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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

Journal of Integrative Plant Biology 2024年第3期66卷 546-578页

作者： Guojin Zhang Hong Ma College of Life Sciences Hunan Normal UniversityChangsha 410081China Department of Biology 510 Mueller LaboratoryHuck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA

Angiosperms(flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,”hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological,and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences,dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families,and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella,Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and ***, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore,we discuss the implicatio

关键词： angiosperms evolution flowering plants nuclear gene phylogenomics phylogeny

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Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

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Journal of Integrative Plant Biology 2024年第2期66卷 228-251页

作者： Yezi Xiang Taikui Zhang Yiyong Zhao Hongjin Dong Hongyi Chen Yi Hu Chien-Hsun Huang Jun Xiang Hong Ma state Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200438China Department of Biology Howard Hughes Medical InstituteDuke UniversityDurhamNC 27708USA Department of Biology the Eberly College of Scienceand the Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA 16802USA Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggang 438000China

Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and *** we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny,with resolved relationships for orders and families with previously uncertain *** this phylogeny as a framework,molecular dating supports a Triassic origin of the crown angiosperms,followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial *** robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types,revealing a trend of parallel carpel fusions during early diversifications in eudicots,monocots,and ***,taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits;such associations of ovary,dry and fleshy fruits define several ovaryfruit"modules"each found in multiple *** of the frequent modules has an ovary containing multiple ovules,capsules and berries,and another with an ovary having one or two ovules,achenes(or other single-seeded dry fruits)and *** new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types,such as capsule and berry,that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules(such as achenes and drupes).Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications,supporting a possible role of whole-genome duplications,in combination with climate changes and animal behaviors,in angiosperm fruit and ovary diversificat

关键词： angiosperm fruit evolution MADS-box molecular clock nuclear phylogeny ovary and fruit developmental genes

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Nuclear phylogenomics of Asteraceae with increased sampling provides new insights into convergent morphological and molecular evolution

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Plant Communications 2024年第6期5卷 117-138页

作者： Guojin Zhang Junbo Yang Caifei Zhang Bohan Jiao JoséL.Panero Jie Cai Zhi-Rong Zhang Lian-Ming Gao Tiangang Gao Hong Ma College of Life Sciences Hunan Normal UniversityChangshaHunan 410081China Department of Biology the Huck Institute of the Life Sciencesthe Pennsylvania State UniversityState CollegePA 16801USA state Key Laboratory of Plant Diversity and Specialty Crops Institute of BotanyChinese Academy of SciencesBeijing 100093China Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Wuhan Botanical Garden and Sino-Africa Joint Research Center Chinese Academy of SciencesWuhan 430074China Department of Integrative Biology University of TexasAustinTX 78712USA CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Lijiang National Forest Biodiversity National Observation and Research Station Kunming Institute of BotanyChinese Academy of SciencesLijiangYunnan 674100China

Convergent morphological evolution is widespread in flowering plants,and understanding this phenomenon relies on well-resolved *** phylogenetic reconstruction using transcriptome datasets has been successful in various angiosperm groups,but it is limited to taxa with available fresh ***,which are one of the two largest angiosperm families and are important for both ecosystems and human livelihood,show multiple examples of convergent *** Asteraceae phylogenies have resolved relationships among most subfamilies and many tribes,but many phylogenetic and evolutionary questions regarding subtribes and genera remain,owing to limited ***,we increased the sampling for Asteraceae phylogenetic reconstruction using transcriptomes and genome-skimming datasets and produced nuclear phylogenetic trees with 706 species representing two-thirds of recognized *** character reconstruction supports multiple convergent evolutionary events in Asteraceae,with gains and losses of bilateral floral symmetry correlated with diversification of some subfamilies and smaller groups,*** of the calyx-related pappus may have been especially important for the success of some subtribes and *** evolutionary analyses support the likely contribution of duplications of MADS-box and TCP floral regulatory genes to innovations in floral morphology,including capitulum inflorescences and bilaterally symmetric flowers,potentially promoting the diversification of *** divergences and reductions in CYC2 gene expression are related to the gain and loss of zygomorphic *** phylogenomic work with greater taxon sampling through inclusion of genome-skimming datasets reveals the feasibility of expanded evolutionary analyses using DNA samples for understanding convergent evolution.

关键词： sunflower family floral symmetry florets capitulescence molecular clock ancestral character pappus subtribe MADS-box TCP CYC2 gene family gene expression

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Machine learning in concrete science:applications,challenges,and best practices

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npj Computational Materials 2022年第1期8卷 1192-1208页

作者： Zhanzhao Li Jinyoung Yoon Rui Zhang Farshad Rajabipour Wil V.Srubar III Ismaila Dabo Aleksandra Radlińska Department of Civil and Environmental Engineering The Pennsylvania State UniversityUniversity ParkPA16802USA Department of Structural Engineering Research Korea Institute of Civil Engineering and Building Technology(KICT)Goyang-si10223Republic of Korea Department of Civil Environmentaland Architectural EngineeringUniversity of Colorado BoulderBoulderCO80309USA Materials Science and Engineering Program University of Colorado BoulderBoulderCO80309USA Department of Materials Science and Engineering The Pennsylvania State UniversityUniversity ParkPA16802USA

Concrete,as the most widely used construction material,is inextricably connected with human *** conceptual and methodological progress in concrete science,concrete formulation for target properties remains a challenging task due to the ever-increasing complexity of cementitious *** the ability to tackle complex tasks autonomously,machine learning(ML)has demonstrated its transformative potential in concrete *** the rapid adoption of ML for concrete mixture design,there is a need to understand methodological limitations and formulate best practices in this emerging computational ***,we review the areas in which ML has positively impacted concrete science,followed by a comprehensive discussion of the implementation,application,and interpretation of ML *** conclude by outlining future directions for the concrete community to fully exploit the capabilities of ML models.

关键词： concrete directions autonomous

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Estimation of environmental effects of photovoltaic generation in North-west China

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Frontiers in Energy 2013年第4期7卷 535-543页

作者： Mengjia REN Anastasia SHCHERBAKOVA Energy and Mineral Engineering Department Pennsylvania State University University Park PA 16802 USA

In estimating emissions reductions brought about by renewables in China, much of existing research assumes that renewables displace coal power. In this paper, this assumption is challenged and the potential environmental effects of photovoltaic （PV） power in North-west China are reevaluated when the marginal generator actually being displaced is taken into account. The annual PV power generation in the North-west Grid is estimated, in this paper, to be as high as 17900GW.h in 2015, roughly equaling to the output of 1.5 nuclear power plants in the US today. The total associated emission reduction in 2015 will at most be 0.36 percent of SO2 and 0.25 percent of NOx emissions from their 2010 levels in China. Further, PV power may render no emissions reduction at all if it displaces hydropower, which is often used to meet peak demand in the North-west Grid in China. These results imply that a more cost-effective area of focus in the short- term may be on desulfurization and denitrification technologies for coal plants.

关键词： photovoltaic (PV) emission reduction North- west China marginal generator

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Survival is negatively associated with glucocorticoids in a wild ungulate neonate

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Integrative Zoology 2021年第2期16卷 214-225页

作者： Tess Michelle GINGERY Duane Richard DIEFENBACH Catharine ElizabethPRITCHARD David Charles ENSMINGER Bret Daniel WALLINGFORD Christopher Scott ROSENBERRY pennsylvania Cooperative Fish and Wildlife Research Unit Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA U.S.Geological Survey Pennsylvania Cooperative Fish and Wildlife Research UnitPennsylvania State UniversityUniversity ParkPennsylvaniaUSA Department of Ecosystem Science and Management Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA pennsylvania Game Commission 2001 Elmerton AvenueHarrisburgPennsylvaniaUSA Department of Integrative Biology University of CaliforniaBerkeleyValley Life Sciences BuildingBerkeleyCaliforniaUSA

It is unknown how ungulate physiological responses to environmental perturbation influence overall population ***,neonatal physiological responses remain poorly studied despite the importance of neonatal survival to population ***(GC)hormones potentially facilitate critical physiological and behavioral responses to environmental ***,elevated GC concentrations over time may compromise body condition and indirectly reduce *** evaluated baseline salivary cortisol(CORT;a primary GC in mammals)concentrations in 19 wild neonatal white-tailed deer(Odocoileus virginianus)in a northern(NS)and southern(SS)area in *** ranking survival models consisting of variables hypothesized to influence neonate survival(***,sex),the probability of neonate survival was best explained by CORT concentrations,where elevated CORT concentrations were associated with reduced survival probability to 12 weeks of *** concentrations were greater in the SS where predation rates and predator densities were *** the first evaluation of baseline CORT concentrations in an ungulate neonate to our knowledge,this is also the first study to demonstrate CORT concentrations are negatively associated with ungulate survival at any life *** hormones could provide a framework in which to better understand susceptibility to mortality in neonatal white-tailed deer.

关键词： neonates salivary cortisol stress survival ungulates

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RNA-Guided Genome Editing in Plants Using a CRISPR-Cas System

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Molecular Plant 2013年第6期6卷 1975-1983页

作者： Kabin Xie Yinong Yang Department of Plant Pathology and Environmental Microbiology The Huck Institute of the Life Sciences Pennsylvania State University University Park PA16802 USA

Precise and straightforward methods to edit the plant genome are much needed for functional genomics and crop improvement. Recently, RNA-guided genome editing using bacterial Type II cluster regularly interspaced short palindromic repeats （CRISPR）-associated nuclease （Cas） is emerging as an efficient tool for genome editing in microbial and animal systems. Here, we report the genome editing and targeted gene mutation in plants via the CRISPR-Cas9 sys- tem. Three guide RNAs （gRNAs） with a 20-22-nt seed region were designed to pair with distinct rice genomic sites which are followed by the protospacer-adjacent motif （PAM）. The engineered gRNAs were shown to direct the Cas9 nuclease for precise cleavage at the desired sites and introduce mutation （insertion or deletion） by error-prone non-homologous end joining DNA repairing. By analyzing the RNA-guided genome-editing events, the mutation efficiency at these target sites was estimated to be 3-8%. In addition, the off-target effect of an engineered gRNA-Cas9 was found on an imper- fectly paired genomic site, but it had lower genome-editing efficiency than the perfectly matched site. Further analysis suggests that mismatch position between gRNA seed and target DNA is an important determinant of the gRNA-Cas9 tar- geting specificity, and specific gRNAs could be designed to target more than 90% of rice genes. Our results demonstrate that the CRISPR-Cas system can be exploited as a powerful tool for gene targeting and precise genome editing in plants.

关键词： CRISPR-Cas gene targeting genome editing.

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Investigations on the Optimization of Contacts Barrier Height for the Improved Performance of ZnO/CdS/CZTS Solar Cells

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Energy Engineering 2023年第8期120卷 1803-1815页

作者： Fatiha Daoudi Abdelkrim Naas Omar Meglali Radia Boudaira Ahmed Gueddim A.M.Saeed Material Science and Informatics Laboratory University of DjelfaDjelfa17000Algeria Faculty of Sciences University of M’silaM’sila28000Algeria Department of Physics University of ConstantineConstantine25000Algeria Department of Physics Division of Science and TechnologyUniversity of EducationLahorePakistan

The numerical simulations were performed using the AMPS-1D simulator to study the effects of the CZTS as an absorber layer and the contacts’barrier height on the performance of four ZnO/CdS/CZTS solar *** obtain the best cell performances,the barrier heights of the back and front contacts were adjusted between 0.01,0.77,0.5,and 1.55 eV,*** simulations,we used the lifetime mode,and the device performances were evaluated under AM1.5 illumination *** found that the efficiency,fill factor,and open-circuit voltage were almost constant at a front contact barrier height of less than 0.31 *** short-current density was not affected by the front contact barrier *** back contact material had a significant impact on the CZTS cells *** best performance was obtained for the CZTS550 cell with JSC=29.53 mA/cm2,VOC=1.07 V,FF=0.88,andη=28.08%at barrier heights of 0.31 and 1.55 eV for front and back contacts,*** conduction band offset at the CZTS550/CdS hetero-junction was found to be spike-like with 0.21 *** obtained conversion efficiency is comparable to those previously reported in the literature.

关键词： CZTS solar cell barrier height AMPS-1D photovoltaic parameters

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Early CD8 T-cell memory precursors and terminal effectors exhibit equipotent in vivo degranulation

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Cellular & Molecular Immunology 2015年第4期12卷 400-408页

作者： Yevgeniy Yuzefpolskiy Florian M. Baumann Vandana Kalia Surojit Sarkar Center for Molecular Immunology and Infectious Diseases Department of Veterinary and Biomedical Sciences and The Huck Institutes of Life Sciences ThePennsylvania State University University Park PA USA

Early after priming, effector CD8 T cells are distinguished into memory precursor and short-lived effector cell subsets （MPECs and SLECs）. Here, we delineated a distinct in vivo heterogeneity in killer cell lectin-like receptor G1 （KLRG-1） expression, which was strongly associated with diverse MPEC and SLEC fates. These in vivo MPECs and SLECs expressed equivalent levels of cytotoxic molecules and effector cytokines. Using a unique in vivodegranulation assay, we found that the MPECs and SLECs similarly encountered infected target cells and elaborated equivalent levels of cytotoxicity in vivo. These data provide direct in vivoevidence that memory-fated ceils pass through a robust effector phase. Additionally, the preferential localization of the MPECs in the lymph nodes, where a lesser degree of cytotoxicity was elaborated, suggests that the MPECs may be protected from excessive stimulation and terminal differentiation by virtue of their differential tissue localization. These data provide novel mechanistic insights into the linear decreasing potential model of memory differentiation.

关键词： CD8 MPEC SLEC in vivo degranulation effector cytotoxicity

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Disinfection byproduct regulatory compliance surrogates and bromide-associated risk

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Journal of Environmental Sciences 2017年第8期29卷 191-207页

作者： Chelsea Kolb Royce A.Francis Jeanne M.VanBriesen Department of Ciuil and Environmental Engineering Carnegie Mellon Uniuersity Pittsburgh PA 15213 USA Department of Engineering Management and Systems Engineering The George Washington University Washington DC 20052 USA Department of Engineering and Public Policy Carnegie Mellon University Pittsburgh PA 15213 USA

Natural and anthropogenic factors can alter bromide concentrations in drinking water sources. Increasing source water bromide concentrations increases the formation and alters the speciation of disinfection byproducts（DBPs） formed during drinking water *** DBPs are more toxic than their chlorinated analogs, and thus have a greater impact on human health. However, DBPs are regulated based on the mass sum of DBPs within a given class（e.g., trihalomethanes and haloacetic acids）, not based on species-specific risk or extent of bromine incorporation. The regulated surrogate measures are intended to protect against not only the species they directly represent, but also against unregulated DBPs that are not routinely measured. Surrogates that do not incorporate effects of increasing bromide may not adequately capture human health risk associated with drinking water when source water bromide is elevated. The present study analyzes trihalomethanes（THMs）, measured as TTHM,with varying source water bromide concentrations, and assesses its correlation with brominated THM, TTHM risk and species-specific THM concentrations and associated *** potential surrogates are evaluated to assess their ability to capture THM risk under different source water bromide concentration conditions. The results of the present study indicate that TTHM does not adequately capture risk of the regulated species when source water bromide concentrations are elevated, and thus would also likely be an inadequate surrogate for many unregulated brominated species. Alternative surrogate measures,including THM3 and the bromodichloromethane concentration, are more robust surrogates for species-specific THM risk at varying source water bromide concentrations.

关键词： Disinfection byproducts Bromide Disinfection byproduct regulation Trihalomethanes Disinfection byproduct risk

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