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Genetic Analyses of Meiotic Recombination in Arabidopsis

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Journal of Integrative plant Biology 2007年第8期49卷 1199-1207页

作者： Asela J.Wijeratne Intercollege Graduate Program in plant Biology Department of Biology and the Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA

Meiosis is essential for sexual reproduction and recombination is a critical step required for normal meiosis. Understanding the underlying molecular mechanisms that regulate recombination is important for medical, agricultural and ecological reasons. Readily available molecular and cytological tools make Arabidopsis an excellent system to study meiosis. Here we review recent developments in molecular genetic analyses on meiotic recombination. These include studies on plant homologs of yeast and animal genes, as well as novel genes that were first identified in plants. The characterizations of these genes have demonstrated essential functions from the initiation of recombination by double-strand breaks to repair of such breaks, from the formation of doubie-HoUiday junctions to possible resolution of these junctions, both of which are critical for crossover formation. The recent advances have ushered a new era in plant meiosis, in which the combination of genetics, genomics, and molecular cytology can uncover important gene functions.

关键词： Arabidopsis crossover formation double-Holliday junction resolution double-strand break repair model interference meioticrecombination

Phylogenetic Analysis of the plant-specific Zinc Finger-Homeobox and Mini Zinc Finger Gene Families

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Journal of Integrative plant Biology 2008年第8期50卷 1031-1045页

作者： Claude W. dePamphilis department of Biology and the huck institutes of the life sciences Pennsylvania State University University ParkPA 16802 USA

Zinc finger-homeodomain proteins （ZHD） are present in many plants; however, the evolutionary history of the ZHD gene family remains largely unknown. We show here that ZHD genes are plant-specific, nearly all intronless, and related to MINI ZINC FINGER （MIF） genes that possess only the zinc finger. Phylogenetic analyses of ZHD genes from representative land plants suggest that *** plant ZHD genes occupy basal positions and angiosperm homologs form seven distinct clades. Several clades contain genes from two or more major angiosperm groups, including eudicots, monocots, magnoliids, and other basal angiosperms, indicating that several duplications occurred before the diversification of flowering plants. In addition, specific lineages have experienced more recent duplications. Unlike the ZHD genes, MIFs are found only from seed plants, possibly derived from ZHDs by loss of the homeodomain before the divergence of seed plants. Moreover, the MIF genes have also undergone relatively recent gene duplications. Finally, genome duplication might have contributed substantially to the expansion of family size in angiosperms and caused a high level of functional redundancy/overlap in these genes.

关键词： gene duplication gene family evolution Mini Zinc Finger Physcomitrella poplar Selaginella zinc finger-homeodomain proteins

Efficient expression of multiple guide RNAs for CRISPR/Cas genome editing

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aBIOTECH 2020年第2期1卷 123-134页

作者： Vicki Hsieh-Feng Yinong Yang Intercollege Graduate Degree Program in plant Biology The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA department of plant pathology and Environmental Microbiology The Pennsylvania State UniversityUniversity ParkPA 16802USA

The Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein system(CRISPR/Cas)has recently become the most powerful tool available for genome engineering in various *** efficient and proper expression of multiple guide RNAs(gRNAs),the CRISPR/Cas system is particularly suitable for multiplex genome *** the past several years,different CRISPR/Cas expression strategies,such as two-component transcriptional unit,single transcriptional unit,and bidirectional promoter systems,have been developed to efficiently express gRNAs as well as Cas *** progress has been made to optimize gRNA production using different types of promoters and RNA processing strategies such as ribozymes,endogenous RNases,and exogenous endoribonuclease(Csy4).Besides being constitutively and ubiquitously expressed,inducible and spatiotemporal regulations of gRNA expression have been demonstrated using inducible,tissue-specific,and/or synthetic promoters for specific research *** recently,the emergence of CRISPR/Cas ribonucleoprotein delivery methods,such as engineered nanoparticles,further revolutionized transgene-free and multiplex genome *** this review,we discuss current strategies and future perspectives for efficient expression and engineering of gRNAs with a goal to facilitate CRISPR/Cas-based multiplex genome editing.

关键词： CRISPR/Cas Gene expression Genome engineering Guide RNA Multiplex editing

Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

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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

Genome-wide Analysis of Kelch Repeatcontaining F-box Family

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Journal of Integrative plant Biology 2007年第6期49卷 940-952页

作者： Yujin Sun Xiaofan Zhou Hong Ma department of Biology and the huck institutes of life sciences Intercollege Graduate Program in Cell and Developmental Biology The Pennsylvania State University University Park PA 16802 USA

The ubiquitin-dependent protein degradation pathway plays diverse roles in eukaryotes. Previous studies indicate that both F-box and Kelch motifs are common in a variety of organisms. F-box proteins are subunits of E3 ubiquitin ligase complexes called SCFs （SKP1, Cullinl, F-box protein, and Rbxl）; they have an N-terminal F-box motif that binds to SKP1 （S-phase kinase associated protein）, and often have C-terminal protein-protein interaction domains, which specify the protein substrates for degradation via the ubiquitin pathway. One of the most frequently found protein interaction domains in F-box proteins is the Kelch repeat domain. Although both the F-box and Kelch repeats are ancient motifs, Kelch repeats-containing F-box proteins （KFB） have only been reported for human and Arabidopsis previously. The recent sequencing of the rice genome and other plant genomes provides an opportunity to examine the possible evolution history of KFB. We carried out extensive BLAST searches to identify putative KFBs in selected organisms, and analyzed their relationships phylogenetically. We also carried out the analysis of both gene duplication and gene expression of the KFBs in rice and Arabidopsis. Our study indicates that the origin of KFBs occurs before the divergence of animals and plants, and plant KFBs underwent rapid gene duplications.

关键词： Arabidopsis thaliana F-box motif Kelch repeats Kelch repeats-containing F-box proteins SCF SKP1 like.

Analyses of functional conservation and divergence reveal requirement of b HLH010/089/091 for pollen development at elevated temperature in Arabidopsis

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Journal of Genetics and Genomics 2020年第8期47卷 477-492页

作者： Ying Fu Mengyu Li Shiting Zhang Qi Yang Engao Zhu Chenjiang You Ji Qi Hong Ma Fang Chang State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and Institute of Biodiversity SciencesInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China department of Biology The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA

The Arabidopsis b HLH010/089/091(basic helix-loop-helix)genes are functionally redundant and are required for both anther development and normal expression of DYT1-activated anther-related *** three genes are conserved in Brassicaceae,suggesting that each of them is under selection pressure;however,little is known about the possible functional differences among these b HLH genes and between the b HLH and DYT1 ***,we compared novel anther transcriptomic data sets from b HLH010/089/091 single and double mutants,with an anther transcriptomic data set from the wild type(WT)and a previously obtained anther transcriptomic data set from the bhlh010 bhlh089 bhlh091 triple *** results revealed molecular phenotypes that support the functional redundancy and divergence of b HLH010,b HLH089,and b HLH091,as well as the functional overlap and difference between them and ***-binding analyses revealed that DYT1 and b HLH089 specifically recognize the TCATGTGC box to activate the expression of target genes,including ATA20,EXL4,and *** addition,among genes whose expression was affected in the bhlh010 bhlh089 double and bhlh010 bhlh089 bhlh091 triple mutants,genes that are involved in the stress response and cell signaling were enriched,which included256 genes whose expression was preferentially induced by heat during early flower ***,the bhlh double mutants exhibited defective pollen development when the plants were grown under elevated temperature,suggesting that b HLH genes are important for anther gene expression under such *** results are consistent with the observation that the heat-induced expression of several genes is less in the bhlh mutants than that in the ***,our results provide important insights into the molecular mechanism underlying the activation of direct targets by DYT1-b HLH089 heterodimers and demonstrate the protective roles of b HLH010/089/091 in maintaining fertility upon heat stress.

关键词： DYT1 bHLH010/089/091 Male fertility Molecular phenotype Transcriptional activation Heat response

Single-nucleotide editing for zebra3 and wsl5 phenotypes in rice using CRISPR/Cas9-mediated adenine base editors

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aBIOTECH 2020年第2期1卷 106-118页

作者： Kutubuddin A.Molla Justin Shih Yinong Yang department of plant pathology and Environmental Microbiology and the huck Institute of the life sciences The Pennsylvania State UniversityUniversity ParkPA 16802USA ICAR-National Rice Research Institute Cuttack 753006India

The CRISPR/Cas9-mediated base editing technology can efficiently generate point mutations in the genome without introducing a double-strand break(DSB)or supplying a DNA donor template for homology-directed repair(HDR).In this study,adenine base editors(ABEs)were used for rapid generation of precise point mutations in two distinct genes,OsWSL5,and OsZEBRA3(Z3),in both rice protoplasts and regenerated *** precisely engineered point mutations were stably inherited to subsequent *** single nucleotide alterations resulted in single amino acid changes and associated wsl5 and z3 phenotypes as evidenced by white stripe leaf and light green/dark green leaf pattern,*** selfing and genetic segregation,transgene-free,base edited wsl5 and z3 mutants were obtained in a short period of *** noticed a novel mutation(V540A)in Z3 locus could also mimic the phenotype of Z3 mutation(S542P).Furthermore,we observed unexpected non-A/G or T/C mutations in the ABE editing window in a few of the edited *** ABE vectors and the method from this study could be used to simultaneously generate point mutations in multiple target genes in a single transformation and serve as a useful base editing tool for crop improvement as well as basic studies in plant biology.

关键词： Adenine base editor CRISPR/Cas9 genome editing plant base editing Precise point mutation Transgene-free rice

Regulation of Arabidopsis Early Anther Development by Putative Cell-Cell Signaling Molecules and Transcriptional Regulators

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Journal of Integrative plant Biology 2007年第1期49卷 60-68页

作者： Yu-Jin Sun Carey LH Hord Chang-Bin Chen Hong Ma department of Biology and the huck institutes of the life sciences Pennsylvania State University University Park PA 16802 USA The Integrative Bioscience Graduate Program Pennsylvania State University University Park PA 16802 USA

Anther development in flowering plants involves the formation of several cell types, including the tapetal and pollen mother cells. The use of genetic and molecular tools has led to the identification and characterization of genes that are critical for normal cell division and differentiation in Arabidopsis early anther development. We review here several recent studies on these genes, including the demonstration that the putative receptor protein kinases BAM1 and BAM2 together play essential roles in the control of early cell division and differentiation. In addition, we discuss the hypothesis that BAM1/2 may form a positive-negative feedback regulatory loop with a previously identified key regulator, SPOROCYTELESS （also called NOZZLE）, to control the balance between sporogenous and somatic cell types in the anther. Furthermore, we summarize the isolation and functional analysis of the DYSFUNCTIONAL TAPETUM1 （DYT1） gene in promoting proper tapetal cell differentiation. Our finding that DYT1 encodes a putative transcription factor of the bHLH family, as well as relevant expression analyses, strongly supports a model that DYT1 serves as a critical link between upstream factors and downstream target genes that are critical for normal tapetum development and function. These studies, together with other recently published works, indicate that cell-cell communication and transcriptional control are key processes essential for cell fate specification in anther development.

关键词： anther development Arabidopsis signaling tapetum transcription factor

Recurrent genome duplication events likely contributed to both the ancient and recent rise of ferns^FA

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Journal of Integrative plant Biology 2020年第4期62卷 433-455页

作者： Chien-Hsun Huang Xinping Qi Duoyuan Chen Ji Qi Hong Ma Ministry of Education Key Laboratory of Biodiversity sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering Collaborative Innovation Center for Genetics and DevelopmentInstitute of Plant BiologyInstitute of Biodiversity SciencesCenter for Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200433China department of Biology The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkUniversity ParkPA 16802USA

Ferns, the second largest group of vascular plants, originated ~400 mil ion years ago(Mya). They became dominant in the ancient Earth landscape before the angiosperms and are stil important in current *** ferns have exceptional y high chromosome numbers,possibly resulting from whole-genome duplications(WGDs).However, WGDs have not been investigated molecularly across fern diversity. Here we detected and dated fern WGDs using a phylogenomic approach and by calculating synonymous substitution rates(Ks). We also investigated a possible correlation between proposed WGDs and shifts in species diversification rates. We identified 19 WGDs: three ancient events along the fern phylogenetic backbone that are shared by 66%–97% of extant ferns, with additional lineage-specific WGDs for eight orders, providing strongevidence for recurring genome duplications across fern evolutionary history. We also observed similar Ks peak values for more than half of these WGDs, with multiple WGDs occurring close to the Cretaceous(~145–66 Mya). Despite the repeated WGD events, the biodiversity of ferns declined during the Cretaceous, implying that other factors probably contributed to the floristic turnover from ferns to angiosperms. This study provides molecular evidence for recurring WGDs in ferns and offers important clues to the genomic evolutionary history of ferns.

关键词： likely Cretaceous backbone