Showing papers by "Detlef Weigel published in 2013"
TL;DR: Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease is demonstrated using a single Cas9 molecule for the first time.
Abstract: Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease
955 citations
Uppsala University1, University of Toronto2, New York University Abu Dhabi3, Max Planck Society4, Institut national de la recherche agronomique5, Chinese Academy of Sciences6, McGill University7, Masaryk University8, University of Utah9, Colby–Sawyer College10, University of California, Irvine11, University of California, Davis12, Princeton University13, Gregor Mendel Institute14, United States Department of Energy15, University of California, Berkeley16
TL;DR: The transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection, similar to that seen in Arabidopsis, which self fertilization evolved about 1 million years ago.
Abstract: The shift from outcrossing to selfing is common in flowering plants(1,2), but the genomic consequences and the speed at which they emerge remain poorly understood. An excellent model for understanding the evolution of self fertilization is provided by Capsella rubella, which became self compatible <200,000 years ago. We report a C. rubella reference genome sequence and compare RNA expression and polymorphism patterns between C. rubella and its outcrossing progenitor Capsella grandiflora. We found a clear shift in the expression of genes associated with flowering phenotypes, similar to that seen in Arabidopsis, in which self fertilization evolved about 1 million years ago. Comparisons of the two Capsella species showed evidence of rapid genome-wide relaxation of purifying selection in C. rubella without a concomitant change in transposable element abundance. Overall we document that the transition to selfing may be typified by parallel shifts in gene expression, along with a measurable reduction of purifying selection.
404 citations
TL;DR: It is proposed that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity, which replaced it outside of Mexico in the 20th century.
Abstract: Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the 19th century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the 20th century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species' center of diversity.
DOI: http://dx.doi.org/10.7554/eLife.00731.001
346 citations
TL;DR: High-throughput sequencing is used to identify changes in DNA sequence and gene expression that differentiate cultivated tomato and its wild relatives and identifies hundreds of candidate genes that have evolved new protein sequences or have changed expression levels in response to natural selection in wild tomato relatives.
Abstract: Although applied over extremely short timescales, artificial selection has dramatically altered the form, physiology, and life history of cultivated plants. We have used RNAseq to define both gene sequence and expression divergence between cultivated tomato and five related wild species. Based on sequence differences, we detect footprints of positive selection in over 50 genes. We also document thousands of shifts in gene-expression level, many of which resulted from changes in selection pressure. These rapidly evolving genes are commonly associated with environmental response and stress tolerance. The importance of environmental inputs during evolution of gene expression is further highlighted by large-scale alteration of the light response coexpression network between wild and cultivated accessions. Human manipulation of the genome has heavily impacted the tomato transcriptome through directed admixture and by indirectly favoring nonsynonymous over synonymous substitutions. Taken together, our results shed light on the pervasive effects artificial and natural selection have had on the transcriptomes of tomato and its wild relatives.
331 citations
TL;DR: In this paper, the authors resequenced the four products of 13 meiotic tetrads along with 10 doubled haploids derived from Arabidopsis thaliana hybrids and revealed an ∼80-kb transposition, which undergoes copy-number changes mediated by meiotic recombination.
Abstract: 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 ∼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 ∼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
201 citations
TL;DR: Overall, this work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants.
Abstract: Transposable elements (TEs) make up the majority of many plant genomes. Their transcription and transposition is controlled through siRNAs and epigenetic marks including DNA methylation. To dissect the interplay of siRNA–mediated regulation and TE evolution, and to examine how TE differences affect nearby gene expression, we investigated genome-wide differences in TEs, siRNAs, and gene expression among three Arabidopsis thaliana accessions. Both TE sequence polymorphisms and presence of linked TEs are positively correlated with intraspecific variation in gene expression. The expression of genes within 2 kb of conserved TEs is more stable than that of genes next to variant TEs harboring sequence polymorphisms. Polymorphism levels of TEs and closely linked adjacent genes are positively correlated as well. We also investigated the distribution of 24-nt-long siRNAs, which mediate TE repression. TEs targeted by uniquely mapping siRNAs are on average farther from coding genes, apparently because they more strongly suppress expression of adjacent genes. Furthermore, siRNAs, and especially uniquely mapping siRNAs, are enriched in TE regions missing in other accessions. Thus, targeting by uniquely mapping siRNAs appears to promote sequence deletions in TEs. Overall, our work indicates that siRNA–targeting of TEs may influence removal of sequences from the genome and hence evolution of gene expression in plants.
150 citations
TL;DR: A family of night light–inducible and clock-regulated genes (LNK) that play a key role linking light regulation of gene expression to the control of daily and seasonal rhythms in Arabidopsis thaliana are described.
Abstract: Light signaling pathways and the circadian clock interact to help organisms synchronize physiological and developmental processes with periodic environmental cycles. The plant photoreceptors responsible for clock resetting have been characterized, but signaling components that link the photoreceptors to the clock remain to be identified. Here we describe a family of night light–inducible and clock-regulated genes (LNK) that play a key role linking light regulation of gene expression to the control of daily and seasonal rhythms in Arabidopsis thaliana. A genomewide transcriptome analysis revealed that most light-induced genes respond more strongly to light during the subjective day, which is consistent with the diurnal nature of most physiological processes in plants. However, a handful of genes, including the homologous genes LNK1 and LNK2, are more strongly induced by light in the middle of the night, when the clock is most responsive to this signal. Further analysis revealed that the morning phased LNK1 and LNK2 genes control circadian rhythms, photomorphogenic responses, and photoperiodic dependent flowering, most likely by regulating a subset of clock and flowering time genes in the afternoon. LNK1 and LNK2 themselves are directly repressed by members of the TIMING OF CAB1 EXPRESSION/PSEUDO RESPONSE REGULATOR family of core-clock genes in the afternoon and early night. Thus, LNK1 and LNK2 integrate early light signals with temporal information provided by core oscillator components to control the expression of afternoon genes, allowing plants to keep track of seasonal changes in day length.
150 citations
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TL;DR: Overall, recombination preferentially targeted non-methylated nucleosome-free regions at gene promoters, which showed significant enrichment of two sequence motifs, and GC detection through short reads has previously been confounded by genomic rearrangements.
Abstract: 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 ~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 ~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.
147 citations
TL;DR: Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, more than 400,000 mapping-by-sequencing experiments are simulated, informing about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.
Abstract: Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific biases, we simulated more than 400,000 mapping-by-sequencing experiments. This allowed us to evaluate a broad range of different types of experiments and to develop general rules for mapping-by-sequencing in Arabidopsis. Most importantly, this informs about the properties of different crossing scenarios, the number of recombinants and sequencing depth needed for successful mapping experiments.
129 citations
TL;DR: This work describes how three evolutionary conserved miRNA-TF pairs interact to form multiple checkpoints during reproductive development of Arabidopsis thaliana and reveals how different miRNAs can be organized into modules that coordinate successive steps in the plant life cycle.
Abstract: The development of multicellular organisms relies on interconnected genetic programs that control progression through their life cycle. MicroRNAs (miRNAs) and transcription factors (TFs) play key roles in such regulatory circuits. Here, we describe how three evolutionary conserved miRNA-TF pairs interact to form multiple checkpoints during reproductive development of Arabidopsis thaliana. Genetic, cellular, and physiological experiments show that miR159- and miR319-regulated MYB and TCP transcription factors pattern the expression of miR167 family members and their ARF6/8 targets. Coordinated action of these miRNA-TF pairs is crucial for the execution of consecutive hormone-dependent transitions during flower maturation. Cross-regulation includes both cis- and trans-regulatory interactions between these miRNAs and their targets. Our observations reveal how different miRNA-TF pairs can be organized into modules that coordinate successive steps in the plant life cycle.
115 citations
TL;DR: KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development and controls through its target genes auxin effects on organ development at different levels.
Abstract: Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN) subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV). A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.
TL;DR: In the Ll-2 Arabidopsis accession, MAF2 var1 was consistent in its effect on reproductive delay under ambient and reduced temperatures, indicating that it acts as a repressor of flowering.
Abstract: The MADS-AFFECTING FLOWERING 2 (MAF2) gene of Arabidopsis thaliana has been characterized as a repressor of flowering. The molecular basis of MAF2 gene function and role of alternative MAF2 transcripts in flowering time modulation is not understood. MAF2 splice variant expression was quantified in cold-acclimated plants by quantitative RT-PCR. Cold influenced the abundance of splice variants and prompted a functional study of splice forms. Individual variants were overexpressed in the Col background and were assayed for their ability to delay flowering. Overexpression of MAF2 variants 2 and 4 had limited effect on flowering time. Overexpression of MAF2 splice variant 1 resulted in early flowering and affected the expression of the endogenous MAF2 gene and its paralogues, confounding functional assessment. In the Ll-2 Arabidopsis accession, a MAF2, MAF3, MAF4 and FLC null line, MAF2 var1 was consistent in its effect on reproductive delay under ambient and reduced temperatures, indicating that it acts as a repressor of flowering.
TL;DR: It is confirmed that active AGO1-miR171a* complexes are common in Arabidopsis and that they trigger silencing of SU(VAR)3-9 HOMOLOG8, a new microRNA target that was acquired very recently in the Arabidops lineage.
Abstract: MicroRNAs (miRNAs) are produced from double-stranded precursors, from which a short duplex is excised. The strand of the duplex that remains more abundant is usually the active form, the miRNA, while steady-state levels of the other strand, the miRNA*, are generally lower. The executive engines of miRNA-directed gene silencing are RNA-induced silencing complexes (RISCs). During RISC maturation, the miRNA/miRNA* duplex associates with the catalytic subunit, an ARGONAUTE (AGO) protein. Subsequently, the guide strand, which directs gene silencing, is retained, while the passenger strand is degraded. Under certain circumstances, the miRNA*s can be retained as guide strands. miR170 and miR171 are prototypical miRNAs in Arabidopsis (Arabidopsis thaliana) with well-defined targets. We found that the corresponding star molecules, the sequence-identical miR170* and miR171a*, have several features of active miRNAs, such as sequence conservation and AGO1 association. We confirmed that active AGO1-miR171a* complexes are common in Arabidopsis and that they trigger silencing of SU(VAR)3-9 HOMOLOG8, a new miR171a* target that was acquired very recently in the Arabidopsis lineage. Our study demonstrates that each miR171a strand can be loaded onto RISC with separate regulatory outcomes.
TL;DR: In this article, it was shown that blue and golden correspond to guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita.
Abstract: Males of the guppy (Poecilia reticulata) vary tremendously in their ornamental patterns, which are thought to have evolved in response to a complex interplay between natural and sexual selection. Although the selection pressures acting on the color patterns of the guppy have been extensively studied, little is known about the genes that control their ontogeny. Over 50 years ago, two autosomal color loci, blue and golden, were described, both of which play a decisive role in the formation of the guppy color pattern. Orange pigmentation is absent in the skin of guppies with a lesion in blue, suggesting a defect in xanthophore development. In golden mutants, the development of the melanophore pattern during embryogenesis and after birth is affected. Here, we show that blue and golden correspond to guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita. Most excitingly, we found that both genes are required for the development of the black ornaments of guppy males, which in the case of csf1ra might be mediated by xanthophore–melanophore interactions. Furthermore, we provide evidence that two temporally and genetically distinct melanophore populations contribute to the adult camouflage pattern expressed in both sexes: one early appearing and kita-dependent and the other late-developing and kita-independent. The identification of csf1ra and kita mutants provides the first molecular insights into pigment pattern formation in this important model species for ecological and evolutionary genetics.
TL;DR: A role for sterol conjugates in cell non-autonomous defense responses against invasive filamentous pathogens is suggested.
Abstract: Summary
Non-host resistance of Arabidopsis thaliana against Phytophthora infestans, the causal agent of late blight disease of potato, depends on efficient extracellular pre- and post-invasive resistance responses. Pre-invasive resistance against P. infestans requires the myrosinase PEN2. To identify additional genes involved in non-host resistance to P. infestans, a genetic screen was performed by re-mutagenesis of pen2 plants. Fourteen independent mutants were isolated that displayed an enhanced response to Phytophthora (erp) phenotype. Upon inoculation with P. infestans, two mutants, pen2-1 erp1-3 and pen2-1 erp1-4, showed an enhanced rate of mesophyll cell death and produced excessive callose deposits in the mesophyll cell layer. ERP1 encodes a phospholipid:sterol acyltransferase (PSAT1) that catalyzes the formation of sterol esters. Consistent with this, the tested T-DNA insertion lines of PSAT1 are phenocopies of erp1 plants. Sterol ester levels are highly reduced in all erp1/psat1 mutants, whereas sterol glycoside levels are increased twofold. Excessive callose deposition occurred independently of PMR4/GSL5 activity, a known pathogen-inducible callose synthase. A similar formation of aberrant callose deposits was triggered by the inoculation of erp1 psat1 plants with powdery mildew. These results suggest a role for sterol conjugates in cell non-autonomous defense responses against invasive filamentous pathogens.
TL;DR: This work shows that indel classification is a necessary step to reduce the number of false positive candidates and demonstrates that missing classification may lead to spurious biological interpretations.
Abstract: One of the major open challenges in next generation sequencing (NGS) is the accurate identification of structural variants such as insertions and deletions (indels) Current methods for indel calling assign scores to different types of evidence or counter-evidence for the presence of an indel, such as the number of split read alignments spanning the boundaries of a deletion candidate or reads that map within a putative deletion Candidates with a score above a manually defined threshold are then predicted to be true indels As a consequence, structural variants detected in this manner contain many false positives Here, we present a machine learning based method which is able to discover and distinguish true from false indel candidates in order to reduce the false positive rate Our method identifies indel candidates using a discriminative classifier based on features of split read alignment profiles and trained on true and false indel candidates that were validated by Sanger sequencing We demonstrate the usefulness of our method with paired-end Illumina reads from 80 genomes of the first phase of the 1001 Genomes Project (
http://www1001genomesorg
) in Arabidopsis thaliana In this work we show that indel classification is a necessary step to reduce the number of false positive candidates We demonstrate that missing classification may lead to spurious biological interpretations The software is available at: http://agkbistuebingenmpgde/Forschung/SV-M/
TL;DR: All editorial decisions at eLife are taken by working scientists in a process that emphasizes fairness, speed and transparency.
Abstract: All editorial decisions at eLife are taken by working scientists in a process that emphasizes fairness, speed and transparency.
01 Jan 2013
TL;DR: In this paper, it was shown that blue and golden correspond to guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita.
Abstract: Males of the guppy (Poecilia reticulata) vary tremendously in their ornamental patterns, which are thought to have evolved in response to a complex interplay between natural and sexual selection. Although the selection pressures acting on the color patterns of the guppy have been extensively studied, little is known about the genes that control their ontogeny. Over 50 years ago, two autosomal color loci, blue and golden, were described, both of which play a decisive role in the formation of the guppy color pattern. Orange pigmentation is absent in the skin of guppies with a lesion in blue, suggesting a defect in xanthophore development. In golden mutants, the development of the melanophore pattern during embryogenesis and after birth is affected. Here, we show that blue and golden correspond to guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita. Most excitingly, we found that both genes are required for the development of the black ornaments of guppy males, which in the case of csf1ra might be mediated by xanthophore-melanophore interactions. Furthermore, we provide evidence that two temporally and genetically distinct melanophore populations contribute to the adult camouflage pattern expressed in both sexes: one early appearing and kita-dependent and the other late-developing and kita-independent. The identification of csf1ra and kita mutants provides the first molecular insights into pigment pattern formation in this important model species for ecological and evolutionary genetics.
Dalhousie University1, Babraham Institute2, University of California, Santa Cruz3, Yale University4, University of Connecticut Health Center5, Fred Hutchinson Cancer Research Center6, Massachusetts Institute of Technology7, Harvard University8, Royal Children's Hospital9, University of Oxford10, Wellcome Trust Sanger Institute11, Beth Israel Deaconess Medical Center12, Cold Spring Harbor Laboratory13, UCL Institute of Neurology14, Laboratory of Molecular Biology15, Max Planck Society16, Washington University in St. Louis17
TL;DR: Sixty years after Watson and Crick published the double helix model of DNA's structure, thirteen members of Genome Biology's Editorial Board select key advances in the field of genome biology subsequent to that discovery.
Abstract: Sixty years after Watson and Crick published the double helix model of DNA's structure, thirteen members of Genome Biology's Editorial Board select key advances in the field of genome biology subsequent to that discovery.
TL;DR: It is proposed that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species’ center of diversity, which replaced it outside of Mexico in the 20th century.
TL;DR: This chapter describes the generation and application of amiRNAs as a gene silencing tool in rice.
Abstract: Artificial microRNAs (amiRNAs) have been shown to facilitate efficient gene silencing with high specificity to the intended target gene(s). For the plant breeder, gene silencing by artificial miRNAs will certainly accelerate gene discovery, because it allows targeting of all genes in a mapping interval, independent of the genetic background. In addition, beneficial knockout phenotypes can easily be transferred between varieties and across incompatibility barriers. This chapter describes the generation and application of amiRNAs as a gene silencing tool in rice.
TL;DR: Improving the peer review process, overcoming the limitations of print journals and providing open access to the very best work in the life and biomedical sciences are three highlights of the journal's first year.
Abstract: Improving the peer review process, overcoming the limitations of print journals and providing open access to the very best work in the life and biomedical sciences are three highlights of our first year.
TL;DR: There are many reasons for submitting your best work to eLife, especially if you are an early career researcher.
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TL;DR: Small, 21–22 nucleotide long RNAs called microRNAs play an essential role in the spatial and temporal regulation of gene expression and have an influence on many developmental pathways during plant development.
Abstract: Small, 21–22 nucleotide long RNAs called microRNAs play an essential role in the spatial and temporal regulation of gene expression. They are often part of complex gene networks. By controlling the stability or translation of their target mRNAs they have an influence on many developmental pathways. Juvenile to adult transition, initiation of flowering or plant architecture and leaf morphology are examples of miRNA-regulated processes during plant development.