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Phylogeny,molecular evolution,and dating of divergences in Lagerstroemia using plastome sequences

Horticultural Plant Journal 2023年第2期9卷 345-355页

作者： Jie Wang Wenchuang He Xuezhu Liao Jin Ma Wei Gao Haoqi Wang Dili Wu luke r.tembrock Zhiqiang Wu Cuihua Gu Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden PlantsCollege of Landscape and ArchitectureZhejiang A&F UniversityHangzhouZhejiang 311300China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenShenzhenGuangdong 518120China Shenzhen Middle School ShenzhenGuangdong 518000China Department of Agricultural Biology Colorado State UniversityFort CollinsCO80523USA Kunpeng Institute of Modern Agriculture at Foshan FoshanGuangdong 528200China

Lagerstroemia L.(Lythraceae)is a widely distributed genus of trees and shrubs native to tropical and subtropical environments from Southeast Asia to Australia,with numerous species highly valued as *** the plastomes of many species in this genus have been sequenced,the rates of functional gene evolution and their effect on phylogenetic analyses have not been thoroughly *** compared three plastome sequence matrices to elucidate how differences in these datasets affected phylogenetic *** phylogenetic relationships for Lagerstroemia species were reconstructed based on different plastome sequence partitions and multiple phylogenetic *** of single-nucleotide variants within different genes also provides basic data on the patterns of functional gene evolution in Lagerstroemia and may provide insights into how those mutations affect protein structure and potentially drive divergence via cytonuclear *** results as well as analyses of non-synonymous and synonymous mutations,indicate that heterotachic modes of evolution are present in functional plastome genes and should be accounted for in the analyses of molecular *** addition,divergence events within the Lagerstroemia were dated for the first *** of the divergence estimates corresponded to well-known Earth history events,such as the reduction in global temperatures at the Eocene/Oligocene *** analyses conducted in Lagerstroemia here dissects the various patterns in the divergence of Lagerstroemia and may provide a useful guide to help plant breeders,as well as the necessity of using plastomic data and as possible as to combine evidence from morphological characteristics to investigate the complicated interspecies relationship and the evolutionary dynamics of species.

关键词： Lagerstroemia L Evolutionary rate Single-nucleotide variants Molecular dating Chloroplast Codon Covarion

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Multi‑integrated genomic data for Passiflora foetida provides insights into genome size evolution and floral development in Passiflora

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Molecular Horticulture 2023年第1期3卷 19-38页

作者： Yi Zou Jie Wang Dan Peng Xiaoni Zhang luke r.tembrock Jinliang Yang Jianli Zhao Hong Liao Zhiqiang Wu Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyLaboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary EcologyInstitute of BiodiversitySchool of Ecology and Environmental ScienceYunnan UniversityKunmingYunnan 650504China College of Agriculture Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhou 350002China Department of Agricultural Biology Colorado State UniversityFort CollinsCO 80523USA Department of Agronomy and Horticulture University of Nebraska-LincolnLincolnNE 68583USA Kunpeng Institute of Modern Agriculture at Foshan Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China

Passiflora is a plant genus known for its extremely distinctive and colorful flowers and a wide range of genome size ***,how genome characteristics are related to flower traits among Passiflora species remains poorly ***,we assembled a chromosome-scale genome of ***,which belongs to the same subgenus as the commercial passionfruit *** genome of *** is smaller(424.16 Mb)and contains fewer copies of long terminal repeat retrotransposons(LTr-rTs).The disparity in LTr-rTs is one of the main contributors to the differences in genome sizes between these two species and possibly in floral ***,we observed variation in insertion times and copy numbers of LTr-rTs across different transposable element(TE)***,by integrating transcriptomic data from 33 samples(eight floral organs and flower buds at three developmental stages)with phylogenomic and metabolomic data,we conducted an in-depth analysis of the expression,phylogeny,and copy number of MIKC-type MADS-box genes and identified essential biosynthetic genes responsible for flower color and scent from glandular bracts and other floral *** study pinpoints LrT-rTs as an important player in genome size variation in Passiflora species and provides insights into future genetic improvement.

关键词： Passiflora foetida Genome assembly Transposable elements MADS-box Floral organ

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The Asian lotus (Nelumbo nucifera) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics

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Ornamental Plant research 2022年第1期2卷 8-17页

作者： Jie Wang Xuezhu Liao Cuihua Gu Kunli Xiang Jie Wang Sen Li luke r.tembrock Zhiqiang Wu Wenchuang He College of Landscape and Architecture Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden PlantsKey Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden PlantsZhejiang Agriculture&Forestry UniversityHangzhou 311300China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China College of Horticulture Shanxi Agricultural UniversityShanxi 030801China Department of Agricultural Biology Colorado State UniversityFort CollinsCO 80523USA

The Asian lotus(Nelumbo nucifera)has a history of cultivation in Asia dating back over 3,000 years where it has been an important food crop producing edible rhizomes and seeds as well as flowers of great aesthetic and cultural ***,we de novo assembled the plastomes of 316 lotus accessions including five North American lotus(***)and 311 Asian lotus(***)to construct a pan-plastome genome map,and investigate the phylogeography and genetic diversity among the only two extant species within this living fossil lineage.A total of 113 unique genes were annotated and plastome sizes varied between 163,457 and 163,672 bp with only minor differences in each of the four major genomic *** most abundant nucleotide differences among plastomes were single nucleotide variants followed by insertions/deletions and block substitutions mainly found in intergenic spacer regions of the large single copy portion of the *** well-supported genetic clusters were resolved using multiple different population structure *** different lotus types(flower,seed,rhizome,or wild)were disproportionally assigned to multiple different genetic *** pattern indicates that the domestication of Asian lotus involved multiple genetic origins and possible matrilineal *** mapping of accessions also revealed that genetic diversity is unevenly distributed with eastern China possessing the highest genetic diversity and regions such as Yunnan,Indonesian,and Thailand possessing unique *** results provide an important maternal history of Nelumbo and necessary groundwork for future studies on intergenomic gene transfer,cytonuclear incompatibility,and conservation genetics.

关键词： flowers divergence insertion

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A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales

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Horticulture research 2023年第8期10卷 85-96页

作者： Lan Lan Huiqi Zhao Suxia Xu Shenglong Kan Xiaoni Zhang Weichao Liu Xuezhu Liao luke rtembrock Yonglin ren Wayne reeve Jun Yang Zhiqiang Wu 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 SciencesShenzhen518120China School of Medical Molecularand Forensic SciencesMurdoch University6150Western Australia90 South StreetMurdochAustralia Kunpeng Institute of Modern Agriculture at Foshan Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518124China Sanya Institute Hainan Academy of Agricultural SciencesSanya572025China Institute of Tropical Horticulture research Hainan Academy of Agricultural SciencesHaikou571100China Fujian Key Laboratory of Subtropical Plant Physiology&Biochemistry Fujian Institute of Subtropical BotanyXiamen361006China Key Laboratory of Horticultural Plant Biology College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan430070China Department of Agricultural Biology Colorado State UniversityFort CollinsCO80523USA

Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the ***,the absence of genome data limits our understanding of the pathways involved in bract coloration and ***,we report a chromosome-level assembly of the giga-genome of Bougainvillea×buttiana‘Mrs Butt’,a cultivar thought to be the origin of many other Bougainvillea *** assembled genome is∼5 Gb with a scaffold N50 of 151756278 bp and contains 86572 genes which have undergone recent whole-genome *** confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales,reconstructed the relationship in the Caryophyllales at whole genome level,and found discordance between species and gene trees as the result of complex introgression *** investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales *** explore the potential formation mechanism of diverse bract colors in Bougainvillea,we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFr genes in all cultivars,which may limit anthocyanin *** findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color,and a higher expression level in the betalain biosynthetic pathway is required for colored *** improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.

关键词： evolutionary insight breeding

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The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation

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aBIOTECH 2022年第3期3卷 178-196页

作者： Xuezhu Liao Yuanjun Ye Xiaoni Zhang Dan Peng Mengmeng Hou Gaofei Fu Jianjun Tan Jianli Zhao rihong Jiang Yechun Xu Jinmei Liu Jinliang Yang Wusheng Liu luke rtembrock Genfa Zhu Zhiqiang Wu 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 SciencesShenzhen518120China Guangdong Provincial Key Lab of Ornamental Plant Germplasm Innovation and Utilization Environmental Horticulture Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou510640China Yunnan Key Laboratory of Plant reproductive Adaptation and Evolutionary Ecology Yunnan UniversityKunming650504China Guangxi Engineering and Technology research Center for Woody Spices Guangxi Key Laboratory for Cultivation and Utilization of Special Non-Timber Forest CropsGuangxi Forestry Research InstituteNanning530002China Department of Agronomy and Horticulture University of Nebraska-LincolnLincolnNE68583USA Department of Horticultural Science North Carolina State UniversityRaleighNC27607USA Department of Agricultural Biology Colorado State UniversityFort CollinsCO80523USA Kunpeng Institute of Modern Agriculture at Foshan Foshan528200China

Compared with most flowers where the showy part comprises specialized leaves(petals)directly subtending the reproductive structures,most Zingiberaceae species produce showy“flowers”through modifications of leaves(bracts)subtending the true flowers throughout an *** alismatifolia,belonging to the Zingiberaceae family,a plant species originating from Southeast Asia,has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different ***,we present the chromosome-scale genome assembly of ***“Chiang Mai Pink”and explore the underlying mechanisms of bract *** genomic analysis revealed *** contains a residual signal of whole-genome *** genes,including pigment-related genes,exhibit functional and structural differentiation resulting in diverse bract colors among *** *** addition,we identified the key genes that produce different colored bracts in ***,such as F3′5'H,DFr,ANS and several transcription factors for anthocyanin synthesis,as well as chlH and CAO in the chlorophyll synthesis pathway by conducting transcriptomic analysis,bulked segregant analysis using both DNA and rNA data,and population genomic *** work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in *** and related *** is also important to understand the variation in the evolution of the Zingiberaceae family.

关键词： Anthocyanin synthesis Siam tulip Floriculture Zingiberaceae Genome evolution

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On the Existence of robot Zombies and our Ethical Obligations to AI Systems

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Journal of Social Computing 2023年第4期4卷 270-274页

作者： luke r.Hansen the Computer Science Department Stanford UniversityStanfordCA 94305USA

As artificial intelligence algorithms improve,we will interact with programs that seem increasingly *** may never know if these algorithms are sentient,yet this quality is crucial to ethical considerations regarding their moral *** will likely have to make important decisions without a full understanding of the relevant issues and *** this ignorance,we ought to take seriously the prospect that some systems are *** would be a moral catastrophe if we were to treat them as if they were not sentient,but,in reality they are.

关键词： artificial intelligence sentience ethics

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Heme oxygenase system in hepatic ischemia-reperfusion injury

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World Journal of Gastroenterology 2010年第48期16卷 6068-6078页

作者： James A richards Stephen J Wigmore luke r Devey Centre for Inflammation research The University of EdinburghThe Queen's Medical Research Institute

Hepatic ischemia-reperfusion injury (IrI) limits access to transplantation. Heme oxygenase-1 (HO-1) is a powerful antioxidant enzyme which degrades free heme into biliverdin,free iron and carbon monoxide. HO-1 and its metabolites have the ability to modulate a wide variety of inflammatory disorders including hepatic IrI. Mechanisms of this protective effect include reduction of oxygen free radicals,alteration of macrophage and T cell phenotype. Further work is required to understand the physiological importance of the many actions of HO-1 identified experimentally,and to harness the protective effect of HO-1 for therapeutic potential.

关键词： Ischemia-reperfusion injury Heme oxygenase Transplantation Ischemic pre-conditioning

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Apologos:A Lightweight Design Method for Sociotechnical Inquiry

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Journal of Social Computing 2021年第4期2卷 297-308页

作者： luke Stark the Faculty of Information and Media Studies Western UniversityLondonN6A 0A2Canada

While scholars involved in studying the ethics and politics flowing from digital information and communication systems have sought to impact the design and deployment of digital technologies,the fast pace and iterative tempo of technical development in these contexts,and the lack of structured engagement with sociotechnical questions,have been major barriers to ensuring values are considered explicitly in the r&D *** I introduce Apologos,a lightweight design methodology informed by the author’s experience of the challenges and opportunities of interdisciplinary collaboration between computational and social sciences over a five-year ***,which is inspired by“design apologetics”,is intended as an initial mechanism to introduce technologists to the process of considering how human values impact the digital design process.

关键词： values in design values sensitive design(VSD) artificial intelligence Values@Play design methods sociotechnical ethics values

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revealing a Transformation-Induced Plasticity(TrIP)Phenomenon in a Medium-Entropy Alloy

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Acta Metallurgica Sinica(English Letters) 2020年第8期33卷 1159-1165页

作者： Ibrahim Ondicho Bernard Alunda Dicken Owino luke Otieno Melody Chepkoech Department of Mechanical Engineering Dedan Kimathi University of TechnologyPrivate Bag-10143NyeriKenya Materials Design and Manufacturing(MADEMA)GroupDedan Kimathi University of TechnologyPrivate Bag-10143Dedan KimathiNyeriKenya Department of Advanced root Industry Engineering Yuengnam UniversityGyeongsanSouth Korea Department of Mining and Minerals Processing Engineering Taita Taveta UniversityP.O.Box 635-80300VoiKenya Department of Mechanical Engineering Inha UniversityIncheonSouth Korea School of Mechanical Engineering Kyungpook National UniversityDaeguSouth Korea Department of Mechanical Engineering Howard UniversityWashingtonDCUSA

A transformation-induced plasticity phenomenon in Fe65(CoCrMnNi)35 medium-entropy alloy was *** to the X-ray diffraction patterns,the as-cast specimen contains a single-phase face-centered cubic(fcc),while low-temperature annealing at 500℃and 600℃leads to the introduction of a body-centered cubic(bcc)phase as a secondary *** increment of the annealing temperature to above 700℃eliminates the bcc phase,and the microstructure was found to contain a single-phase *** 20%true strain,an fcc-to-bcc phase transformation is observed;whereas,at 28%true strain,an fccto-hcp phase transformation takes place as an additional deformation *** strain-induced phase transformation phenomenon leads to improved tensile properties of this alloy.

关键词： Phase transformation X-ray diffraction Mechanical behavior Microstructure evolution Multicomponent alloys

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Functional genomics studies on the innate immunity of disease vectors

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Insect Science 2008年第1期15卷 15-27页

作者： luke A. Baton Lindsey Garver Zhiyong Xi George Dimopoulos W. Harry Feinstone Department of Molecular Microbiology and Immunology Malaria Research Institute Bloomberg School of Pubfic Health Johns Hopkins University Baltimore Maryland USA

The increasing availability of genome sequences and the development of highthroughput techniques for gene expression profiling and functional characterization are transforming the study of innate immunity and other areas of insect biology. Already, functional genomic approaches have enabled a quantum advance in the characterization of mosquito immune responses to malaria parasite infection, and similar high-throughput functional genomic studies of other vector-pathogen interactions can be expected in the near future. The application of microarray-based and other expression analyses provide genomewide transcriptional profiles that can be used to identify insect immune system components that are differentially regulated upon exposure to various classes of pathogens, including many important etiologic agents of human and animal diseases. The role of infection-responsive or other candidate immune genes identified through comparative genomic approaches can then be functionally characterized, either in vivo, for instance in adult mosquitoes, or in vitro using cell lines. In most insect vectors of human pathogens, germ-line transgenesis is still technically difficult and maintenance of multiple transgenic lines logistically demanding. Consequently, transient rNA interference （rNAi）-mediated gene-silencing has rapidly become the method of choice for functional characterization of candidate innate immune genes. The powerful combination of transcriptional profiling in conjunction with assays using rNAi to determine gene function, and identify regulatory pathways, together with downstream cell biological approaches to determine protein localization and interactions, will continue to provide novel insights into the role of insect innate immunity in a variety of vector-pathogen interactions. Here we review advances in functional genomics studies of innate immunity in the insect disease vectors, over the past decade, with a particular focus on the Anopheles mosquito and its respo

关键词： Anopheles genomics innate immunity insect mosquito malaria microarray,parasite Plasmodium rNA interference transcriptomics transgenesis vector

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