript sequences,preferential allele expression,and structural variation that collectively result in a highly complex transcriptome and predicted proteome,which are distributed across the homologous *** species contribute to the extensive allelic diversity in tetraploid cultivars,demonstrating ancestral introgressions predating modern breeding *** a clonally propagated autotetraploid that undergoes limited meiosis,dysfunctional and deleterious alleles are not purged in tetraploid *** a quarter of the loci bore mutations are predicted to have a high negative impact on protein function,complicating breeder’s efforts to reduce genetic *** StCDF1 locus controls maturity,and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent *** of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous,diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.

关键词： potato allele diversity phased assembly polyploid pan-genome wild introgressions

Efficient Algorithm forMany-Electron Angular Momentum and Spin Diagonalization on Atomic Subshells

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Communications in Computational Physics 2016年第1期19卷 192-204页

作者： christian b.Mendl Zentrum Mathematik Technische Universitat MunchenBoltzmannstraße 385748 Garching bei MunchenGermany

we devise an efficient algorithm for the symbolic calculation of irreducible angular momentum and spin(LS)eigenspaces within the n-fold antisymmetrized tensor product∧^(n)V_(u),where n is the number of electrons and u=s,p,d,…denotes the atomic *** is an essential step for dimension reduction in configurationinteraction(CI)methods applied to atomic many-electron quantum *** algorithm relies on the observation that each Lz eigenstate with maximal eigenvalue is also an L2 eigenstate(equivalently for Sz and S2),as well as the traversal of LS eigenstates using the lowering operators L−and S−.Iterative application to the remaining states in∧^(n)V_(u)leads to an implicit simultaneous diagonalization.A detailed complexity analysis for fixed n and increasing subshell number u yields run time O(u^(3n−2)).A symbolic computer algebra implementation is available online.

关键词： Angular momentum and spin symmetry atomic many-electron quantum systems symbolic computation

Pollination interactions reveal direct costs and indirect benefits of plant-plant facilitation for ecosystem engineers

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Journal of Plant Ecology 2020年第1期13卷 107-113页

作者： Gianalberto Losapio christian Schöb Department of Evolutionary biology and Environmental Studies University of ZurichZurichSwitzerland Department of Environmental Systems Science ETH ZurichZurichSwitzerland

Aims Ecosystem engineers substantially modify the environment via their impact on abiotic conditions and the biota,resulting in facilitation of associated species that would not otherwise ***,reciprocal effects are poorly understood as studies of plant–plant interactions usually estimate only benefits for associated species,while how another trophic level may mediate direct and indirect feedback effects for ecosystem engineers is hardly *** we ran a field experiment with two ecosystem engineers(Arenaria tetraquetra and Hormathophylla spinosa)blooming either alone or with associated plants to decompose net effects and to test the hypothesis that pollinator-mediated interactions provide benefits that balance costs of facilitation by ecosystem *** Findings we found that net costs of facilitation are accompanied by pollinator-mediated *** ecosystem engineers producing fewer flowers per plant,they were visited by more and more diverse pollinators per flower when blooming with associated plants than when blooming *** seed production per plant was higher when ecosystem engineers bloomed alone,fruit set and seed set varied between *** one case(***),fruit and seed sets were negatively affected by the presence of associated plants,whereas,in another case(***),fruit set and seed set were higher and unaffected when ecosystem engineers bloomed with associated plants,*** findings suggest that besides experiencing direct costs,ecosystem engineers can also benefit from facilitating other species via increasing their own visibility to ***,we highlight that pollination interactions can compensate for costs of facilitation depending on ecosystem engineer *** study illuminates how the outcome of direct plant–plant interactions might be mediated by indirect interactions including third players.

关键词： biodiversity commensalism ecosystem engineering mutualism niche construction three-way interactions

COVID-19:Insights into long-term manifestations and lockdown impacts

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Journal of Sport and Health Science 2023年第4期12卷 438-463页

作者： Erika Hilbold christian bär Thomas Thum Institute of Molecular and Translational Therapeutic Strategies(IMTTS) Hannover Medical SchoolHannover 30625Germany Fraunhofer Cluster of Excellence Immune-Mediated Diseases(CIMD) Hannover 30625Germany Fraunhofer Institute for Toxicology and Experimental Medicine(ITEM) Hannover 30625Germany

Coronaviruses are pathogens thought to primarily affect the respiratory tracts of *** outbreak of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)in 2019 was also marked mainly by its symptoms of respiratory illness,which were named coronavirus disease 2019(COVID-19).Since its initial discovery,many other symptoms have been linked to acute SARS-CoV-2 infections as well as to the long-term outcomes of COVID-19 *** these symptoms are different categories of cardiovascular diseases(CVDs),which continue to be the main cause of death *** world Health Organization estimates that 17.9 million people die from CVDs each year,accounting for~32%of all deaths *** inactivity is one of the most important behavioral risk factors for *** COVID-19 pandemic has affected CVDs as well as the physical activity in different ***,we provide an overview of the current status as well as future challenges and possible solutions.

关键词： Cardiovascular disease COVID-19 Long COVID Physical activity Return to play

Ecological intensification of agriculture through biodiversity management:introduction

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Journal of Plant Ecology 2023年第6期16卷 1-4页

作者： bernhard Schmid christian Schöb Department of Geography Remote Sensing LaboratoriesUniversity of ZurichWinterthurerstrasse 1908057 ZürichSwitzerland Universidad Rey Juan Carlos Calle Tulipán s/n28933 MóstolesSpain

A major feature of humans is that they can attain much higher population densities than any non-domestic animal species of similar body size(Damuth 1987).This is most likely due to the invention of agriculture(Herrera and Garcia-bertrand 2018),which allowed humans to manage ecosystems in such a way that as much biomass as possible is converted into food(Vitousek et al.1986).

关键词： Ecological likely agriculture

Rationality of quotients by linear actions of affine groups

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Science China Mathematics 2011年第8期54卷 1521-1532页

作者： bOGOMOLOV Fedor bHNING christian GRAF VON bOTHMER Hans-christian Department of Mathematics Courant Institute of Mathematical Sciences New York University Mathematisches Institut University of Gottingen

LetG = SLn(C)Cn be the (special) affine group. In this paper we study the representation theory of G and in particular the question of rationality for V/G, where V is a generically free G-representation. we show that the answer to this question is positive (Theorem 6.1) if the dimension of V is sufficiently large and V is indecomposable. we explicitly characterize two-step extensions 0 → S → V → Q → 0, with completely reducible S and Q, whose rationality cannot be obtained by the methods presented here (Theorem 5.3).

关键词： rationality linear group quotients affine groups

Three-Dimensional Sub-100 nm Super-Resolution Imaging of biological Samples Using a Phase Ramp in the Objective Pupil

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Nano Research 2011年第6期4卷 589-598页

作者： David baddeley Mark b. Cannell christian Soeller Department of Physiology University of Auckland Private Bag 92019 Auckland 1142 New Zealand

Localisation microscopy overcomes the diffraction limit by measuring the position of individual molecules to obtain optical images with a lateral resolution better than 30 nm. Single molecule localisation microscopy was originally demonstrated only in two dimensions but has recently been extended to three dimensions. Here we develop a new approach to three-dimensional （3D） localisation microscopy by engineering of the point-spread function （PSF） of a fluorescence microscope. by introducing a linear phase gradient between the two halves of the objective pupil plane the PSF is split into two lateral lobes whose relative position depends on defocus. Calculations suggested that the phase gradient resulting from the very small tolerances in parallelism of conventional slides made from float glass would be sufficient to generate a two-lobed PSF. we demonstrate that insertion of a suitably chosen microscope slide that occupies half the objective aperture combined with a novel fast fitting algorithm for 3D localisation estimation allows nanoscopic imaging with detail resolution well below 100 nm in all three dimensions （standard deviations of 20, 16, and 42 nm in x, y, and z directions, respectively）. The utility of the approach is shown by imaging the complex 3D distribution of microtubules in cardiac muscle cells that were stained with conventional near infrared fluorochromes. The straightforward optical setup, minimal hardware requirements and large axial localisation range make this approach suitable for many nanoscopic imaging applications.

关键词： Single molecules nanoscopy point-spread function engineering immunocytochemistry localisation microscopy

Quantizing Euclidean Motions via Double-Coset Decomposition

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Research 2019年第1期2019卷 525-540页

作者： christian wülker Sipu Ruan Gregory S.Chirikjian Johns Hopkins University BaltimoreMDUSA Department of Mechanical Engineering National University of SingaporeSingapore

Concepts from mathematical crystallography and group theory are used here to quantize the group of rigid-body motions,resulting in a“motion alphabet”with which robot motion primitives are *** these primitives it is possible to develop a dictionary of physical *** with an alphabet of the sort developed here,intelligent actions of robots in the world can be approximated with fnite sequences of characters,thereby forming the foundation of a language in which robot motion is *** particular,we use the discrete handedness-preserving symmetries of macromolecular crystals(known in mathematical crystallography as Sohncke space groups)to form a coarse discretization of the space SE(3)of rigid-body *** discretization is made fner by subdividing using the concept of double-coset *** specifcally,a very efcient,equivolumetric quantization of spatial motion can be defned using the group-theoretic concept of a double-coset decomposition of the formΓ\SE(3)/Δ,whereΓis a Sohncke space group andΔis a fnite group of rotational symmetries such as those of the *** resulting discrete alphabet is based on a very uniform sampling of SE(3)and is a tool for describing the continuous trajectories of robots and *** efcient coarse-to-fne search algorithm is presented to round of any motion sampled from the continuous group of motions to the nearest element of our *** is shown that our alphabet and this efcient rounding algorithm can be used as a geometric data structure to accelerate the performance of other sampling schemes designed for desirable dispersion or discrepancy ***,the general“signals to symbols”problem in artifcial intelligence is cast in this framework for robots moving continuously in the world.

关键词： robot primitive thereby