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Phylogenetically Distinct Cellulose Synthase Genes Support Secondary Wall Thickening in Arabidopsis Shoot Trichomes and Cotton f.ber

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Journal of.Integrative Plant Biology 2010年第2期52卷 205-220页

作者： Lissete Betancur Bir Singh Ryan A.Rapp jonathan f.wendel M. David Marks Alison W.Roberts Candace H.Haigler Department of.Plant Biology North Carolina State University Department of.Crop Science North Carolina State University EEOB Department Iowa State University Department of.Plant Biology University of Minnesota Department of.Biological Sciences CBLSUniversity of Rhode Island

Through exploring potential analogies between cotton seed trichomes （or cotton f.ber） and arabidopsis shoot trichomes we discovered that CesAs f.om either the primary or secondary wall phylogenetic clades can support secondary wall thickening. CesA genes that typically support primary wall synthesis, AtCesA 1,2,3,5, and 6, underpin expansion and secondary wall thickening of.arabidopsis shoot trichomes. In contrast, apparent orthologs of.CesA genes that support secondary wall synthesis in arabidopsis xylem, AtCesA4,7, and 8, are up-regulated f.r cotton f.ber secondary wall deposition. These conclusions arose f.om：（a） analyzing the expression of.CesA genes in arabidopsis shoot trichomes; （b） observing biref.ingent secondary walls in arabidopsis shoot trichomes with mutations in AtCesA4, 7, or 8; （c） assaying up-regulated genes during dif.erent stages of.cotton f.ber development; and （d） comparing genes that were *** with primary or secondary wall CesAs in arabidopsis with genes up- regulated in arabidopsis trichomes, arabidopsis secondary xylem, or cotton f.ber during primary or secondary wall deposition. Cumulatively, the data show that：（a） the xylem of.arabidopsis provides the best model f.r secondary wall cellulose synthesis in cotton f.ber; and （b） CesA genes within a ＂cell wall toolbox＂ are used in diverse ways f.r the construction of.particular specialized cell walls.

关键词： Phylogenetically Distinct Cellulose Synthase Genes Support Secondary Wall Thickening in Arabidopsis Shoot Trichomes and Cotton f.ber GUS

维普期刊数据库

A Malvaceae mystery: A mallow maelstrom of.genome multiplications and maybe misleading methods?

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Journal of.Integrative Plant Biology 2019年第1期61卷 12-31页

作者： Justin L.Conover Nisa Karimi Noah Stenz Cecile Ane Corrinne E.Grover Cynthia Skema Jennif.r A.Tate Kirsten Wolf. Samuel A.Logan jonathan f.wendel David A.Baum Department of.Ecology Evolutionand Organismal BiologyIowa State University Department of.Botany University of Wisconsin Madison Department of.Statistics University of Wisconsin Madison Morris Arboretum of.the University of.Pennsylvania Institute of.f.ndamental Sciences Massey University School of.Natural and Environmental Sciences Newcastle University Wisconsin Institute f.r Discovery

Previous research suggests that Gossypium has undergone a 5-to 6-f.ld multiplication f.llowing its divergence f.om Theobroma. However, the number of.events, or where they occurred in the Malvaceae phylogeny remains unknown. We analyzed transcriptomic and genomic data f.om representatives of.eight of.the nine Malvaceae subf.milies. Phylogenetic analysis of.nuclear data placed Dombeya(Dombeyoideae) as sister to the rest of.Malvadendrina clade, but the plastid DNA tree strongly supported Durio(Helicteroideae) in this position. Intraspecif.c Ks plots indicated that all sampled taxa, except Theobroma(Byttnerioideae), Corchorus(Grewioideae), and Dombeya(Dombeyoideae), have experienced whole genome multiplications(WGMs). Quartet analysis suggested WGMs were shared by Malvoideae-Bombacoideae and Sterculioideae-Tilioideae, but did not resolve whether these are shared with each other or Helicteroideae(Durio).Gene tree reconciliation and Bayesian concordance analysis suggested a complex history. Alternative hypotheses are suggested, each involving two independent autotetraploid and one allopolyploid event. They dif.er in that one entails an allopolyploid origin f.r the Durio lineage,whereas the other invokes an allopolyploid origin f.r Malvoideae-Bombacoideae. We highlight the need f.r more genomic inf.rmation in the Malvaceae and improved methods to resolve complex evolutionary histories that may include allopolyploidy, incomplete lineage sorting, and variable rates of.gene and genome evolution.

关键词： research data

维普期刊数据库

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

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

作者： Ying Wu f.n 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 f.rmed allopolyploid species typically suf.er f.om extreme genetic bottlenecks. One escape f.om 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 f.om the f.urth self.d generation f.llowing chromosomal doubling of.reciprocal f. hybrids of.crosses between rice subspecies, using whole-genome sequencing. We describe rampant occurrence of.HEs that, by overcoming incompatibility or conf.rring 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 af.ects known-f.nction genes and their complex genetic interactions, in the process creating extraordinary phenotypic diversity at the population level f.llowing 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 f.els rapid phenotypic diversif.cation accompanying the initial stages of.allopolyploid evolution.

关键词： nascent allopolyploidy homoeologous recombination phenotypic diversity plant evolution GWAS dosage ef.ects epistasis

The miR319-Targeted GhTCP4 Promotes the Transition f.om Cell Elongation to Wall Thickening in Cotton f.ber

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Molecular Plant 2020年第7期13卷 1063-1077页

作者： Jun-f.ng Cao Bo Zhao Chao-Chen Huang Zhi-Wen Chen Ting Zhao Hong-Ru Liu Guan-Jing Hu Xiao-Xia Shangguan Chun-Min Shan- Ling-Jian Wang Tian-Zhen Zhang jonathan f.wendel Xue-Ying Guan Xiao-Ya Chen National Key Laboratory of.Plant Molecular Genetics Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China Plant Stress Biology Center Institute of Plant Physiology and Ecology/CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China University of.Chinese Academy of.Sciences Shanghai 200032China School of.Lif. Science and Technology ShanghaiTech UniversityShanghai 201210China Agronomy Department College of Agriculture and BiotechnologyZhejiang UniversityHangzhouZhejiang 310058China Department of.Ecology Evolution and Organismal BiologyIowa State UniversityAmesIA 50011.USA Plant Science Research Center Shanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghai 201602China

Plant cell growth involves a complex interplay among cell-wall expansion, biosynthesis, and, in specif.c tissues, secondary cell wall (SCW) deposition, yet the coordination of.these processes remains elusive. Cotton f.ber cells are developmentally synchronous, highly elongated, and contain nearly pure cellulose when mature. Here, we report that the transcription f.ctor GhTCP4 plays an important role in balancing cotton f.ber cell elongation and wall synthesis. During f.ber development the expression of.miR319 declines while GhTCP4 transcript levels increase, with high levels of.the latter promoting SCW deposition. GhTCP4 interacts with a homeobox-containing f.ctor, GhHOX3, and repressing its transcriptional activity. GhTCP4 and GhHOX3 f.nction antagonistically to regulate cell elongation, thereby establishing temporal control of.f.ber cell transition to the SCW stage. We f.und that overexpression of.GhTCP4A upregulated and accelerated activation of.the SCW biosynthetic pathway in f.ber cells, as revealed by transcriptome and promoter activity analyses, resulting in shorter f.bers with varied lengths and thicker walls. In contrast, GhTCP4 downregulation led to slightly longer f.bers and thinner cell walls. The GhHOX3–GhTCP4 complex may represent a general mechanism of.cellular development in plants since both are conserved f.ctors in many species, thus providing us a potential molecular tool f.r the design of.f.ber traits.

关键词： cell elongation secondary cell wall cotton f.ber Gossypium hirsutum TCP microRNA

Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice

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Segmental allotetraploidy generates extensive homoeologous e...

Machine learning using the extreme gradient boosting (XGBoost) algorithm predicts 5-day delta of.SOf. score at ICU admission in COVID-19 patients

中国植物学会第十六次全国会员代表大会暨85周年学术年会

作者： Yue Sun Ying Wu Chunwu Yang Shuai Sun Xiuyun Lin Lixia Liu Chunming Xu jonathan f.wendel Lei Gong Bao Liu Key Laboratory of.Molecular Epigenetics of.the Ministry of.Education (MOE) Northeast Normal University Jilin Academy of.Agriculture Department of.Ecology Evolutionand Organismal BiologyIowa State University

Allopolyploidization,that is,concomitant merging and doubling of.two or more divergent genomes in a common nucleus/cytoplasm,is known to instantly alter genomewide transcriptome dynamics,a phenomenon ref.rred to as "transcriptomic shock." However,the immediate ef.ects of.transcriptomic alteration in generating phenotypic diversity at the population level remain ***,we employed the MassARRAY-based Sequenom platf.rm to assess and compare orthologous,allelic and homoeologous gene expression status in two tissues（leaf.and root） of.a set of.randomly chosen individuals f.om populations of.parental rice subspecies（indica and japonica）,in vitro "hybrids"（parental mixes）,reciprocal f. hybrids and reciprocal tetraploids at the 5 th-self.d generation（S5）.We show that hybridization and whole genome duplication（WGD） have opposing ef.ects on allelic and homoeologous expression in the f. hybrids and tetraploids,*** hybridization exerts strong attenuating ef.ects on allelic expression dif.erences in diploid hybrids,WGD augments the intrinsic parental dif.erences and generates extensive and variable homoeolog content which triggers diversif.cation in expression patterning among the tetraploid *** with the vast phenotypic diversity observed among the tetraploid individuals,our results provide experimental evidence in support of.the notion that allopolyploidy catalyses rapid phenotypic diversif.cation in higher *** data f.rther suggest that largely stochastic homoeolog content reshuf.ling rather than alteration in total expression level may be an important f.ature of.evolution in young segmental allopolyploids,which underlies rapid expression diversity at the population level.

关键词： homoeolog expression diversif.cation homoeolog reshuf.ling phenotypic diversity segmental allopolyploidy population transcriptomic shock

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Journal of.Intensive Medicine 2021年第2期1卷 110-116页

作者： jonathan Montomoli Luca Romeo Sara Moccia Michele Bernardini Lucia Migliorelli Daniele Berardini Abele Donati Andrea Carsetti Maria Grazia Bocci Pedro David wendel Garcia Thierry f.meaux Philippe Guerci Reto Andreas Schüpbach Can Ince Emanuele f.ontoni Matthias Peter Hilty RISC-19-ICU Investigators Department of.Anaesthesia and Intensive Care Infermi HospitalAUSL della RomagnaRimini 47923Italy Department of.Inf.rmation Engineering UniversitàPolitecnica delle MarcheAncona 60131Italy The BioRobotics Institute and Department of.Excellence in Robotics and AI Scuola Superiore Sant’AnnaPisa 56127Italy Anesthesia and Intensive Care Unit Azienda Ospedaliero Universitaria Ospedali RiunitiAncona 60126Italy Department of.Biomedical Sciences and Public Health UniversitàPolitecnica delle MarcheAncona 60126Italy Department of.Anaesthesia and Intensive Care Fondazione Policlinico Universitario A.Gemelli IRCCSUniversitàCattolica del Sacro CuoreRome 00168Italy Institute of.Intensive Care Medicine University Hospital of ZurichZurich 8091Switzerland Swiss Society of.Intensive Care Medicine Basel 4001Switzerland Department of.Anesthesiology and Critical Care Medicine University Hospital of NancyNancy 54511France Department of.Intensive Care Erasmus MC University Medical Center RotterdamRotterdam3015 GDNetherlands 不详

Background:Accurate risk stratif.cation of.critically ill patients with coronavirus disease 2019(COVID-19)is essential f.r optimizing resource allocation,delivering targeted interventions,and maximizing patient survival *** learning(ML)techniques are attracting increased interest f.r the development of.prediction models as they excel in the analysis of.complex signals in data-rich environments such as critical ***:We retrieved data on patients with COVID-19 admitted to an intensive care unit(ICU)between March and October 2020 f.om the RIsk Stratif.cation in COVID-19 patients in the Intensive Care Unit(RISC-19-ICU)*** applied the Extreme Gradient Boosting(XGBoost)algorithm to the data to predict as a binary out-come the increase or decrease in patients’Sequential Organ f.ilure Assessment(SOf.)score on day 5 af.er ICU *** model was iteratively cross-validated in dif.erent subsets of.the study ***:The f.nal study population consisted of.675 *** XGBoost model correctly predicted a decrease in SOf. score in 320/385(83%)critically ill COVID-19 patients,and an increase in the score in 210/290(72%)*** area under the mean receiver operating characteristic curve f.r XGBoost was signif.cantly higher than that f.r the logistic regression model(0.86 vs.0.69,Pf.dence interval]).Conclusions:The XGBoost model predicted the change in SOf. score in critically ill COVID-19 patients admitted to the ICU and can guide clinical decision support systems(CDSSs)aimed at optimizing available resources.

关键词： Machine learning Extreme gradient boosting(XGBoost) COVID-19 Multiple organ f.ilure Clinical decision support system(CDSS) Organ dysf.nction score