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  • 1
    Language: English
    In: The Plant cell, 2006-05-01, Vol.18 (5), p.1121-1133
    Description: Plant microRNAs (miRNAs) affect only a small number of targets with high sequence complementarity, while animal miRNAs usually have hundreds of targets with limited complementarity. We used artificial miRNAs (amiRNAs) to determine whether the narrow action spectrum of natural plant miRNAs reflects only intrinsic properties of the plant miRNA machinery or whether it is also due to past selection against natural miRNAs with broader specificity. amiRNAs were designed to target individual genes or groups of endogenous genes. Like natural miRNAs, they had varying numbers of target mismatches. Previously determined parameters of target selection for natural miRNAs could accurately predict direct targets of amiRNAs. The specificity of amiRNAs, as deduced from genome-wide expression profiling, was as high as that of natural plant miRNAs, supporting the notion that extensive base pairing with targets is required for plant miRNA function. amiRNAs make an effective tool for specific gene silencing in plants, especially when several related, but not identical, target genes need to be downregulated. We demonstrate that amiRNAs are also active when expressed under tissue-specific or inducible promoters, with limited nonautonomous effects. The design principles for amiRNAs have been generalized and integrated into a Web-based tool (http://wmd.weigelworld.org).
    Subject(s): Arabidopsis ; Arabidopsis - anatomy & histology ; Arabidopsis - genetics ; Arabidopsis - metabolism ; Base Pairing ; Flowering ; Gene Silencing ; Genes ; Genetic aspects ; Genomes ; Inflorescences ; Messenger RNA ; MicroRNA ; MicroRNAs - chemistry ; MicroRNAs - metabolism ; MicroRNAs - physiology ; Phenotype ; Plant cells ; Plant genetics ; Plants ; Research ; RNA ; RNA, Plant - chemistry ; RNA, Plant - metabolism ; RNA, Plant - physiology ; Sequence Analysis, RNA ; Small interfering RNA ; Software
    ISSN: 1040-4651
    E-ISSN: 1532-298X
    Source: JSTOR Life Sciences
    Source: JSTOR Ecology & Botany II
    Source: Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals
    Source: Alma/SFX Local Collection
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  • 2
    Language: English
    In: Nature genetics, 2011, Vol.43 (10), p.956-963
    Description: The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.
    Subject(s): Alleles ; Arabidopsis - genetics ; Arabidopsis thaliana ; Biological and medical sciences ; Biological Sciences ; Biologiska vetenskaper ; Chromosome Mapping ; Chromosomes, Plant ; DNA, Plant - genetics ; Evolutionary Biology ; Evolutionsbiologi ; Fundamental and applied biological sciences. Psychology ; Genetic aspects ; Genetic Loci ; Genetics of eukaryotes. Biological and molecular evolution ; Genetics, Population ; Genome, Plant ; Genomes ; Geography ; Linkage Disequilibrium ; Mutation ; Natural Sciences ; Naturvetenskap ; Nucleotide sequencing ; Phenotype ; Polymorphism, Single Nucleotide ; Research ; Selection, Genetic ; Sequence Analysis, DNA - methods ; Usage
    ISSN: 1061-4036
    ISSN: 1546-1718
    E-ISSN: 1546-1718
    Source: Academic Search Ultimate
    Source: Alma/SFX Local Collection
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  • 3
    Language: English
    In: Science (American Association for the Advancement of Science), 2010-01-01, Vol.327 (5961), p.92-94
    Description: To take complete advantage of information on within-species polymorphism and divergence from close relatives, one needs to know the rate and the molecular spectrum of spontaneous mutations. To this end, we have searched for de novo spontaneous mutations in the complete nuclear genomes of five Arabidopsis thaliana mutation accumulation lines that had been maintained by single-seed descent for 30 generations. We identified and validated 99 base substitutions and 17 small and large insertions and deletions. Our results imply a spontaneous mutation rate of 7 x 10⁻⁹ base substitutions per site per generation, the majority of which are G: C-» A: T transitions. We explain this very biased spectrum of base substitution mutations as a result of two main processes: deamination of methylated cytosines and ultraviolet light-induced mutagenesis.
    Subject(s): Agronomy. Soil science and plant productions ; Analysis ; Arabidopsis - genetics ; Arabidopsis - radiation effects ; Arabidopsis thaliana ; Biological and medical sciences ; Cytosine - metabolism ; Deamination ; DNA Methylation ; DNA, Intergenic ; DNA, Plant - genetics ; Fundamental and applied biological sciences. Psychology ; Gene mutations ; Genetic aspects ; Genetic mutation ; Genetic polymorphisms ; Genetics and breeding of economic plants ; Genome, Plant ; Genomes ; INDEL Mutation ; Intergenic DNA ; Introns ; Methylation ; Molecular spectra ; Mutagenesis ; Mutation ; Natural selection ; Plant breeding: fundamental aspects and methodology ; Reports ; Research ; Sequence Analysis, DNA ; Sequence Deletion ; Sequencing ; Ultraviolet Rays ; Untranslated regions
    ISSN: 0036-8075
    E-ISSN: 1095-9203
    Source: JSTOR Life Sciences
    Source: Academic Search Ultimate
    Source: Alma/SFX Local Collection
    Source: Get It Now
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  • 4
    Language: English
    In: PloS one, 2008-03-19, Vol.3 (3), p.e1829-e1829
    Description: Endogenous microRNAs (miRNAs) are potent negative regulators of gene expression in plants and animals. Artificial miRNAs (amiRNAs)-designed to target one or several genes of interest-provide a new and highly specific approach for effective post-transcriptional gene silencing (PTGS) in plants. We devised an amiRNA-based strategy for both japonica and indica type strains of cultivated rice, Oryza sativa. Using an endogenous rice miRNA precursor and customized 21mers, we designed amiRNA constructs targeting three different genes (Pds, Spl11, and Eui1/CYP714D1). Upon constitutive expression of these amiRNAs in the varieties Nipponbare (japonica) and IR64 (indica), the targeted genes are down-regulated by amiRNA-guided cleavage of the transcripts, resulting in the expected mutant phenotypes. The effects are highly specific to the target gene, the transgenes are stably inherited and they remain effective in the progeny. Our results not only show that amiRNAs can efficiently trigger gene silencing in a monocot crop, but also that amiRNAs can effectively modulate agronomically important traits in varieties used in modern breeding programs. We provide all software tools and a protocol for the design of rice amiRNA constructs, which can be easily adapted to other crops. The approach is suited for candidate gene validation, comparative functional genomics between different varieties, and for improvement of agronomic performance and nutritional value.
    Subject(s): Acids ; Agricultural Biotechnology ; Agronomy ; Bioinformatics ; Biotechnology ; Breeding ; Complex Traits ; Crops ; Developmental biology ; Domestication ; Gene Discovery ; Gene Expression ; Gene Function ; Gene Silencing ; Genes ; Genes, Plant ; Genetic aspects ; Genetic engineering ; Genetic transcription ; Genetics ; Genetics and Genomics ; Genomes ; Genomics ; Grain cultivation ; Mathematical models ; MicroRNA ; MicroRNAs ; MicroRNAs - chemistry ; MicroRNAs - physiology ; miRNA ; Molecular biology ; Mutagenesis ; Nucleic Acid Conformation ; Oryza - genetics ; Plant Biology ; Plant Biotechnology ; Plant breeding ; Plant genetics ; Plant Genetics and Gene Expression ; Plant Growth and Development ; Post-transcription ; Progeny ; Regulators ; Reverse Transcriptase Polymerase Chain Reaction ; Ribonucleic acid ; Rice ; RNA ; Software development tools ; Transgenes ; Trends
    ISSN: 1932-6203
    E-ISSN: 1932-6203
    Source: Academic Search Ultimate
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 5
    Language: English
    In: Nature biotechnology, 2021-04, Vol.39 (4), p.422-430
    Description: Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very high quality at low computational cost. We demonstrate de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms to improve assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50: 17.24-80.64 Mb), few assembly errors (contig NGA50: 11.8-59.59 Mb), good consensus quality (QV: 27.84-42.88) and high gene completeness (BUSCO complete: 94.6-95.2%), while consuming low computational resources (CPU hours: 187-1,200). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64 Mb (NGA50: 59.59 Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88 Mb).
    Subject(s): Algorithms ; Analysis ; Bioinformatics ; Computational Biology - methods ; Computational biology and bioinformatics ; Computer programs ; Computer Science ; Contig Mapping - methods ; Genetic algorithms ; Genome assembly algorithms ; Genome, Human ; Genomes ; Genomics ; Haploidy ; High-Throughput Nucleotide Sequencing ; Human genome ; Humans ; Hybridization ; Life Sciences ; Methods ; Science ; Sequence Analysis, DNA ; Software ; Usage
    ISSN: 1087-0156
    E-ISSN: 1546-1696
    Source: Get It Now
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  • 6
    Language: English
    In: Nature (London), 2009-09-17, Vol.461 (7262), p.427-430
    Description: Retrotransposons are mobile genetic elements that populate chromosomes, where the host largely controls their activities. In plants and mammals, retrotransposons are transcriptionally silenced by DNA methylation, which in Arabidopsis is propagated at CG dinucleotides by METHYLTRANSFERASE 1 (MET1). In met1 mutants, however, mobilization of retrotransposons is not observed, despite their transcriptional activation. A post-transcriptional mechanism therefore seems to be preventing retrotransposition. Here we show that a copia-type retrotransposon (Évadé, French for 'fugitive') evaded suppression of its movement during inbreeding of hybrid epigenomes consisting of met1- and wild-type-derived chromosomes. Évadé (EVD) reinsertions caused a series of developmental mutations that allowed its identification. Genetic testing of host control of the EVD life cycle showed that transcriptional suppression occurred by CG methylation supported by RNA-directed DNA methylation. On transcriptional reactivation, subsequent steps of the EVD cycle were inhibited by plant-specific RNA polymerase IV/V and the histone methyltransferase KRYPTONITE (KYP). Moreover, genome resequencing demonstrated retrotransposition of EVD but no other potentially active retroelements when this combination of epigenetic mechanisms was compromised. Our results demonstrate that epigenetic control of retrotransposons extends beyond transcriptional suppression and can be individualized for particular elements.
    Subject(s): Agronomy. Soil science and plant productions ; Alleles ; Arabidopsis ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - metabolism ; Biological and medical sciences ; DNA (Cytosine-5-)-Methyltransferases - genetics ; DNA Methylation ; DNA-Directed RNA Polymerases - metabolism ; Epigenesis, Genetic - genetics ; Epigenetic inheritance ; Fundamental and applied biological sciences. Psychology ; Gene Silencing ; Genetic aspects ; Genetics and breeding of economic plants ; Genome, Plant - genetics ; Histone-Lysine N-Methyltransferase - metabolism ; Inbreeding ; Life Sciences ; Methylation ; Mutagenesis, Insertional - genetics ; Observations ; Properties ; Recombination, Genetic - genetics ; Research ; Retroelements - genetics ; Retrotransposons ; Suppression, Genetic ; Terminal Repeat Sequences - genetics ; Transcription, Genetic - genetics
    ISSN: 0028-0836
    E-ISSN: 1476-4687
    E-ISSN: 1476-4679
    Source: Academic Search Ultimate
    Source: Nature Journals Online
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  • 7
    Language: English
    In: Nature methods, 2009-08, Vol.6 (8), p.550-551
    Subject(s): Applications software ; Arabidopsis - genetics ; Arabidopsis - growth & development ; Chromosome Mapping ; Gene Frequency ; Gene mutations ; Genome-Wide Association Study - methods ; Identification and classification ; Methods ; Mutation - genetics ; Nucleotide sequencing ; Plant Leaves - genetics ; Software ; Usage
    ISSN: 1548-7091
    E-ISSN: 1548-7105
    Source: Academic Search Ultimate
    Source: Nature Journals Online
    Source: Get It Now
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  • 8
    Language: English
    In: eLife, 2013, Vol.2, p.e01426-e01426
    Description: Knowledge of the exact distribution of meiotic crossovers (COs) and gene conversions (GCs) is essential for understanding many aspects of population genetics and evolution, from haplotype structure and long-distance genetic linkage to the generation of new allelic variants of genes. To this end, we resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids. GC detection through short reads has previously been confounded by genomic rearrangements. Rigid filtering for misaligned reads allowed GC identification at high accuracy and revealed an approximately 80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination. Non-crossover associated GCs were extremely rare most likely due to their short average length of approximately 25-50 bp, which is significantly shorter than the length of CO-associated GCs. Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs. DOI: http://dx.doi.org/10.7554/eLife.01426.001.
    Subject(s): Arabidopsis ; Arabidopsis - genetics ; Chromosomes ; Conversion ; Crossing Over, Genetic ; Developmental biology ; dna methylation ; double strand break repair ; Gene Conversion ; Genetic recombination ; Genome, Plant ; Genomes ; Genomics and Evolutionary Biology ; Genètica ; Genòmica ; Haploidy ; Haplotypes ; Hybrids ; Meiosis ; Meiosis - genetics ; meiotic recombination ; meiotic tetrad ; meiotic tetrads ; mouse ; Mutation ; next generation sequencing ; Plant Biology ; Population genetics ; populations ; Recombination ; recombination landscape ; reveals ; saccharomyces-cerevisiae ; sex ; short reads ; Tetrads ; Transposition ; yeast
    ISSN: 2050-084X
    E-ISSN: 2050-084X
    Source: PubMed Central
    Source: DOAJ Directory of Open Access Journals - Not for CDI Discovery
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  • 9
    Language: English
    In: Plant physiology (Bethesda), 2011-10-01, Vol.157 (2), p.757-769
    Description: Plants, like animals, use several lines of defense against pathogen attack. Prominent among genes that confer disease resistance are those encoding nucleotide-binding site-leucine-rich repeat (NB-LRR) proteins. Likely due to selection pressures caused by pathogens, NB-LRR genes are the most variable gene family in plants, but there appear to be species-specific limits to the number of NB-LRR genes in a genome. Allelic diversity within an individual is also increased by obligatory outcrossing, which leads to genome-wide heterozygosity. In this study, we compared the NB-LRR gene complement of the selfer Arabidopsis thaliana and its outcrossing close relative Arabidopsis lyrata. We then complemented and contrasted the interspecific patterns with studies of NB-LRR diversity within A. thaliana. Three important insights are as follows: (1) that both species have similar numbers of NB-LRR genes; (2) that loci with single NB-LRR genes are less variable than tandem arrays; and (3) that presenceabsence polymorphisms within A. thaliana are not strongly correlated with the presence or absence of orthologs in A. lyrata. Although A. thaliana individuals are mostly homozygous and thus potentially less likely to suffer from aberrant interaction of NB-LRR proteins with newly introduced alíeles, the number of NB-LRR genes is similar to that in A. lyrata. In intraspecific and interspecific comparisons, NB-LRR genes are also more variable than receptor-like protein genes. Finally, in contrast to Drosophila, there is a clearly positive relationship between interspecific divergence and intraspecific polymorphisms.
    Subject(s): Alleles ; Arabidopsis ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis Proteins - metabolism ; Binding Sites - genetics ; Biological and medical sciences ; Biological diversity ; Disease resistance ; Evolution ; Evolution, Molecular ; Fundamental and applied biological sciences. Psychology ; Gene conversion ; Genes ; Genes, Plant ; Genetic aspects ; Genetic loci ; GENETICS, GENOMICS, AND MOLECULAR EVOLUTION ; Genome, Plant ; Genomes ; Genomics ; Multigene Family ; Nucleotides - metabolism ; Phylogeny ; Physiological aspects ; Plant physiology and development ; Polymorphism, Genetic ; Proteins ; Proteins - genetics ; Proteins - metabolism ; Research ; Statistical median
    ISSN: 0032-0889
    E-ISSN: 1532-2548
    Source: American Society of Plant Biologists
    Source: JSTOR Life Sciences
    Source: JSTOR Ecology & Botany II
    Source: Alma/SFX Local Collection
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  • 10
    Language: English
    In: Genome medicine, 2020-05-27, Vol.12 (1), p.49-14
    Description: Mosaic mutations acquired during early embryogenesis can lead to severe early-onset genetic disorders and cancer predisposition, but are often undetectable in blood samples. The rate and mutational spectrum of embryonic mosaic mutations (EMMs) have only been studied in few tissues, and their contribution to genetic disorders is unknown. Therefore, we investigated how frequent mosaic mutations occur during embryogenesis across all germ layers and tissues. Mosaic mutation detection in 49 normal tissues from 570 individuals (Genotype-Tissue Expression (GTEx) cohort) was performed using a newly developed multi-tissue, multi-individual variant calling approach for RNA-seq data. Our method allows for reliable identification of EMMs and the developmental stage during which they appeared. The analysis of EMMs in 570 individuals revealed that newborns on average harbor 0.5-1 EMMs in the exome affecting multiple organs (1.3230 × 10 per nucleotide per individual), a similar frequency as reported for germline de novo mutations. Our multi-tissue, multi-individual study design allowed us to distinguish mosaic mutations acquired during different stages of embryogenesis and adult life, as well as to provide insights into the rate and spectrum of mosaic mutations. We observed that EMMs are dominated by a mutational signature associated with spontaneous deamination of methylated cytosines and the number of cell divisions. After birth, cells continue to accumulate somatic mutations, which can lead to the development of cancer. Investigation of the mutational spectrum of the gastrointestinal tract revealed a mutational pattern associated with the food-borne carcinogen aflatoxin, a signature that has so far only been reported in liver cancer. In summary, our multi-tissue, multi-individual study reveals a surprisingly high number of embryonic mosaic mutations in coding regions, implying novel hypotheses and diagnostic procedures for investigating genetic causes of disease and cancer predisposition.
    Subject(s): Aflatoxins ; Age ; Bias ; Carcinogens ; Cell division ; Deamination ; Embryogenesis ; Embryonic Development - genetics ; Gastrointestinal tract ; Genetic disorders ; Genetic mosaicism ; Genomes ; Genotype & phenotype ; Genotypes ; Human embryogenesis ; Humans ; Liver cancer ; Mosaic mutation rate ; Mosaicism ; Mutation ; Neonates ; Quality ; Ribonucleic acid--RNA ; RNA-Seq ; Whole Exome Sequencing
    ISSN: 1756-994X
    E-ISSN: 1756-994X
    Source: BioMedCentral Open Access
    Source: Academic Search Ultimate
    Source: PubMed Central
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