1
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Hauptfeld E, Pappas N, van Iwaarden S, Snoek BL, Aldas-Vargas A, Dutilh BE, von Meijenfeldt FAB. Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes. Nat Commun 2024; 15:3373. [PMID: 38643272 PMCID: PMC11032395 DOI: 10.1038/s41467-024-47155-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/20/2024] [Indexed: 04/22/2024] Open
Abstract
Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.
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Affiliation(s)
- Ernestina Hauptfeld
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sandra van Iwaarden
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Andrea Aldas-Vargas
- Environmental Technology, Wageningen University & Research, P.O. Box 17, 6700, EV Wageningen, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University, Rosalind Franklin Strasse 1, 07743, Jena, Germany.
| | - F A Bastiaan von Meijenfeldt
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Department of Marine Microbiology and Biogeochemistry (MMB), NIOZ Royal Netherlands Institute for Sea Research, PO Box 59, 1790AB, Den Burg, The Netherlands.
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2
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Oskam L, Snoek BL, Pantazopoulou CK, van Veen H, Matton SEA, Dijkhuizen R, Pierik R. A low-cost open-source imaging platform reveals spatiotemporal insight into leaf elongation and movement. Plant Physiol 2024:kiae097. [PMID: 38401532 DOI: 10.1093/plphys/kiae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/08/2024] [Accepted: 01/25/2024] [Indexed: 02/26/2024]
Abstract
Plant organs move throughout the diurnal cycle, changing leaf and petiole positions to balance light capture, leaf temperature, and water loss under dynamic environmental conditions. Upward movement of the petiole, called hyponasty, is one of several traits of the shade avoidance syndrome (SAS). SAS traits are elicited upon perception of vegetation shade signals such as far-red light (FR) and improve light capture in dense vegetation. Monitoring plant movement at a high temporal resolution allows studying functionality and molecular regulation of hyponasty. However, high temporal resolution imaging solutions are often very expensive, making this unavailable to many researchers. Here, we present a modular and low-cost imaging set-up, based on small Raspberry Pi computers, that can track leaf movements and elongation growth with high temporal resolution. We also developed an open-source, semi-automated image analysis pipeline. Using this setup we followed responses to FR enrichment, light intensity, and their interactions. Tracking both elongation and the angle of the petiole, lamina, and entire leaf in Arabidopsis (Arabidopsis thaliana) revealed insight into R:FR sensitivities of leaf growth and movement dynamics and the interactions of R:FR with background light intensity. The detailed imaging options of this system allowed us to identify spatially separate bending points for petiole and lamina positioning of the leaf.
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Affiliation(s)
- Lisa Oskam
- Plant Environment-Signaling, Dept. Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Basten L Snoek
- Theoretical Biology & Bioinformatics, Dept. Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Chrysoula K Pantazopoulou
- Plant Environment-Signaling, Dept. Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hans van Veen
- Plant Environment-Signaling, Dept. Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Sanne E A Matton
- Laboratory of Molecular Biology, Wageningen University, 6700 AA Wageningen, the Netherlands
| | - Rens Dijkhuizen
- Plant Environment-Signaling, Dept. Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Ronald Pierik
- Plant Environment-Signaling, Dept. Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
- Laboratory of Molecular Biology, Wageningen University, 6700 AA Wageningen, the Netherlands
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3
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van Eijnatten AL, Sterken MG, Kammenga JE, Nijveen H, Snoek BL. The effect of developmental variation on expression QTLs in a multi parental Caenorhabditis elegans population. G3 (Bethesda) 2024; 14:jkad273. [PMID: 38015660 PMCID: PMC10849341 DOI: 10.1093/g3journal/jkad273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 09/21/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023]
Abstract
Regulation of gene expression plays a crucial role in developmental processes and adaptation to changing environments. expression quantitative trait locus (eQTL) mapping is a technique used to study the genetic regulation of gene expression using the transcriptomes of recombinant inbred lines (RILs). Typically, the age of the inbred lines at the time of RNA sampling is carefully controlled. This is necessary because the developmental process causes changes in gene expression, complicating the interpretation of eQTL mapping experiments. However, due to genetics and variation in ambient micro-environments, organisms can differ in their "developmental age," even if they are of the same chronological age. As a result, eQTL patterns are affected by developmental variation in gene expression. The model organism Caenorhabditis elegans is particularly suited for studying the effect of developmental variation on eQTL mapping patterns. In a span of days, C. elegans transitions from embryo through 4 larval stages to adult while undergoing massive changes to its transcriptome. Here, we use C. elegans to investigate the effect of developmental age variation on eQTL patterns and present a normalization procedure. We used dynamical eQTL mapping, which includes the developmental age as a cofactor, to separate the variation in development from genotypic variation and explain variation in gene expression levels. We compare classical single marker eQTL mapping and dynamical eQTL mapping using RNA-seq data of ∼200 multi-parental RILs of C. elegans. The results show that (1) many eQTLs are caused by developmental variation, (2) most trans-bands are developmental QTLs, and (3) dynamical eQTL mapping detects additional eQTLs not found with classical eQTL mapping. We recommend that correction for variation in developmental age should be strongly considered in eQTL mapping studies given the large impact of processes like development on the transcriptome.
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Affiliation(s)
- Abraham L van Eijnatten
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8,3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Laboratory of Bioinformatics, Wageningen University, Droevendaalsesteeg 1, Radix West, Building 107, 6708 PB Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8,3584 CH Utrecht, The Netherlands
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4
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van Wijk MH, Riksen JAG, Elvin M, Poulin GB, Maulana MI, Kammenga JE, Snoek BL, Sterken MG. Cryptic genetic variation of eQTL architecture revealed by genetic perturbation in C. elegans. G3 (Bethesda) 2023; 13:7067301. [PMID: 36861370 PMCID: PMC10151397 DOI: 10.1093/g3journal/jkad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 12/27/2022] [Accepted: 02/07/2023] [Indexed: 03/03/2023]
Abstract
Genetic perturbation in different genetic backgrounds can cause a range of phenotypes within a species. These phenotypic differences can be the result of the interaction between the genetic background and the perturbation. Previously we reported that perturbation of gld-1, an important player in developmental control of C. elegans, released cryptic genetic variation affecting fitness in different genetic backgrounds. Here we investigated the change in transcriptional architecture. We found 414 genes with a cis-eQTL and 991 genes with a trans-eQTL that were specifically found in the gld-1 RNAi treatment. In total, we detected 16 eQTL-hotspots, of which 7 were only found in the gld-1 RNAi treatment. Enrichment analysis of those 7 hotspots showed that the regulated genes were associated with neurons and the pharynx. Furthermore, we found evidence of accelerated transcriptional aging in the gld-1 RNAi treated nematodes. Overall, our results illustrate that studying CGV leads to the discovery of hidden polymorphic regulators.
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Affiliation(s)
- Marijke H van Wijk
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Mark Elvin
- Peak Proteins, Alderley Park, Macclesfield, Cheshire, SK10 4TG, United Kingdom
| | - Gino B Poulin
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, M13 9PL, United Kingdom
| | - Muhammad I Maulana
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
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5
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Sterken MG, Nijveen H, van Zanten M, Jiménez-Gómez JM, Geshnizjani N, Willems LAJ, Rienstra J, Hilhorst HWM, Ligterink W, Snoek BL. Plasticity of maternal environment-dependent expression-QTLs of tomato seeds. Theor Appl Genet 2023; 136:28. [PMID: 36810666 PMCID: PMC9944408 DOI: 10.1007/s00122-023-04322-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 10/27/2022] [Indexed: 06/18/2023]
Abstract
Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depend on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to construct a linkage map and measure gene expression of seeds of a tomato recombinant inbred line (RIL) population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments, i.e., on high phosphorus or low nitrogen. The obtained single-nucleotide polymorphisms (SNPs) were subsequently used to construct a genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.
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Affiliation(s)
- Mark G. Sterken
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Laboratory of Bioinformatics, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Martijn van Zanten
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Jose M. Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Nafiseh Geshnizjani
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Leo A. J. Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Juriaan Rienstra
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Henk W. M. Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University, 6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity, Utrecht University, 3584 CH Utrecht, The Netherlands
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6
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Hauptfeld E, Pelkmans J, Huisman TT, Anocic A, Snoek BL, von Meijenfeldt FAB, Gerritse J, van Leeuwen J, Leurink G, van Lit A, van Uffelen R, Koster MC, Dutilh BE. A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater. Water Res 2022; 221:118767. [PMID: 35777321 DOI: 10.1016/j.watres.2022.118767] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/18/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Biodegradation of pollutants is a sustainable and cost-effective solution to groundwater pollution. Here, we investigate microbial populations involved in biodegradation of poly-contaminants in a pipeline for heavily contaminated groundwater. Groundwater moves from a polluted park to a treatment plant, where an aerated bioreactor effectively removes the contaminants. While the biomass does not settle in the reactor, sediment is collected afterwards and used to seed the new polluted groundwater via a backwash cycle. The pipeline has successfully operated since 1999, but the biological components in the reactor and the contaminated park groundwater have never been described. We sampled seven points along the pipeline, representing the entire remediation process, and characterized the changing microbial communities using genome-resolved metagenomic analysis. We assembled 297 medium- and high-quality metagenome-assembled genome sequences representing on average 46.3% of the total DNA per sample. We found that the communities cluster into two distinct groups, separating the anaerobic communities in the park groundwater from the aerobic communities inside the plant. In the park, the community is dominated by members of the genus Sulfuricurvum, while the plant is dominated by generalists from the order Burkholderiales. Known aromatic compound biodegradation pathways are four times more abundant in the plant-side communities compared to the park-side. Our findings provide a genome-resolved portrait of the microbial community in a highly effective groundwater treatment system that has treated groundwater with a complex contamination profile for two decades.
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Affiliation(s)
- Ernestina Hauptfeld
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands
| | - Jordi Pelkmans
- Department of Molecular Microbiology, Science for Life, Utrecht University, the Netherlands
| | - Terry T Huisman
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands
| | - Armin Anocic
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands
| | | | | | | | | | | | | | - Margot C Koster
- Department of Molecular Microbiology, Science for Life, Utrecht University, the Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, the Netherlands; Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, Germany.
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7
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Oyserman BO, Flores SS, Griffioen T, Pan X, van der Wijk E, Pronk L, Lokhorst W, Nurfikari A, Paulson JN, Movassagh M, Stopnisek N, Kupczok A, Cordovez V, Carrión VJ, Ligterink W, Snoek BL, Medema MH, Raaijmakers JM. Disentangling the genetic basis of rhizosphere microbiome assembly in tomato. Nat Commun 2022; 13:3228. [PMID: 35710629 PMCID: PMC9203511 DOI: 10.1038/s41467-022-30849-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/19/2022] [Indexed: 12/31/2022] Open
Abstract
Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating ‘microbiomics’ and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs. Genetics factors involved in rhizosphere microbiomes assembly remain largely elusive. Here, the authors integrate microbiomics and quantitative plant genetics to reveal genetic loci associated with specific microbes and rhizobacterial traits underlying microbiome assembly in tomato.
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Affiliation(s)
- Ben O Oyserman
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. .,Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.
| | - Stalin Sarango Flores
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Thom Griffioen
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Xinya Pan
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Elmar van der Wijk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Lotte Pronk
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Wouter Lokhorst
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Azkia Nurfikari
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Joseph N Paulson
- Department of Data Sciences, Genentech, Inc. South San Francisco, South San Francisco, CA, USA
| | - Mercedeh Movassagh
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Data Sciences Dana Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Nejc Stopnisek
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Anne Kupczok
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Víctor J Carrión
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.,Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands. .,Institute of Biology, Leiden University, Leiden, The Netherlands.
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8
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van Sluijs L, Bosman KJ, Pankok F, Blokhina T, Wilten JIHA, te Molder DM, Riksen JAG, Snoek BL, Pijlman GP, Kammenga JE, Sterken MG. Balancing Selection of the Intracellular Pathogen Response in Natural Caenorhabditis elegans Populations. Front Cell Infect Microbiol 2022; 11:758331. [PMID: 35174100 PMCID: PMC8841876 DOI: 10.3389/fcimb.2021.758331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/21/2021] [Indexed: 12/17/2022] Open
Abstract
Genetic variation in host populations may lead to differential viral susceptibilities. Here, we investigate the role of natural genetic variation in the Intracellular Pathogen Response (IPR), an important antiviral pathway in the model organism Caenorhabditis elegans against Orsay virus (OrV). The IPR involves transcriptional activity of 80 genes including the pals-genes. We examine the genetic variation in the pals-family for traces of selection and explore the molecular and phenotypic effects of having distinct pals-gene alleles. Genetic analysis of 330 global C. elegans strains reveals that genetic diversity within the IPR-related pals-genes can be categorized in a few haplotypes worldwide. Importantly, two key IPR regulators, pals-22 and pals-25, are in a genomic region carrying signatures of balancing selection, suggesting that different evolutionary strategies exist in IPR regulation. We infected eleven C. elegans strains that represent three distinct pals-22 pals-25 haplotypes with Orsay virus to determine their susceptibility. For two of these strains, N2 and CB4856, the transcriptional response to infection was also measured. The results indicate that pals-22 pals-25 haplotype shapes the defense against OrV and host genetic variation can result in constitutive activation of IPR genes. Our work presents evidence for balancing genetic selection of immunity genes in C. elegans and provides a novel perspective on the functional diversity that can develop within a main antiviral response in natural host populations.
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Affiliation(s)
- Lisa van Sluijs
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Kobus J. Bosman
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Frederik Pankok
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Tatiana Blokhina
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Jop I. H. A. Wilten
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Dennie M. te Molder
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Gorben P. Pijlman
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
| | - Mark G. Sterken
- Laboratory of Nematology, Wageningen University and Research, Wageningen, Netherlands
- Laboratory of Virology, Wageningen University and Research, Wageningen, Netherlands
- *Correspondence: Mark G. Sterken,
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9
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van Schijndel L, Snoek BL, ten Tusscher K. Embodiment in distributed information processing: "Solid" plants versus "liquid" ant colonies. Quant Plant Biol 2022; 3:e27. [PMID: 37077985 PMCID: PMC10095861 DOI: 10.1017/qpb.2022.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 05/02/2023]
Abstract
Information processing is an essential part of biology, enabling coordination of intra-organismal processes such as development, environmental adaptation and inter-organismal communication. Whilst in animals with specialised brain tissue a substantial amount of information processing occurs in a centralised manner, most biological computing is distributed across multiple entities, such as cells in a tissue, roots in a root system or ants in a colony. Physical context, called embodiment, also affects the nature of biological computing. While plants and ant colonies both perform distributed computing, in plants the units occupy fixed positions while individual ants move around. This distinction, solid versus liquid brain computing, shapes the nature of computations. Here we compare information processing in plants and ant colonies, highlighting how similarities and differences originate in, as well as make use of, the differences in embodiment. We end with a discussion on how this embodiment perspective may inform the debate on plant cognition.
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Affiliation(s)
- Laura van Schijndel
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Basten L. Snoek
- Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Kirsten ten Tusscher
- Computational Developmental Biology Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
- Author for correspondence: K. ten Tusscher, E-mail:
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10
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Pavlova P, van Zanten M, Snoek BL, de Jong H, Fransz P. Correction to: 2D morphometric analysis of Arabidopsis thaliana nuclei reveals characteristic profiles of different cell types and accessions. Chromosome Res 2021; 30:25-27. [PMID: 34962631 DOI: 10.1007/s10577-021-09677-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Penka Pavlova
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Paul Fransz
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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11
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Courbier S, Snoek BL, Kajala K, Li L, van Wees SCM, Pierik R. Mechanisms of far-red light-mediated dampening of defense against Botrytis cinerea in tomato leaves. Plant Physiol 2021; 187:1250-1266. [PMID: 34618050 PMCID: PMC8566310 DOI: 10.1093/plphys/kiab354] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Plants detect neighboring competitors through a decrease in the ratio between red and far-red light (R:FR). This decreased R:FR is perceived by phytochrome photoreceptors and triggers shade avoidance responses such as shoot elongation and upward leaf movement (hyponasty). In addition to promoting elongation growth, low R:FR perception enhances plant susceptibility to pathogens: the growth-defense tradeoff. Although increased susceptibility in low R:FR has been studied for over a decade, the associated timing of molecular events is still unknown. Here, we studied the chronology of FR-induced susceptibility events in tomato (Solanum lycopersicum) plants pre-exposed to either white light (WL) or WL supplemented with FR light (WL+FR) prior to inoculation with the necrotrophic fungus Botrytis cinerea (B.c.). We monitored the leaf transcriptional changes over a 30-h time course upon infection and followed up with functional studies to identify mechanisms. We found that FR-induced susceptibility in tomato is linked to a general dampening of B.c.-responsive gene expression, and a delay in both pathogen recognition and jasmonic acid-mediated defense gene expression. In addition, we found that the supplemental FR-induced ethylene emissions affected plant immune responses under the WL+FR condition. This study improves our understanding of the growth-immunity tradeoff, while simultaneously providing leads to improve tomato resistance against pathogens in dense cropping systems.
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Affiliation(s)
- Sarah Courbier
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity, Utrecht University, The Netherlands
| | - Kaisa Kajala
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Linge Li
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Saskia C M van Wees
- Plant-Microbe Interactions, Institute of Environmental Biology, Utrecht University, The Netherlands
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, The Netherlands
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12
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Snoek BL, Sterken MG, Nijveen H, Volkers RJM, Riksen J, Rosenstiel PC, Schulenburg H, Kammenga JE. The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population. G3 (Bethesda) 2021; 11:6347583. [PMID: 34568931 PMCID: PMC8496280 DOI: 10.1093/g3journal/jkab258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022]
Abstract
Studying genetic variation of gene expression provides a powerful way to unravel the molecular components underlying complex traits. Expression quantitative trait locus (eQTL) studies have been performed in several different model species, yet most of these linkage studies have been based on the genetic segregation of two parental alleles. Recently, we developed a multiparental segregating population of 200 recombinant inbred lines (mpRILs) derived from four wild isolates (JU1511, JU1926, JU1931, and JU1941) in the nematode Caenorhabditis elegans. We used RNA-seq to investigate how multiple alleles affect gene expression in these mpRILs. We found 1789 genes differentially expressed between the parental lines. Transgression, expression beyond any of the parental lines in the mpRILs, was found for 7896 genes. For expression QTL mapping almost 9000 SNPs were available. By combining these SNPs and the RNA-seq profiles of the mpRILs, we detected almost 6800 eQTLs. Most trans-eQTLs (63%) co-locate in six newly identified trans-bands. The trans-eQTLs found in previous two-parental allele eQTL experiments and this study showed some overlap (17.5–46.8%), highlighting on the one hand that a large group of genes is affected by polymorphic regulators across populations and conditions, on the other hand, it shows that the mpRIL population allows identification of novel gene expression regulatory loci. Taken together, the analysis of our mpRIL population provides a more refined insight into C. elegans complex trait genetics and eQTLs in general, as well as a starting point to further test and develop advanced statistical models for detection of multiallelic eQTLs and systems genetics studying the genotype–phenotype relationship.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Rita J M Volkers
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Joost Riksen
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
| | - Philip C Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, 24098 Kiel, Germany.,Competence Centre for Genomic Analysis (CCGA) Kiel, University of Kiel, 24098 Kiel, Germany
| | - Hinrich Schulenburg
- Zoological Institute, University of Kiel, 24098 Kiel, Germany.,Max Planck Institute for Evolutionary Biology, 24306 Ploen, Germany
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, NL-6708 PB Wageningen, The Netherlands
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13
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van der Woude L, Piotrowski M, Klaasse G, Paulus JK, Krahn D, Ninck S, Kaschani F, Kaiser M, Novák O, Ljung K, Bulder S, van Verk M, Snoek BL, Fiers M, Martin NI, van der Hoorn RAL, Robert S, Smeekens S, van Zanten M. The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases. Plant J 2021; 106:1523-1540. [PMID: 33768644 PMCID: PMC8360157 DOI: 10.1111/tpj.15250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
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Affiliation(s)
- Lennard van der Woude
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of PlantsFaculty of Biology and BiotechnologyUniversitätsstraße 150Bochum44801Germany
| | - Gruson Klaasse
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
| | - Judith K. Paulus
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Ondřej Novák
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
- Laboratory of Growth RegulatorsThe Czech Academy of Sciences & Faculty of ScienceInstitute of Experimental BotanyPalacký UniversityŠlechtitelů 27Olomouc78371Czech Republic
| | - Karin Ljung
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Suzanne Bulder
- Bejo Zaden B.V.Trambaan 1Warmenhuizen1749 CZthe Netherlands
| | - Marcel van Verk
- Plant‐Microbe InteractionsInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- KeygeneAgro Business Park 90Wageningen6708 PWthe Netherlands
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn Fiers
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
- Biological Chemistry GroupSylvius LaboratoriesInstitute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEthe Netherlands
| | - Renier A. L. van der Hoorn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Stéphanie Robert
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Sjef Smeekens
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn van Zanten
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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14
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Meisner A, Snoek BL, Nesme J, Dent E, Jacquiod S, Classen AT, Priemé A. Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles. ISME J 2021; 15:1207-1221. [PMID: 33408369 PMCID: PMC8115648 DOI: 10.1038/s41396-020-00844-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Climate change alters frequencies and intensities of soil drying-rewetting and freezing-thawing cycles. These fluctuations affect soil water availability, a crucial driver of soil microbial activity. While these fluctuations are leaving imprints on soil microbiome structures, the question remains if the legacy of one type of weather fluctuation (e.g., drying-rewetting) affects the community response to the other (e.g., freezing-thawing). As both phenomenons give similar water availability fluctuations, we hypothesized that freezing-thawing and drying-rewetting cycles have similar effects on the soil microbiome. We tested this hypothesis by establishing targeted microcosm experiments. We created a legacy by exposing soil samples to a freezing-thawing or drying-rewetting cycle (phase 1), followed by an additional drying-rewetting or freezing-thawing cycle (phase 2). We measured soil respiration and analyzed soil microbiome structures. Across experiments, larger CO2 pulses and changes in microbiome structures were observed after rewetting than thawing. Drying-rewetting legacy affected the microbiome and CO2 emissions upon the following freezing-thawing cycle. Conversely, freezing-thawing legacy did not affect the microbial response to the drying-rewetting cycle. Our results suggest that drying-rewetting cycles have stronger effects on soil microbial communities and CO2 production than freezing-thawing cycles and that this pattern is mediated by sustained changes in soil microbiome structures.
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Affiliation(s)
- Annelein Meisner
- grid.4514.40000 0001 0930 2361Microbial Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62 Lund, Sweden ,grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.418375.c0000 0001 1013 0288Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, Wageningen, The Netherlands ,grid.4818.50000 0001 0791 5666Present Address: Wageningen University & Research, Droevendaalsesteeg 4, Wageningen, The Netherlands
| | - Basten L. Snoek
- grid.5477.10000000120346234Theoretical Biology and Bioinformatics, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Joseph Nesme
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Elizabeth Dent
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
| | - Samuel Jacquiod
- grid.5613.10000 0001 2298 9313Agroécologie, AgroSup Dijon, INRAE Centre Dijon, Université de Bourgogne Franche-Comté, Dijon, France
| | - Aimée T. Classen
- grid.214458.e0000000086837370Ecology and Evolutionary Biology Department, University of Michigan, Ann Arbor, MI 48109 USA ,grid.59062.380000 0004 1936 7689The Gund Institute for Environment, University of Vermont, Burlington, VT USA ,grid.5254.60000 0001 0674 042XThe Center for Macroecology, Evolution and Climate, The University of Copenhagen, Copenhagen Ø, Denmark
| | - Anders Priemé
- grid.5254.60000 0001 0674 042XDepartment of Biology, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark ,grid.5254.60000 0001 0674 042XDepartment of Geosciences and Natural Resource Management, Center for Permafrost (CENPERM), University of Copenhagen, Øster Voldgade 10, 1350 Copenhagen, Denmark
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15
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Yu K, Stringlis IA, van Bentum S, de Jonge R, Snoek BL, Pieterse CMJ, Bakker PAHM, Berendsen RL. Transcriptome Signatures in Pseudomonas simiae WCS417 Shed Light on Role of Root-Secreted Coumarins in Arabidopsis-Mutualist Communication. Microorganisms 2021; 9:microorganisms9030575. [PMID: 33799825 PMCID: PMC8000642 DOI: 10.3390/microorganisms9030575] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/22/2022] Open
Abstract
Pseudomonas simiae WCS417 is a root-colonizing bacterium with well-established plant-beneficial effects. Upon colonization of Arabidopsis roots, WCS417 evades local root immune responses while triggering an induced systemic resistance (ISR) in the leaves. The early onset of ISR in roots shows similarities with the iron deficiency response, as both responses are associated with the production and secretion of coumarins. Coumarins can mobilize iron from the soil environment and have a selective antimicrobial activity that impacts microbiome assembly in the rhizosphere. Being highly coumarin-tolerant, WCS417 induces the secretion of these phenolic compounds, likely to improve its own niche establishment, while providing growth and immunity benefits for the host in return. To investigate the possible signaling function of coumarins in the mutualistic Arabidopsis-WCS417 interaction, we analyzed the transcriptome of WCS417 growing in root exudates of coumarin-producing Arabidopsis Col-0 and the coumarin-biosynthesis mutant f6′h1. We found that coumarins in F6′H1-dependent root exudates significantly affected the expression of 439 bacterial genes (8% of the bacterial genome). Of those, genes with functions related to transport and metabolism of carbohydrates, amino acids, and nucleotides were induced, whereas genes with functions related to cell motility, the bacterial mobilome, and energy production and conversion were repressed. Strikingly, most genes related to flagellar biosynthesis were down-regulated by F6′H1-dependent root exudates and we found that application of selected coumarins reduces bacterial motility. These findings suggest that coumarins’ function in the rhizosphere as semiochemicals in the communication between the roots and WCS417. Collectively, our results provide important novel leads for future functional analysis of molecular processes in the establishment of plant-mutualist interactions.
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Affiliation(s)
- Ke Yu
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475004, China
| | - Ioannis A. Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
| | - Sietske van Bentum
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Basten L. Snoek
- Theoretical Biology & Bioinformatics, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
| | - Peter A. H. M. Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
| | - Roeland L. Berendsen
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; (K.Y.); (I.A.S.); (S.v.B.); (R.d.J.); (C.M.J.P.); (P.A.H.M.B.)
- Correspondence: ; Tel.: +31-3025-36860
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16
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Sterken MG, Bevers RPJ, Volkers RJM, Riksen JAG, Kammenga JE, Snoek BL. Dissecting the eQTL Micro-Architecture in Caenorhabditis elegans. Front Genet 2020; 11:501376. [PMID: 33240309 PMCID: PMC7670075 DOI: 10.3389/fgene.2020.501376] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/13/2020] [Indexed: 01/11/2023] Open
Abstract
The study of expression quantitative trait loci (eQTL) using natural variation in inbred populations has yielded detailed information about the transcriptional regulation of complex traits. Studies on eQTL using recombinant inbred lines (RILs) led to insights on cis and trans regulatory loci of transcript abundance. However, determining the underlying causal polymorphic genes or variants is difficult, but ultimately essential for the understanding of regulatory networks of complex traits. This requires insight into whether associated loci are single eQTL or a combination of closely linked eQTL, and how this QTL micro-architecture depends on the environment. We addressed these questions by testing for independent replication of previously mapped eQTL in Caenorhabditis elegans using new data from introgression lines (ILs). Both populations indicate that the overall heritability of gene expression, number, and position of eQTL differed among environments. Across environments we were able to replicate 70% of the cis- and 40% of the trans-eQTL using the ILs. Testing eight different simulation models, we suggest that additive effects explain up to 60-93% of RIL/IL heritability for all three environments. Closely linked eQTL explained up to 40% of RIL/IL heritability in the control environment whereas only 7% in the heat-stress and recovery environments. In conclusion, we show that reproducibility of eQTL was higher for cis vs. trans eQTL and that the environment affects the eQTL micro-architecture.
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Affiliation(s)
- Mark G. Sterken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Roel P. J. Bevers
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Rita J. M. Volkers
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Joost A. G. Riksen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University & Research, Wageningen, Netherlands
- Theoretical Biology & Bioinformatics, Utrecht University, Utrecht, Netherlands
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17
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Lindhout FW, Kooistra R, Portegies S, Herstel LJ, Stucchi R, Snoek BL, Altelaar AFM, MacGillavry HD, Wierenga CJ, Hoogenraad CC. Quantitative mapping of transcriptome and proteome dynamics during polarization of human iPSC-derived neurons. eLife 2020; 9:e58124. [PMID: 32940601 PMCID: PMC7498259 DOI: 10.7554/elife.58124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
The differentiation of neuronal stem cells into polarized neurons is a well-coordinated process which has mostly been studied in classical non-human model systems, but to what extent these findings are recapitulated in human neurons remains unclear. To study neuronal polarization in human neurons, we cultured hiPSC-derived neurons, characterized early developmental stages, measured electrophysiological responses, and systematically profiled transcriptomic and proteomic dynamics during these steps. The neuron transcriptome and proteome shows extensive remodeling, with differential expression profiles of ~1100 transcripts and ~2200 proteins during neuronal differentiation and polarization. We also identified a distinct axon developmental stage marked by the relocation of axon initial segment proteins and increased microtubule remodeling from the distal (stage 3a) to the proximal (stage 3b) axon. This developmental transition coincides with action potential maturation. Our comprehensive characterization and quantitative map of transcriptome and proteome dynamics provides a solid framework for studying polarization in human neurons.
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Affiliation(s)
- Feline W Lindhout
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Robbelien Kooistra
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Sybren Portegies
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Lotte J Herstel
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Riccardo Stucchi
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht UniversityUtrechtNetherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht UniversityUtrechtNetherlands
| | - AF Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht UniversityUtrechtNetherlands
| | - Harold D MacGillavry
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Corette J Wierenga
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
| | - Casper C Hoogenraad
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht UniversityUtrechtNetherlands
- Department of Neuroscience, Genentech, IncSan FranciscoUnited States
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18
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Koorem K, Snoek BL, Bloem J, Geisen S, Kostenko O, Manrubia M, Ramirez KS, Weser C, Wilschut RA, van der Putten WH. Community-level interactions between plants and soil biota during range expansion. J Ecol 2020; 108:1860-1873. [PMID: 32999508 PMCID: PMC7508040 DOI: 10.1111/1365-2745.13409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Plant species that expand their range in response to current climate change will encounter soil communities that may hinder, allow or even facilitate plant performance. It has been shown repeatedly for plant species originating from other continents that these plants are less hampered by soil communities from the new than from the original range. However, information about the interactions between intra-continental range expanders and soil communities is sparse, especially at community level.Here we used a plant-soil feedback experiment approach to examine if the interactions between range expanders and soil communities change during range expansion. We grew communities of range-expanding and native plant species with soil communities originating from the original and new range of range expanders. In these conditioned soils, we determined the composition of fungi and bacteria by high-throughput amplicon sequencing of the ITS region and the 16S rRNA gene respectively. Nematode community composition was determined by microscopy-based morphological identification. Then we tested how these soil communities influence the growth of subsequent communities of range expanders and natives.We found that after the conditioning phase soil bacterial, fungal and nematode communities differed by origin and by conditioning plant communities. Despite differences in bacterial, fungal and nematode communities between original and new range, soil origin did not influence the biomass production of plant communities. Both native and range expanding plant communities produced most above-ground biomass in soils that were conditioned by plant communities distantly related to them. Synthesis. Communities of range-expanding plant species shape specific soil communities in both original and new range soil. Plant-soil interactions of range expanders in communities can be similar to the ones of their closely related native plant species.
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Affiliation(s)
- Kadri Koorem
- Netherlands Institute of Ecology Wageningen The Netherlands
- Department of Botany Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia
| | - Basten L Snoek
- Netherlands Institute of Ecology Wageningen The Netherlands
- Theoretical Biology and Bioinformatics Utrecht University Utrecht The Netherlands
- Laboratory of Nematology Wageningen University Wageningen The Netherlands
| | - Janneke Bloem
- Netherlands Institute of Ecology Wageningen The Netherlands
- Department of Plant Sciences Wageningen University Wageningen The Netherlands
| | - Stefan Geisen
- Netherlands Institute of Ecology Wageningen The Netherlands
- Laboratory of Nematology Wageningen University Wageningen The Netherlands
| | - Olga Kostenko
- Netherlands Institute of Ecology Wageningen The Netherlands
| | - Marta Manrubia
- Netherlands Institute of Ecology Wageningen The Netherlands
| | | | - Carolin Weser
- Netherlands Institute of Ecology Wageningen The Netherlands
| | - Rutger A Wilschut
- Netherlands Institute of Ecology Wageningen The Netherlands
- Ecology, Department of Biology University of Konstanz Konstanz Germany
| | - Wim H van der Putten
- Netherlands Institute of Ecology Wageningen The Netherlands
- Laboratory of Nematology Wageningen University Wageningen The Netherlands
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19
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Geshnizjani N, Snoek BL, Willems LAJ, Rienstra JA, Nijveen H, Hilhorst HWM, Ligterink W. Detection of QTLs for genotype × environment interactions in tomato seeds and seedlings. Plant Cell Environ 2020; 43:1973-1988. [PMID: 32419153 PMCID: PMC7496158 DOI: 10.1111/pce.13788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/01/2020] [Accepted: 05/12/2020] [Indexed: 05/17/2023]
Abstract
Seed quality and seedling establishment are the most important factors affecting successful crop development. They depend on the genetic background and are acquired during seed maturation and therefor, affected by the maternal environment under which the seeds develop. There is little knowledge about the genetic and environmental factors that affect seed quality and seedling establishment. The aim of this study is to identify the loci and possible molecular mechanisms involved in acquisition of seed quality and how these are controlled by adverse maternal conditions. For this, we used a tomato recombinant inbred line (RIL) population consisting of 100 lines which were grown under two different nutritional environmental conditions, high phosphate and low nitrate. Most of the seed germination traits such as maximum germination percentage (Gmax ), germination rate (t50 ) and uniformity (U8416 ) showed ample variation between genotypes and under different germination conditions. This phenotypic variation leads to identification of quantitative trait loci (QTLs) which were dependent on genetic factors, but also on the interaction with the maternal environment (QTL × E). Further studies of these QTLs may ultimately help to predict the effect of different maternal environmental conditions on seed quality and seedling establishment which will be very useful to improve the production of high-performance seeds.
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Affiliation(s)
- Nafiseh Geshnizjani
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsUtrecht UniversityUtrechtThe Netherlands
- Laboratory of NematologyWageningen UniversityWageningenThe Netherlands
| | - Leo A. J. Willems
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Juriaan A. Rienstra
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Harm Nijveen
- Bioinformatics GroupWageningen UniversityWageningenThe Netherlands
| | - Henk W. M. Hilhorst
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant PhysiologyWageningen UniversityWageningenThe Netherlands
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20
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Snoek BL, Sterken MG, Hartanto M, van Zuilichem AJ, Kammenga JE, de Ridder D, Nijveen H. WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans. Database (Oxford) 2020; 2020:baz149. [PMID: 31960906 PMCID: PMC6971878 DOI: 10.1093/database/baz149] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/30/2019] [Accepted: 12/13/2019] [Indexed: 12/19/2022]
Abstract
Quantitative genetics provides the tools for linking polymorphic loci to trait variation. Linkage analysis of gene expression is an established and widely applied method, leading to the identification of expression quantitative trait loci (eQTLs). (e)QTL detection facilitates the identification and understanding of the underlying molecular components and pathways, yet (e)QTL data access and mining often is a bottleneck. Here, we present WormQTL2, a database and platform for comparative investigations and meta-analyses of published (e)QTL data sets in the model nematode worm C. elegans. WormQTL2 integrates six eQTL studies spanning 11 conditions as well as over 1000 traits from 32 studies and allows experimental results to be compared, reused and extended upon to guide further experiments and conduct systems-genetic analyses. For example, one can easily screen a locus for specific cis-eQTLs that could be linked to variation in other traits, detect gene-by-environment interactions by comparing eQTLs under different conditions, or find correlations between QTL profiles of classical traits and gene expression. WormQTL2 makes data on natural variation in C. elegans and the identified QTLs interactively accessible, allowing studies beyond the original publications. Database URL: www.bioinformatics.nl/WormQTL2/.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Margi Hartanto
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Albert-Jan van Zuilichem
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
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21
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Pascoal S, Risse JE, Zhang X, Blaxter M, Cezard T, Challis RJ, Gharbi K, Hunt J, Kumar S, Langan E, Liu X, Rayner JG, Ritchie MG, Snoek BL, Trivedi U, Bailey NW. Field cricket genome reveals the footprint of recent, abrupt adaptation in the wild. Evol Lett 2019; 4:19-33. [PMID: 32055408 PMCID: PMC7006468 DOI: 10.1002/evl3.148] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 10/21/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022] Open
Abstract
Evolutionary adaptation is generally thought to occur through incremental mutational steps, but large mutational leaps can occur during its early stages. These are challenging to study in nature due to the difficulty of observing new genetic variants as they arise and spread, but characterizing their genomic dynamics is important for understanding factors favoring rapid adaptation. Here, we report genomic consequences of recent, adaptive song loss in a Hawaiian population of field crickets (Teleogryllus oceanicus). A discrete genetic variant, flatwing, appeared and spread approximately 15 years ago. Flatwing erases sound‐producing veins on male wings. These silent flatwing males are protected from a lethal, eavesdropping parasitoid fly. We sequenced, assembled and annotated the cricket genome, produced a linkage map, and identified a flatwing quantitative trait locus covering a large region of the X chromosome. Gene expression profiling showed that flatwing is associated with extensive genome‐wide effects on embryonic gene expression. We found that flatwing male crickets express feminized chemical pheromones. This male feminizing effect, on a different sexual signaling modality, is genetically associated with the flatwing genotype. Our findings suggest that the early stages of evolutionary adaptation to extreme pressures can be accompanied by greater genomic and phenotypic disruption than previously appreciated, and highlight how abrupt adaptation might involve suites of traits that arise through pleiotropy or genomic hitchhiking.
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Affiliation(s)
- Sonia Pascoal
- Department of Zoology University of Cambridge Cambridge CB2 3EJ United Kingdom
| | - Judith E Risse
- Division of Bioinformatics, Department of Plant Sciences Wageningen University & Research Wageningen 6708 PB The Netherlands.,Animal Ecology Netherlands Institute of Ecology Wageningen 6700 AB The Netherlands
| | - Xiao Zhang
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Mark Blaxter
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,Institute of Evolutionary Biology University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Timothee Cezard
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Richard J Challis
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Karim Gharbi
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,Earlham Institute Norwich Research Park Norwich NR4 7UZ United Kingdom
| | - John Hunt
- School of Science and Health and the Hawkesbury Institute for the Environment Western Sydney University Penrith NSW 2751 Australia.,Centre for Ecology and Conservation University of Exeter Penryn TR10 9FE United Kingdom
| | - Sujai Kumar
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Emma Langan
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom.,School of Environmental Sciences University of East Anglia Norwich NR4 7UZ United Kingdom
| | - Xuan Liu
- Centre for Genomic Research University of Liverpool Liverpool L69 7ZB United Kingdom
| | - Jack G Rayner
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Michael G Ritchie
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics Utrecht University Utrecht 3584 CH The Netherlands.,Terrestrial Ecology Netherlands Institute of Ecology Wageningen 6700 AB The Netherlands
| | - Urmi Trivedi
- Edinburgh Genomics University of Edinburgh Edinburgh EH9 3JT United Kingdom
| | - Nathan W Bailey
- School of Biology University of St Andrews St Andrews Fife KY16 9TH United Kingdom
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22
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Jovic K, Grilli J, Sterken MG, Snoek BL, Riksen JAG, Allesina S, Kammenga JE. Transcriptome resilience predicts thermotolerance in Caenorhabditis elegans. BMC Biol 2019; 17:102. [PMID: 31822273 PMCID: PMC6905072 DOI: 10.1186/s12915-019-0725-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The detrimental effects of a short bout of stress can persist and potentially turn lethal, long after the return to normal conditions. Thermotolerance, which is the capacity of an organism to withstand relatively extreme temperatures, is influenced by the response during stress exposure, as well as the recovery process afterwards. While heat-shock response mechanisms have been studied intensively, predicting thermal tolerance remains a challenge. RESULTS Here, we use the nematode Caenorhabditis elegans to measure transcriptional resilience to heat stress and predict thermotolerance. Using principal component analysis in combination with genome-wide gene expression profiles collected in three high-resolution time series during control, heat stress, and recovery conditions, we infer a quantitative scale capturing the extent of stress-induced transcriptome dynamics in a single value. This scale provides a basis for evaluating transcriptome resilience, defined here as the ability to depart from stress-expression dynamics during recovery. Independent replication across multiple highly divergent genotypes reveals that the transcriptional resilience parameter measured after a spike in temperature is quantitatively linked to long-term survival after heat stress. CONCLUSION Our findings imply that thermotolerance is an intrinsic property that pre-determines long-term outcome of stress and can be predicted by the transcriptional resilience parameter. Inferring the transcriptional resilience parameters of higher organisms could aid in evaluating rehabilitation strategies after stresses such as disease and trauma.
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Affiliation(s)
- Katharina Jovic
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Jacopo Grilli
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA
- Santa Fe Institute, 1399 Hyde Park Rd, Santa Fe, NM, 87501, USA
- The Abdus Salam International Center for Theoretical Physics (ICTP), Strada Costiera 11, I-34014, Trieste, Italy
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
| | - Stefano Allesina
- Department of Ecology and Evolution, University of Chicago, 1101 E 57th St, Chicago, IL, 60637, USA.
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.
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23
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Veen GF(C, Snoek BL, Bakx‐Schotman T, Wardle DA, Putten WH. Relationships between fungal community composition in decomposing leaf litter and home‐field advantage effects. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13351] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- G. F. (Ciska) Veen
- Department of Terrestrial Ecology Netherlands Institute of Ecology Wageningen The Netherlands
| | - Basten L. Snoek
- Department of Terrestrial Ecology Netherlands Institute of Ecology Wageningen The Netherlands
- Theoretical Biology and Bioinformatics Utrecht University Utrecht The Netherlands
- Laboratory of Nematology Wageningen University Wageningen The Netherlands
| | - Tanja Bakx‐Schotman
- Department of Terrestrial Ecology Netherlands Institute of Ecology Wageningen The Netherlands
| | - David A. Wardle
- Asian School of the Environment Nanyang Technological University Singapore Singapore
- Department of Forest Ecology and Management Swedish University of Agricultural Sciences Umeå Sweden
| | - Wim H. Putten
- Department of Terrestrial Ecology Netherlands Institute of Ecology Wageningen The Netherlands
- Laboratory of Nematology Wageningen University Wageningen The Netherlands
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24
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Geshnizjani N, Sarikhani Khorami S, Willems LAJ, Snoek BL, Hilhorst HWM, Ligterink W. The interaction between genotype and maternal nutritional environments affects tomato seed and seedling quality. J Exp Bot 2019; 70:2905-2918. [PMID: 30828721 DOI: 10.1093/jxb/erz101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 03/02/2019] [Indexed: 05/16/2023]
Abstract
Seed and seedling traits are affected by the conditions of the maternal environment, such as light, temperature, and nutrient availability. In this study, we have investigated whether different maternally applied nitrate and phosphate concentrations affect the seed and seedling performance of two closely related tomato species: Solanum lycopersicum cv. Money maker and Solanum pimpinellifolium accession CGN14498. We observed large differences for seed and seedling traits between the two species. Additionally, we have shown that for nitrate most of the seed and seedling traits were significantly affected by genotype-environment interactions (G×E). The effect of the maternal environment was clearly visible in the primary metabolites of the dry seeds. For example, we could show that the amount of γ-aminobutyric acid (GABA) in Money maker seeds was affected by the differences in the maternal environments and was positively correlated with seed germination under high temperature. Overall, compared with phosphate, nitrate had a larger effect on seed and seedling performance in tomato. In general, the different responses to the maternal environments of the two tomato species showed a major role for G×E in shaping seed and seedling traits.
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Affiliation(s)
- Nafiseh Geshnizjani
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg, PB Wageningen, The Netherlands
| | | | - Leo A J Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg, PB Wageningen, The Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg, PB Wageningen, The Netherlands
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan, Utrecht, The Netherlands
| | - Henk W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg, PB Wageningen, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg, PB Wageningen, The Netherlands
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25
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Kurm V, van der Putten WH, Weidner S, Geisen S, Snoek BL, Bakx T, Hol WHG. Competition and predation as possible causes of bacterial rarity. Environ Microbiol 2019; 21:1356-1368. [PMID: 30803145 PMCID: PMC6850713 DOI: 10.1111/1462-2920.14569] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 02/21/2019] [Indexed: 12/05/2022]
Abstract
We assembled communities of bacteria and exposed them to different nutrient concentrations with or without predation by protists. Taxa that were rare in the field were less abundant at low nutrient concentrations than common taxa, independent of predation. However, some taxa that were rare in the field became highly abundant in the assembled communities, especially under ample nutrient availability. This high abundance points at a possible competitive advantage of some rare bacterial taxa under nutrient-rich conditions. In contrast, the abundance of most rare bacterial taxa decreased at low resource availability. Since low resource availability will be the prevailing situation in most soils, our data suggests that under those conditions poor competitiveness for limiting resources may contribute to bacterial rarity. Interestingly, taxa that were rare in the field and most successful under predator-free conditions in the lab also tended to be more reduced by predation than common taxa. This suggests that predation contributes to rarity of bacterial taxa in the field. We further discuss whether there may be a trade-off between competitiveness and predation resistance. The substantial variability among taxa in their responses to competition and predation suggests that other factors, for example abiotic conditions and dispersal ability, also influence the local abundance of soil bacteria.
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Affiliation(s)
- Viola Kurm
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Wim H. van der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
- Laboratory of NematologyWageningen UniversityP.O. Box 8123, 6700 ES, WageningenThe Netherlands
| | - Simone Weidner
- Institute of Environmental Biology, Ecology and BiodiversityUtrecht UniversityPadualaan 8, 3584 CH, UtrechtThe Netherlands
| | - Stefan Geisen
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Basten L. Snoek
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
- Laboratory of NematologyWageningen UniversityP.O. Box 8123, 6700 ES, WageningenThe Netherlands
- Theoretical Biology and BioinformaticsUtrecht UniversityPadualaan 8, 3584 CH, UtrechtThe Netherlands
| | - Tanja Bakx
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
| | - Wilhelmina H. Gera Hol
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)P.O. Box 50, 6700 AB, WageningenThe Netherlands
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26
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Wang YA, Snoek BL, Sterken MG, Riksen JAG, Stastna JJ, Kammenga JE, Harvey SC. Genetic background modifies phenotypic and transcriptional responses in a C. elegans model of α-synuclein toxicity. BMC Genomics 2019; 20:232. [PMID: 30894116 PMCID: PMC6427842 DOI: 10.1186/s12864-019-5597-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 03/11/2019] [Indexed: 11/13/2022] Open
Abstract
Background Accumulation of protein aggregates are a major hallmark of progressive neurodegenerative disorders such as Parkinson’s disease and Alzheimer’s disease. Transgenic Caenorhabditis elegans nematodes expressing the human synaptic protein α-synuclein in body wall muscle show inclusions of aggregated protein, which affects similar genetic pathways as in humans. It is not however known how the effects of α-synuclein expression in C. elegans differs among genetic backgrounds. Here, we compared gene expression patterns and investigated the phenotypic consequences of transgenic α-synuclein expression in five different C. elegans genetic backgrounds. Results Transcriptome analysis indicates that α-synuclein expression effects pathways associated with nutrient storage, lipid transportation and ion exchange and that effects vary depending on the genetic background. These gene expression changes predict that a range of phenotypes will be affected by α-synuclein expression. We confirm this, showing that α-synuclein expression delayed development, reduced lifespan, increased rate of matricidal hatching, and slows pharyngeal pumping. Critically, these phenotypic effects depend on the genetic background and coincide with the core changes in gene expression. Conclusions Together, our results show genotype-specific effects and core alterations in both gene expression and in phenotype in response to α-synuclein expression. We conclude that the effects of α-synuclein expression are substantially modified by the genetic background, illustrating that genetic background needs to be considered in C. elegans models of neurodegenerative disease. Electronic supplementary material The online version of this article (10.1186/s12864-019-5597-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yiru A Wang
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK.,Laboratory of Nematology, Wageningen University, 6708, PB, Wageningen, The Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University, 6708, PB, Wageningen, The Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, 6708, PB, Wageningen, The Netherlands
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University, 6708, PB, Wageningen, The Netherlands
| | - Jana J Stastna
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, 6708, PB, Wageningen, The Netherlands
| | - Simon C Harvey
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK.
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27
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Snoek BL, Volkers RJM, Nijveen H, Petersen C, Dirksen P, Sterken MG, Nakad R, Riksen JAG, Rosenstiel P, Stastna JJ, Braeckman BP, Harvey SC, Schulenburg H, Kammenga JE. A multi-parent recombinant inbred line population of C. elegans allows identification of novel QTLs for complex life history traits. BMC Biol 2019; 17:24. [PMID: 30866929 PMCID: PMC6417139 DOI: 10.1186/s12915-019-0642-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/26/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The nematode Caenorhabditis elegans has been extensively used to explore the relationships between complex traits, genotypes, and environments. Complex traits can vary across different genotypes of a species, and the genetic regulators of trait variation can be mapped on the genome using quantitative trait locus (QTL) analysis of recombinant inbred lines (RILs) derived from genetically and phenotypically divergent parents. Most RILs have been derived from crossing two parents from globally distant locations. However, the genetic diversity between local C. elegans populations can be as diverse as between global populations and could thus provide means of identifying genetic variation associated with complex traits relevant on a broader scale. RESULTS To investigate the effect of local genetic variation on heritable traits, we developed a new RIL population derived from 4 parental wild isolates collected from 2 closely located sites in France: Orsay and Santeuil. We crossed these 4 genetically diverse parental isolates to generate a population of 200 multi-parental RILs and used RNA-seq to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the 4 genotypes with an average spacing of 11 kb, doubling the mapping resolution relative to currently available RIL panels for many loci. The SNPs were used to construct a genetic map to facilitate QTL analysis. We measured life history traits such as lifespan, stress resistance, developmental speed, and population growth in different environments, and found substantial variation for most traits. We detected multiple QTLs for most traits, including novel QTLs not found in previous QTL analysis, including those for lifespan and pathogen responses. This shows that recombining genetic variation across C. elegans populations that are in geographical close proximity provides ample variation for QTL mapping. CONCLUSION Taken together, we show that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates facilitates the detection of QTLs. The use of multi-parent RIL populations can further enhance our understanding of local adaptation and life history trade-offs.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands. .,Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Rita J M Volkers
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Harm Nijveen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Carola Petersen
- Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Philipp Dirksen
- Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Rania Nakad
- Zoological Institute, University of Kiel, 24098, Kiel, Germany
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, University of Kiel, 24098, Kiel, Germany
| | - Jana J Stastna
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK
| | - Bart P Braeckman
- Department of Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000, Ghent, Belgium
| | - Simon C Harvey
- Biomolecular Research Group, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU, UK
| | - Hinrich Schulenburg
- Zoological Institute, University of Kiel, 24098, Kiel, Germany. .,Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.
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Dröge-Laser W, Snoek BL, Snel B, Weiste C. The Arabidopsis bZIP transcription factor family-an update. Curr Opin Plant Biol 2018; 45:36-49. [PMID: 29860175 DOI: 10.1016/j.pbi.2018.05.001] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/30/2018] [Accepted: 05/02/2018] [Indexed: 05/18/2023]
Abstract
The basic (region) leucine zippers (bZIPs) are evolutionarily conserved transcription factors in eukaryotic organisms. Here, we have updated the classification of the Arabidopsis thaliana bZIP-family, comprising 78 members, which have been assorted into 13 groups. Arabidopsis bZIPs are involved in a plethora of functions related to plant development, environmental signalling and stress response. Based on the classification, we have highlighted functional and regulatory aspects of selected well-studied bZIPs, which may serve as prototypic examples for the particular groups.
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Affiliation(s)
- Wolfgang Dröge-Laser
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg 97082, Germany.
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Christoph Weiste
- Department of Pharmaceutical Biology, Julius-von-Sachs-Institute, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg 97082, Germany.
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29
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van Herwijnen MJC, Driedonks TAP, Snoek BL, Kroon AMT, Kleinjan M, Jorritsma R, Pieterse CMJ, Hoen ENMN', Wauben MHM. Abundantly Present miRNAs in Milk-Derived Extracellular Vesicles Are Conserved Between Mammals. Front Nutr 2018; 5:81. [PMID: 30280098 PMCID: PMC6153340 DOI: 10.3389/fnut.2018.00081] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/20/2018] [Indexed: 12/22/2022] Open
Abstract
Mammalian milk is not only a source of nutrition for the newborn, but also contains various components that regulate further development. For instance, milk is an abundant source of microRNAs (miRNAs), which are evolutionary conserved small non-coding RNAs that are involved in post-transcriptional regulation of target mRNA. MiRNAs present in milk can occur in extracellular vesicles (EVs), which are nanosized membrane vesicles released by many cell types as a means of intercellular communication. The membrane of EVs protects enclosed miRNAs from degradation and harbors molecules that allow specific targeting to recipient cells. Although several studies have investigated the miRNA content in milk EVs from individual species, little is known about the evolutionary conserved nature of EV-associated miRNAs among different species. In this study, we profiled the miRNA content of purified EVs from human and porcine milk. These data were compared to published studies on EVs from human, cow, porcine, and panda milk to assess the overlap in the top 20 most abundant miRNAs. Interestingly, several abundant miRNAs were shared between species (e.g., let-7 family members let-7a, let-7b, let-7f, and miR-148a). Moreover, these miRNAs have been implicated in immune-related functions and regulation of cell growth and signal transduction. The conservation of these miRNA among species, not only in their sequence homology, but also in their incorporation in milk EVs of several species, suggests that they are evolutionarily selected to regulate cell function in the newborn.
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Affiliation(s)
- Martijn J C van Herwijnen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Tom A P Driedonks
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Department of Biology, Science4Life Utrecht University, Utrecht, Netherlands
| | - A M Theresa Kroon
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Marije Kleinjan
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Ruurd Jorritsma
- Department of Farm Animal Health, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life Utrecht University, Utrecht, Netherlands
| | - Esther N M Nolte-'t Hoen
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
| | - Marca H M Wauben
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine Utrecht University, Utrecht, Netherlands
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30
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Ramirez KS, Geisen S, Morriën E, Snoek BL, van der Putten WH. Network Analyses Can Advance Above-Belowground Ecology. Trends Plant Sci 2018; 23:759-768. [PMID: 30072227 DOI: 10.1016/j.tplants.2018.06.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 06/05/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
An understanding of above-belowground (AG-BG) ecology is important for evaluating how plant interactions with enemies, symbionts, and decomposers affect species diversity and will respond to global changes. However, research questions and experiments often focus on only a limited number of interactions, creating an incomplete picture of how entire communities may be involved in AG-BG community ecology. Therefore, a pressing challenge is to formulate hypotheses of AG-BG interactions when considering communities in their full complexity. Here we discuss how network analyses can be a powerful tool to progress AG-BG research, link across scales from individual to community and ecosystem, visualize community interactions between the two (AG and BG) subsystems, and develop testable hypotheses.
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Affiliation(s)
- Kelly S Ramirez
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands.
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700 ES, Wageningen, The Netherlands
| | - Elly Morriën
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Institute of Biodiversity and Ecosystem Dynamics, Department of Ecosystem and Landscape Dynamics (IBED-ELD), University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands
| | - Basten L Snoek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700 ES, Wageningen, The Netherlands; Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB, Wageningen, The Netherlands; Laboratory of Nematology, Wageningen University, P.O. Box 8123, 6700 ES, Wageningen, The Netherlands
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31
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Gao AW, Sterken MG, Uit de Bos J, van Creij J, Kamble R, Snoek BL, Kammenga JE, Houtkooper RH. Natural genetic variation in C. elegans identified genomic loci controlling metabolite levels. Genome Res 2018; 28:1296-1308. [PMID: 30108180 PMCID: PMC6120624 DOI: 10.1101/gr.232322.117] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/20/2018] [Indexed: 12/31/2022]
Abstract
Metabolic homeostasis is sustained by complex biological networks that respond to nutrient availability. Genetic and environmental factors may disrupt this equilibrium, leading to metabolic disorders, including obesity and type 2 diabetes. To identify the genetic factors controlling metabolism, we performed quantitative genetic analysis using a population of 199 recombinant inbred lines (RILs) in the nematode Caenorhabditis elegans We focused on the genomic regions that control metabolite levels by measuring fatty acid (FA) and amino acid (AA) composition in the RILs using targeted metabolomics. The genetically diverse RILs showed a large variation in their FA and AA levels with a heritability ranging from 32% to 82%. We detected strongly co-correlated metabolite clusters and 36 significant metabolite quantitative trait loci (mQTL). We focused on mQTL displaying highly significant linkage and heritability, including an mQTL for the FA C14:1 on Chromosome I, and another mQTL for the FA C18:2 on Chromosome IV. Using introgression lines (ILs), we were able to narrow down both mQTL to a 1.4-Mbp and a 3.6-Mbp region, respectively. RNAi-based screening focusing on the Chromosome I mQTL identified several candidate genes for the C14:1 mQTL, including lagr-1, Y87G2A.2, nhr-265, nhr-276, and nhr-81 Overall, this systems approach provides us with a powerful platform to study the genetic basis of C. elegans metabolism. Furthermore, it allows us to investigate interventions such as nutrients and stresses that maintain or disturb the regulatory network controlling metabolic homeostasis, and identify gene-by-environment interactions.
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Affiliation(s)
- Arwen W Gao
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Jelmi Uit de Bos
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Jelle van Creij
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Rashmi Kamble
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, 1105 AZ Amsterdam, The Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, 1105 AZ Amsterdam, The Netherlands
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32
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Meisner A, Jacquiod S, Snoek BL, Ten Hooven FC, van der Putten WH. Drought Legacy Effects on the Composition of Soil Fungal and Prokaryote Communities. Front Microbiol 2018; 9:294. [PMID: 29563897 PMCID: PMC5845876 DOI: 10.3389/fmicb.2018.00294] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/08/2018] [Indexed: 12/14/2022] Open
Abstract
It is increasingly acknowledged that climate change is influencing terrestrial ecosystems by increased drought and rainfall intensities. Soil microbes are key drivers of many processes in terrestrial systems and rely on water in soil pores to fulfill their life cycles and functions. However, little is known on how drought and rainfall fluctuations, which affect the composition and structure of microbial communities, persist once original moisture conditions have been restored. Here, we study how simulated short-term drying and re-wetting events shape the community composition of soil fungi and prokaryotes. In a mesocosm experiment, soil was exposed to an extreme drought, then re-wetted to optimal moisture (50% WHC, water holding capacity) or to saturation level (100% WHC). Composition, community structure and diversity of microbes were measured by sequencing ITS and 16S rRNA gene amplicons 3 weeks after original moisture content had been restored. Drying and extreme re-wetting decreased richness of microbial communities, but not evenness. Abundance changes were observed in only 8% of prokaryote OTUs, and 25% of fungal OTUs, whereas all other OTUs did not differ between drying and re-wetting treatments. Two specific legacy response groups (LRGs) were observed for both prokaryotes and fungi. OTUs belonging to the first LRG decreased in relative abundance in soil with a history of drought, whereas OTUs that increased in soil with a history of drought formed a second LRG. These microbial responses were spread among different phyla. Drought appeared to be more important for the microbial community composition than the following extreme re-wetting. 16S profiles were correlated with both inorganic N concentration and basal respiration and ITS profiles correlated with fungal biomass. We conclude that a drying and/or an extreme re-wetting history can persist in soil microbial communities via specific response groups composed of members with broad phylogenetic origins, with possible functional consequences on soil processes and plant species. As a large fraction of OTUs responding to drying and re-wetting belonged to the rare biosphere, our results suggest that low abundant microbial species are potentially important for ecosystem responses to extreme weather events.
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Affiliation(s)
- Annelein Meisner
- Microbial Ecology, Department of Biology, Lund University, Lund, Sweden.,Sections of Microbiology and Terrestrial Ecology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | | | - Basten L Snoek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
| | - Freddy C Ten Hooven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, Wageningen, Netherlands.,Laboratory of Nematology, Wageningen University, Wageningen, Netherlands
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33
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Snoek BL, Pavlova P, Tessadori F, Peeters AJM, Bourbousse C, Barneche F, de Jong H, Fransz PF, van Zanten M. Genetic Dissection of Morphometric Traits Reveals That Phytochrome B Affects Nucleus Size and Heterochromatin Organization in Arabidopsis thaliana. G3 (Bethesda) 2017; 7:2519-2531. [PMID: 28592555 PMCID: PMC5555459 DOI: 10.1534/g3.117.043539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/31/2017] [Indexed: 02/05/2023]
Abstract
Microscopically visible chromatin is partitioned into two major components in Arabidopsis thaliana nuclei. On one hand, chromocenters are conspicuous foci of highly condensed "heterochromatic" domains that contain mostly repeated sequences. On the other hand, less condensed and gene-rich "euchromatin" emanates from these chromocenters. This differentiation, together with the dynamic nature of chromatin compaction in response to developmental and environmental stimuli, makes Arabidopsis a powerful system for studying chromatin organization and dynamics. Heterochromatin dynamics can be monitored by measuring the Heterochromatin Index, i.e., the proportion of nuclei displaying well-defined chromocenters, or the DNA fraction of chromocenters (relative heterochromatin fraction). Both measures are composite traits, thus their values represent the sum of effects of various underlying morphometric properties. We exploited genetic variation between natural occurring accessions to determine the genetic basis of individual nucleus and chromocenter morphometric parameters (area, perimeter, density, roundness, and heterogeneity) that together determine chromatin compaction. Our novel reductionist genetic approach revealed quantitative trait loci (QTL) for all measured traits. Genomic colocalization among QTL was limited, which suggests a complex genetic regulation of chromatin compaction. Yet genomic intervals of QTL for nucleus size (area and perimeter) both overlap with a known QTL for heterochromatin compaction that is explained by natural polymorphism in the red/far-red light and temperature receptor Phytochrome B. Mutant analyses and genetic complementation assays show that Phytochrome B is a negative regulator of nucleus size, revealing that perception of climatic conditions by a Phytochrome-mediated hub is a major determinant for coordinating nucleus size and heterochromatin compaction.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, 6708 PB, The Netherlands
- Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity
| | - Penka Pavlova
- Laboratory of Genetics, Wageningen University, 6708 PB, The Netherlands
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM, The Netherlands
| | - Federico Tessadori
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, 3584 CT, The Netherlands
| | - Anton J M Peeters
- Department of Biology, Institute of Education, Utrecht University, 3584 CH, The Netherlands
| | - Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, F-75005, France
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale U1024, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, F-75005, France
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, 6708 PB, The Netherlands
| | - Paul F Fransz
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM, The Netherlands
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, The Netherlands
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Snoek BL, Sterken MG, Bevers RPJ, Volkers RJM, Van't Hof A, Brenchley R, Riksen JAG, Cossins A, Kammenga JE. Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans. BMC Genomics 2017; 18:500. [PMID: 28662696 PMCID: PMC5492678 DOI: 10.1186/s12864-017-3899-8] [Citation(s) in RCA: 247] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022] Open
Abstract
Background Cryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematode Caenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population. Results We measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. The cis-eQTL were highly shared across treatments. A considerable fraction of the trans-eQTL (40–57%) mapped to 19 treatment specific trans-bands. In contrast to cis-eQTL, trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of the trans-eQTL were only induced in a single treatment, with heat-stress showing the most unique trans-eQTL. Conclusions These results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 h) and that CGV is mainly determined by response related trans regulatory eQTL. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3899-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Roel P J Bevers
- Laboratory of Nematology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Rita J M Volkers
- Laboratory of Nematology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Arjen Van't Hof
- Centre for Genome research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Rachel Brenchley
- Centre for Genome research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Joost A G Riksen
- Laboratory of Nematology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Andrew Cossins
- Centre for Genome research, Institute of Integrative Biology, Biosciences Building, University of Liverpool, L69 7ZB, Liverpool, UK
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
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Nijveen H, Ligterink W, Keurentjes JJB, Loudet O, Long J, Sterken MG, Prins P, Hilhorst HW, de Ridder D, Kammenga JE, Snoek BL. AraQTL - workbench and archive for systems genetics in Arabidopsis thaliana. Plant J 2017; 89:1225-1235. [PMID: 27995664 DOI: 10.1111/tpj.13457] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/24/2016] [Accepted: 12/06/2016] [Indexed: 06/06/2023]
Abstract
Genetical genomics studies uncover genome-wide genetic interactions between genes and their transcriptional regulators. High-throughput measurement of gene expression in recombinant inbred line populations has enabled investigation of the genetic architecture of variation in gene expression. This has the potential to enrich our understanding of the molecular mechanisms affected by and underlying natural variation. Moreover, it contributes to the systems biology of natural variation, as a substantial number of experiments have resulted in a valuable amount of interconnectable phenotypic, molecular and genotypic data. A number of genetical genomics studies have been published for Arabidopsis thaliana, uncovering many expression quantitative trait loci (eQTLs). However, these complex data are not easily accessible to the plant research community, leaving most of the valuable genetic interactions unexplored as cross-analysis of these studies is a major effort. We address this problem with AraQTL (http://www.bioinformatics.nl/Ara QTL/), an easily accessible workbench and database for comparative analysis and meta-analysis of all published Arabidopsis eQTL datasets. AraQTL provides a workbench for comparing, re-using and extending upon the results of these experiments. For example, one can easily screen a physical region for specific local eQTLs that could harbour candidate genes for phenotypic QTLs, or detect gene-by-environment interactions by comparing eQTLs under different conditions.
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Affiliation(s)
- Harm Nijveen
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Joost J B Keurentjes
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, 78000, France
| | - Jiao Long
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Pjotr Prins
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Henk W Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
| | - Basten L Snoek
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, Wageningen, NL-6708 PB, The Netherlands
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Zych K, Snoek BL, Elvin M, Rodriguez M, Van der Velde KJ, Arends D, Westra HJ, Swertz MA, Poulin G, Kammenga JE, Breitling R, Jansen RC, Li Y. reGenotyper: Detecting mislabeled samples in genetic data. PLoS One 2017; 12:e0171324. [PMID: 28192439 PMCID: PMC5305221 DOI: 10.1371/journal.pone.0171324] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/19/2017] [Indexed: 12/11/2022] Open
Abstract
In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples seriously reduce the power to detect the genetic basis of phenotypic variation. We have developed an approach to detect potential mislabeling, recover the “ideal” genotype and identify “best-matched” labels for mislabeled samples. On average, we identified 4% of samples as mislabeled in eight published datasets, highlighting the necessity of applying a “data cleaning” step before standard data analysis.
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Affiliation(s)
- Konrad Zych
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - Basten L. Snoek
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Mark Elvin
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Miriam Rodriguez
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - K. Joeri Van der Velde
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Danny Arends
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - Harm-Jan Westra
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Morris A. Swertz
- Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gino Poulin
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Jan E. Kammenga
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Ritsert C. Jansen
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
| | - Yang Li
- Groningen Bioinformatics Centre, University of Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- * E-mail:
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