Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Methanol based chain elongation with acetate to n-butyrate and isobutyrate at varying selectivities dependent on pH
    Leeuw, Kasper de; Smit, Sanne de; Oossanen, Sabine van; Moerland, Merijn ; Buisman, Cees ; Strik, David - \ 2020
    Wageningen University & Research
    PRJEB36205 - ERP119366 - metagenome
    Biomass fermentation technologies offer alternative methods to produce platform chemicals that currently originate from fossil sources. This research showed that an enriched microbiome was capable to produce iso-butyric acid via methanol based chain elongation of acetate. A long term continuous reactor experiment showed that the selectivity for isobutyrate (i-C4) and/or n-butyrate (n-C4) could be reversibly adjusted by changing the reactor pH. A reactor pH of 6.75 led to formation of (carbon per total carbon of products) of 0.78 n-C4 and 0.024 i-C4, whereas a reactor pH of 5.2 led to a selectivity of 0.25 n-C4 and 0.63 i-C4 . This shift in product spectrum was also represented by a shift in microbial composition. The results suggest that an Eubacterium genus is responsible for the formation of n-C4, whereas a Clostridium luticellarii strain is responsible for the formation of a mixture of i-C4 and n¬¬-C4. The formation of n and i-C4 at a low pH was observed to be coupled according to the thermodynamics of isomerization. At a reactor pH of 5.5 and 5.2 the product ratio of i-C4:n-C4 approached the ratio of 0.684 i-C4 : 0.316 n-C4, which is the theoretical ratio that would be achieved when i-C4 and n-C4 would be formed at amounts determined by the equilibrium of isomerization. Various batch experiments at pH 5.5 and 5.2 confirmed that addition of either n-C4 or i-C4 at the start of the batch would immediately lead to the formation of the other butyrate component. Moreover, batch experiments performed at pH 6.5 immediately produced mainly n-C4 and led to the development of a completely different microbiome. The imposed pH as a strong selective pressure can immediately facilitate changes in product selectivities for n-C4 and i-C4 during methanol based chain elongation of acetate.
    Whole genome sequencing of Fusarium fujikuroi species complex members
    Brankovics, Balázs ; Diepeningen, Anne van; Hoog, G.S. de; Lee, Theo van der; Waalwijk, Cees - \ 2020
    Wageningen University & Research
    PRJEB38038 - ERP121406 - Fusarium redolens - Fusarium sacchari - Fusarium concentricum - Fusarium annulatum - Fusarium globosum - Fusarium acutatum - Fusarium verticillioides - Fusarium musae - Fusarium andiyazi - Fusarium napiforme - Fusarium ramigenum - Fusarium pseudocircinatum - Fusarium lactis - Fusarium brevicatenulatum - Fusarium pseudonygamai - Fusarium nygamai - Fusarium bactridioides - Fusarium anthophilum - Fusarium begoniae - Fusarium ananatum - Fusarium guttiforme - Fusarium foetens - Fusarium oxysporum - Fusarium ficicrescens - Fusarium pseudoanthophilum - Fusarium denticulatum
    In total, 23 Fusarium fujikuroi species complex member species and 3 outgroup species were whole genome sequenced. FFSC: Fusarium sacchari CBS:147.25, Fusarium concentricum CBS:450.97, Fusarium annulatum CBS:258.54, Fusarium globosum CBS:428.97, Fusarium acutatum CBS:402.97, Fusarium verticillioides CBS:576.78, Fusarium musae CBS:624.87, Fusarium andiyazi CBS:119857, Fusarium napiforme CBS:748.97, Fusarium ramigenum CBS:418.97, Fusarium pseudocircinatum CBS:449.97, Fusarium lactis CBS:411.97, Fusarium ficicrescens CBS:125178, Fusarium brevicatenulatum CBS:404.97, Fusarium pseudoanthophilum CBS:414.97, Fusarium pseudonygamai CBS:417.97, Fusarium nygamai CBS:749.97, Fusarium bactridioides CBS:100057, Fusarium anthophilum CBS:119858, Fusarium begoniae CBS:452.97, Fusarium ananatum CBS:118516, Fusarium guttiforme CBS:409.97, Fusarium denticulatum CBS:407.97. Outgroup: Fusarium foetens CBS:110286, Fusarium oxysporum CBS:130302, and Fusarium redolens CBS:743.97
    Propionate converting anaerobic microbial communities enriched from distinct biogeochemical zones of Aarhus Bay, Denmark under sulfidogenic and methanogenic conditions
    Ozuolmez, Derya ; Stams, Fons ; Plugge, Caroline - \ 2020
    Wageningen University
    PRJEB36640 - ERP119855 - Propionate conversion - uncultured marine microorganism
    The relationship between predominant physiological types of prokaryotes in marine sediments and propionate degradation through sulfate reduction, fermentation, and methanogenesis was studied in marine sediments. Propionate conversion was assessed in slurries containing sediment from three different biogeochemical zones of Aarhus Bay, Denmark. Sediment slurries were amended with 0, 3 or 20 mM sulfate and incubated at 25°C and 10°C for 514 - 571 days. At the end of the incubation period, methanogenesis in the sulfate zone and sulfate reduction in the methane zone slurries was observed. Both processes occurred simultaneously in enrichments originating from samples along the whole sediment. Bacterial community analysis revealed dominance of Desulfobacteraceae and Desulfobulbaceae members in sulfate-amended slurries incubated at 25°C and 10°C. Cryptanaerobacter belonging to Peptococcaceae family dominated sulfate-free, methanogenic slurries at 25°C whereas bacteria related to Desulfobacteraceae were dominant at 10°C. Archaeal community analysis revealed prevalence of different genera belonging to Methanomicrobiales in slurries incubated at different temperatures and amended with different sulfate concentrations. Methanosarcinaceae were observed only in the absence of sulfate. In summary, Aarhus Bay sediment zones contain sulfate reducers, syntrophs and methanogens interacting with each other in the conversion of propionate . Our results indicate that in Aarhus Bay sediments Cryptanaerobacter degrade propionate in syntrophic association with methanogens.
    Archaeal diversity in sediment slurries degrading butyrate or propionate derived from Aarhus Bay
    Ozuolmez, Derya ; Stams, Fons ; Plugge, Caroline - \ 2020
    Wageningen University
    PRJEB36882 - ERP120135 - uncultured marine microorganism - Propionate degradation - Butyrate degradation
    The relationship between predominant physiological types of prokaryotes in marine sediments and propionate degradation through sulfate reduction, fermentation, and methanogenesis was studied in marine sediments. Propionate conversion was assessed in slurries containing sediment from three different biogeochemical zones of Aarhus Bay, Denmark. Sediment slurries were amended with 0, 3 or 20 mM sulfate and incubated at 25°C and 10°C for 514 - 571 days. Methanogenesis in the sulfate zone and sulfate reduction in the methane zone slurries was observed. Both processes occurred simultaneously in enrichments originating from samples along the whole sediment. Bacterial community analysis revealed dominance of Desulfobacteraceae and Desulfobulbaceae members in sulfate-amended slurries incubated at 25°C and 10°C. Cryptanaerobacter belonging to Peptococcaceae family dominated sulfate-free, methanogenic slurries at 25°C, whereas bacteria related to Desulfobacteraceae were dominant at 10°C. Archaeal community analysis revealed prevalence of different genera belonging to Methanomicrobiales in slurries incubated at different temperatures and amended with different sulfate concentrations. Methanosarcinaceae were only detected in the absence of sulfate. In summary, Aarhus Bay sediment zones contain sulfate reducers, syntrophs and methanogens interacting with each other in the conversion of propionate. Our results indicate that in Aarhus Bay sediments Cryptanaerobacter degrades propionate in syntrophic association with methanogens.
    Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation
    Ottenburghs, Jente ; Honka, Johanna ; Müskens, Gerhard ; Ellegren, Hans - \ 2020
    Wageningen University
    PRJEB35788 - ERP118901 - Anser fabalis - Anser serrirostris - Bean Goose - Genomics
    Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes of closely related species. Specifically, genetic differentiation is often concentrated in particular genomic regions (“islands of differentiation”) that might contain barrier loci contributing to reproductive isolation, whereas the rest of the genome is homogenized by introgression. Alternatively, linked selection can produce differentiation islands in allopatry without introgression. We explored the influence of introgression on the landscape of genetic differentiation in two hybridizing goose taxa: the Taiga Bean Goose (Anser fabalis) and the Tundra Bean Goose (A. serrirostris). Using a combination of population genomic summary statistics and demographic modelling, we reconstructed the evolutionary history of these birds and quantified the impact of introgression on the build-up and maintenance of genetic differentiation. We found evidence for a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Subsequent introgression events led to high levels of gene flow, mainly from the Tundra Bean Goose into the Taiga Bean Goose. This scenario resulted in a largely undifferentiated genomic landscape (genome-wide FST = 0.033) with a few notable differentiation peaks that were scattered across chromosomes. The summary statistics indicated that some peaks might contain barrier loci while others arose in allopatry through linked selection. Finally, based on the low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argue that the Taiga and the Tundra Bean Goose should be treated as subspecies.
    Soil Microbial Communities on the anode and 2-m distance of Tubular Plant Microbial Fuel Cell in a Paddy Field in West Kalimantan, Indonesia
    Sudirjo, Emilius ; Jager, Pim de; Buisman, Cees ; Strik, David - \ 2020
    Wageningen University
    PRJEB34787 - ERP117748 - metagenome - Plant Microbial Fuel Cell - Soil Microbial Communities - Paddy Field
    Soil samples were collected (on 30 June 2018) from 6 different locations for microbial community analysis from a paddy field in West Kalimantan, Indonesia (0.919215N, 109.468182E; elevation 100m above sea level). Sample A: Soil that attached on the anode from mid of Plant-MFC 1Sample B: soil that attached on the anode from end of the plant-MFC 1Sample C: Soil that attached on the anode from mid of Plant-MFC 2Sample D: soil that attached on the anode from end of the plant-MFC 2Sample E: soil from 2 m distance at northen side of plant-MFC 1 & 2Sample F: soil from 2 m distance at southern side of plant-MFC 1 & 2Samples were grouped into 3: Group I (Samples A and C) was soil that attached on the anode from mid plant-MFC; Group II (samples B and D) was soil that attached on the anode from end of the plant-MFC; and Group III (samples E and F) was from soil with 2 m distance from plant-MFC 1 and 2. After collection, samples were kept in a 30ml-tube container and keep in 40C fridge. The next day samples were transported for 48hours with a cool-ice box for DNA extraction to Genetika Lab, Jakarta (PT. Genetika Science Indonesia), a partner company from 1st BASE Axil Scientific Pte Ltd, Singapore. Sequencing steps were performed by 1st BASEas following: the universal primers that targeted the V3V4 regions were used for amplification. The quantity and quality of the PCR product that targeted the V3V4 regions were measured using Tapestation 4200, picogreen and nanodrop. All the samples passed the QC measurement and proceed straight for a library preparation. The libraries were prepared using Illumina 16s metagenomics library prep kit and their quality and quantity were determine using Agilent Tapestation 4200, Picogreen and qPCR. These libraries were then pooled according to the protocol recommended by the Illumina and proceed straight to sequencing using MiSeq platform at 2x301PE format by 1st BASE Axil Scientific Pte Ltd, Singapore.
    Lactate formation and subsequent chain elongation in repeated-batch food waste fermentation
    Contreras Davila, Carlos ; Carrión, Víctor J. ; Vonk, Vincent R. ; Buisman, Cees ; Strik, David - \ 2020
    Wageningen University & Research
    PRJEB33791 - ERP116611 - metagenome - lactate - n-caproate - food waste - fermentation
    The production of biochemicals, materials and biofuels from renewables through biorefinery processes is important to reduce the anthropogenic impact on the environment. Chain elongation processes based on open microbiomes have been successfully developed to produce medium-chain fatty acids (versatile platform products) from organic waste streams. Yet, the sustainability of chain elongation can still be improved by reducing the use of electron donors and reducing chemicals use. This work aimed to in situ produce the electron donor lactate coupled to subsequent chain elongation for n-caproate production with decreased chemicals use for pH control. Food waste was used as substrate in repeated-batch fermentation experiments.
    Differences exist in the faecal microbiota of domesticated equines
    Edwards, Joan ; Schennink, Angeline ; Burden, F. ; Long, S. ; Doorn, D.A. van; Pellikaan, Wilbert ; Dijkstra, Jan ; Saccenti, Edoardo ; Smidt, Hauke - \ 2020
    Wageningen University
    PRJEB32772 - ERP115488 - Metagenome - Equine species - faecal microbiota - Comparison
    Background: Compared to horses and ponies, donkeys have increased degradation of dietary fiber. The longer total mean retention time of feed in the donkey gut has been proposed to be the basis of this, because of the increased time available for feed to be acted upon by enzymes and the gut microbiota. However, differences in terms of microbial concentrations and/or community composition in the hindgut may also underpin this. Therefore, a study was conducted to determine the effect of equine type on the faecal microbiota of three types of domesticated equines: pony, donkey and pony × donkey hybrid (i.e. mule/hinny).Results: Equine type had no significant effect on faecal dry matter content or faecal concentrations of bacteria, archaea and anaerobic fungi. However, equine type did significantly affect the faecal community composition of prokaryotes and anaerobic fungi. Two bacterial genera were significantly higher in donkey compared to both pony and pony x donkey: Lachnoclostridium 10 and ‘probable genus 10’ from the Lachnospiraceae family. Equine type also significantly affected the anaerobic fungal community composition. Piromyces was significantly lower in donkey compared to pony × donkey, with pony not significantly differing from either equine type. In contrast, the uncultivated genus SK3 was only found in donkey (4 of the 8 animals), and not at all in pony or pony × donkey. Anaerobic fungal diversity, as indicated by the number of OTUs, was also significantly higher in donkey, with no significant differences found between pony and pony × donkey.Conclusions: Donkey faecal microbiota differed from that of both pony and pony × donkey. These differences related to an increase in the relative abundance and diversity of taxa with known, or speculated, roles in plant material degradation. These findings are consistent with the previously reported increased fiber degradation in donkeys compared to ponies, and suggests that the hindgut microbiota play a role as well as differences in total retention time of feed. This offers novel opportunities to generate more energy from dietary fiber, decreasing the need for energy dense feeds which are a risk factor for gut-mediated disease.
    Parallel genetic origin of foot feathering in birds
    Bortoluzzi, Chiara ; Megens, Hendrik-Jan ; Bosse, Mirte ; Derks, Martijn ; Dibbits, Bert ; Laport, Kimberley ; Weigend, Steffen ; Groenen, Martien ; Crooijmans, Richard - \ 2020
    Wageningen University
    PRJEB36674 - ERP119891 - chicken - parallel evolution - foot feathering - Gallus gallus
    Understanding the genetic basis of similar phenotypes shared between lineages is a long-lasting research interest. Even though animal evolution offers many examples of parallelism, for many phenotypes little is known about the underlying genes and mutations. We here use a combination of whole-genome sequencing, expression analyses, and comparative genomics to study the parallel genetic origin of ptilopody (Pti) in chicken. Ptilopody (or foot feathering) is a polygenic trait that can be observed in domesticated and wild avian species and is characterized by the partial or complete development of feathers on the ankle and feet. In domesticated birds, ptilopody is easily selected to fixation, though extensive variation in the type and level of feather development is often observed. By mean of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17 kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways. Our study confirms that ptilopody has evolved through parallel evolution in chicken and pigeon.
    Genomics of Rapid Evolution in Field Crickets
    Pascoal, Sonia ; Risse, Judith ; Zhang, Xiao ; Blaxter, Mark ; Cezard, Timothee ; Challis, Richard J. ; Gharbi, Karim ; Hunt, John ; Kumar, Sujai ; Langan, Emma ; Liu, Xuan ; Rayner, Jack G. ; Ritchie, Michael G. ; Snoek, Basten ; Trivedi, Urmi ; Bailey, Nathan W. - \ 2020
    University of Edinburgh
    PRJEB24786 - ERP106639 - Teleogryllus oceanicus - cricket - genomics
    This study reveals the genomic architecture of a rapidly evolving mutation which segregates as a single-locus, X-linked trait -- flatwing -- in wild Hawaiian field crickets (Teleogryllus oceanicus). Flatwingsilences males by eliminating sound-producing structures on their forewings. Silence protects them from an acoustically-orienting parasitoid fly (Ormia ochracea), but interferes with their ability to attract and court females for mating. Silent crickets spread rapidly on several Hawaiian islands under pressure from the flies, representing one of the fastest rates of evoutionary change documented in the wild. Here we present an annotated genome sequence of T. oceanicus along with a linkage map and QTL analysis of the trait derived from RAD-sequencing of a backcrossed mapping population. RNA-seq was used to probe the functional pathways affected by the mutation during early development, and pleiotropic effects on another signaling trait, cuticular hydrocarbons, were assessed and genetically mapped.
    Focus op optimalisatie
    Doornewaard, G.J. ; Haan, M.H.A. de - \ 2020
    V-focus 17 (2020)3. - ISSN 1574-1575 - p. 12 - 14.
    In het Noord-Brabantse Maren-Kessel ligt het melkveebedrijf van Koeien & Kansen-deelnemers Maurice en Ankie van Erp. Na een periode van groei ligt de focus van het bedrijf nu vooral op optimalisatie en het verder verbeteren van de technische en economische prestaties, waarbij de ondernemers ook nadrukkelijk rekening willen houden met de wensen van de consument.
    Circadian misalignment imposed by nocturnal feeding tends to increase fat deposition in pigs
    Erp, Rik J.J. Van; Vries, Sonja De; Kempen, Theo A.T.G. Van; Hartog, Leo A. Den; Gerrits, Walter J.J. - \ 2020
    The British journal of nutrition 123 (2020)5. - ISSN 0007-1145 - p. 529 - 536.
    Circadian clock - Energy metabolism - Feed intake patterns - Heat production - Methane production

    Misalignment of day/night and feeding rhythms has been shown to increase fat deposition and the risk for metabolic disorders in humans and rodents. In most studies, however, food intake and intake patterns are not controlled. We studied the effects of circadian misalignment on energy expenditure in pigs while controlling for food intake as well as intake patterns. Twelve groups of five male pigs were housed in respiration chambers and fed either during the day (10.00-18.00 hours; DF) or night (22.00-06.00 hours; NF), bihourly the same sequential meals, representing 15, 10, 25, 30 and 20 % of the daily allowance. Paired feeding was applied to ensure equal gross energy intake between treatments. Apparent total tract digestibility, energy balances and heat partitioning were measured and analysed using a mixed linear model. Apparent total tract energy and DM digestibility tended to be lower for NF-pigs than DF-pigs (P < 0·10). Heat production was 3 % lower for NF-pigs than DF-pigs (P < 0·026), increasing fat retention by 7 % in NF-pigs (P = 0·050). NF-pigs were less active than DF-pigs during the feeding period, but more active during the fasting period. RMR was greater for DF-pigs than NF-pigs during the fasting period. Methane production was 30 % greater in NF-pigs than DF-pigs (P < 0·001). In conclusion, circadian misalignment has little effect on nutrient digestion, but alters nutrient partitioning, ultimately increasing fat deposition. The causality of the association between circadian misalignment and methane production rates remains to be investigated.

    Feed intake patterns nor growth rates of pigs are affected by dietary resistant starch, despite marked differences in digestion
    Erp, R.J.J. Van; Vries, S. De; Kempen, T.A.T.G. Van; Hartog, L.A. Den; Gerrits, W.J.J. - \ 2020
    Animal 14 (2020)7. - ISSN 1751-7311 - p. 1402 - 1412.
    digesta passage rate - feeding behavior - fermented starch - net energy value - swine

    Current feed evaluation systems often assume that fermented starch (i.e. resistant starch (RS)) yields less energy than digested starch. However, growth rates of pigs fed low and high RS diets are often the same when feed is available ad libitum. This may be explained by its effect on digestive processes changing feeding behavior, and consequently energy utilization. This study aims to investigate the effect of RS on nutrient digestion and digesta passage rate in pigs, in combination with its effect on feeding behavior and growth performance under ad libitum conditions. In experiment 1, 20 male pigs (40 ± 2.82 kg) were fed diets containing either 50% waxy maize starch (low in RS (LRS)) or high-amylose maize starch (high in RS (HRS)), and soluble and insoluble indigestible markers. After 14 days of adaptation to the diets, pigs were fed hourly to reach steady state (6 h), dissected, and digesta were collected from eight segments. From the collected samples, nutrient digestion and passage rate of the solid and liquid digesta fraction were determined. In experiment 2, 288 pigs (80 ± 0.48 kg; sex ratio per pen 1: 1; boar: gilt) were housed in groups of 6. Pigs were ad libitum-fed one of the experimental diets, and slaughtered at approximately 115 kg. Feed intake, growth and carcass parameters were measured. Ileal starch digestibility was greater for LRS-fed than for HRS-fed pigs (98.0% v. 74.0%; P < 0.001), where the additional undigested starch in HRS-fed pigs was fermented in the large intestine. No effects of RS on digesta passage rate of the solid or liquid digesta fraction and on feeding behavior were observed. Growth rate and feed intake did not differ between diets, whereas feed efficiency of HRS-fed pigs was 1%-unit higher than that of LRS-fed pigs (P = 0.041). The efficiency of feed used for carcass gain did not differ between diets indicating that the difference in feed efficiency was determined by the non-carcass fraction. Despite a 30% greater RS intake (of total starch) with HRS than with LRS, carcass gain and feed efficiency used for carcass gain were unaffected. RS did not affect digesta passage rate nor feeding behavior suggesting that the difference in energy intake between fermented and digested starch is compensated for post-absorptively. Our results indicate that the net energy value of fermented starch currently used in pig feed evaluation systems is underestimated and should be reconsidered.

    Metagenomic survey of chloroform fate in hypersaline lake Strawbridge in western Australia
    Peng, Peng ; Lu, Yue ; Bosma, Tom ; Nijenhuis, Ivonne ; Nijsse, Bart ; Shetty, Sudarshan ; Ruecker, Alexander ; Umanetc, Alexander ; Ramiro Garcia, Javier ; Kappler, Andreas ; Sipkema, Detmer ; Smidt, Hauke ; Atashgahi, Siavash - \ 2019
    Wageningen University
    PRJEB32090 - ERP114723 - Chloroform degradation - Hypersaline lakes - Sediment metagenome
    Chloroform (CF) is an environmental contaminant that can be naturally formed in hypersaline lake Strawbridge in western Australia. Anaerobic enrichment cultures using sediments from this lake showed CF degradation to dichloromethane (DCM) and CO2. The potential microbes and genes involved in CF degradation were investigated using metagenome sequencing. Known organohalide-respiring bacteria and their reductive dehalogenase genes were not detected. Rather, acetogens like Clostridium and methanogens like Methanosarcina that are capable for co-metabolically degrading CF to DCM and CO2 were detected in the sediment microcosms and enrichment cultures. Additionally, haloalkane dehalogenase and oxygenase that are possibly involved in further aerobic degradation of DCM were also detected in the sediment microcosms and enrichment cultures. These findings show that microbiota may act as a filter for CF emission from hypersaline lakes to the atmosphere.
    The ability to manipulate ROS metabolism in pepper may affect aphid virulence
    Sun, Mengjing ; Voorrips, Roeland ; Kaauwen, Martijn van; Visser, Richard ; Vosman, Ben - \ 2019
    Wageningen University & Research
    PRJEB35311 - ERP118348 - Myzus persicae
    Myzus persicae has severe economic impact on pepper (Capsicum) cultivation. We tested two populations of M. persicae, NL and SW (avirulent and virulent) respectively on C. baccatum accession PB2013071. The transcriptomics approach used in the current study, which is the first study to explore the pepper-aphid interaction at the whole genome gene expression level, revealed genes whose expression is differentially regulated in pepper accession PB2013071 upon infestation with these M. persicae populations. The NL population induced ROS production genes, while the SW population induced ROS scavenging genes and repressed ROS production genes. We also found that the SW population can induce the removal of ROS which accumulated in response to pre-infestion with the NL population, and that pre-infestation with the SW population significantly improved the performance of the NL population.
    Reciprocal cybrids reveal how organellar genomes affect plant phenotypes - RNA Sequencing
    Flood, Padraic ; Theeuwen, Tom ; Schneeberger, Korbinian ; Keizer, Paul ; Kruijer, Willem ; Severing, Edouard ; Kouklas, Evangelos ; Hageman, Jos ; Wijfjes, Raul ; Calvo Baltanas, Vanesa ; Becker, Frank ; Schnabel, Sabine ; Willems, Leo ; Ligterink, Wilco ; Arkel, Jeroen van; Mumm, Roland ; Gualberto, José M. ; Savage, Linda ; Kramer, David M. ; Keurentjes, Joost ; Eeuwijk, Fred van; Koornneef, Maarten ; Harbinson, Jeremy ; Aarts, Mark ; Wijnker, Erik - \ 2019
    Wageningen University
    PRJEB35324 - ERP118362 - Arabidopsis thaliana - RNA Sequencing - Cybrids
    Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions. We show that natural variation in the plasmotype results in additive as well as epistatic effects across all phenotypic categories. Plasmotypes which induce more additive phenotypic changes also cause more significant epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multilevel Nucleotype x Plasmotype x Environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation which is predominantly exposed under certain conditions. The production of cybrids using haploid inducers is a quick and precise method for assessing the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in nucleotype-plasmotype interactions and identify favourable combinations to improve plant performance.
    Reciprocal cybrids reveal how organellar genomes affect plant phenotypes - Whole Genome Sequencing
    Flood, Padraic ; Theeuwen, Tom ; Schneeberger, Korbinian ; Keizer, Paul ; Kruijer, Willem ; Severing, Edouard ; Kouklas, Evangelos ; Hageman, Jos ; Wijfjes, Raul ; Calvo Baltanas, Vanesa ; Becker, Frank ; Schnabel, Sabine ; Willems, Leo ; Ligterink, Wilco ; Arkel, Jeroen van; Mumm, Roland ; Gualberto, José M. ; Savage, Linda ; Kramer, David M. ; Keurentjes, Joost ; Eeuwijk, Fred van; Koornneef, Maarten ; Harbinson, Jeremy ; Aarts, Mark ; Wijnker, Erik - \ 2019
    Wageningen University
    PRJEB29654 - ERP111970 - Arabidopsis thaliana - Whole Genome Sequencing - Cybrids
    Assessing the impact of variation in chloroplast and mitochondrial DNA (collectively termed the plasmotype) on plant phenotypes is challenging due to the difficulty in separating their effect from nuclear derived variation (the nucleotype). Haploid inducer lines can be used as efficient plasmotype donors to generate new plasmotype-nucleotype combinations (cybrids). We generated a panel comprising all possible cybrids of seven Arabidopsis thaliana accessions and extensively phenotyped these lines for 1859 phenotypes under stable and fluctuating conditions. We show that natural variation in the plasmotype results in additive as well as epistatic effects across all phenotypic categories. Plasmotypes which induce more additive phenotypic changes also cause more significant epistatic effects, suggesting a possible common basis for both additive and epistatic effects. On average epistatic interactions explained twice as much of the variance in phenotypes as additive plasmotype effects. The impact of plasmotypic variation was also more pronounced under fluctuating and stressful environmental conditions. Thus, the phenotypic impact of variation in plasmotypes is the outcome of multilevel Nucleotype x Plasmotype x Environment interactions and, as such, the plasmotype is likely to serve as a reservoir of variation which is predominantly exposed under certain conditions. The production of cybrids using haploid inducers is a quick and precise method for assessing the phenotypic effects of natural variation in organellar genomes. It will facilitate efficient screening of unique nucleotype-plasmotype combinations to both improve our understanding of natural variation in nucleotype-plasmotype interactions and identify favourable combinations to improve plant performance.
    The Synchytrium endobioticum AvrSen1 triggers a Hypersensitive Response in Sen1 potatoes while natural variants evade detection
    Vossenberg, Bart van de; Prodhomme, Charlotte ; Arkel, Gert van; Gent-Pelzer, Marga van; Bergervoet-van Deelen, Marjan ; Brankovics, Balázs ; Przetakiewicz, J. ; Visser, Richard ; Lee, Theo van der; Vossen, Jack - \ 2019
    Wageningen University and Research
    PRJEB31420 - ERP113980 - Synchytrium endobioticum
    Synchytrium endobioticum is an obligate biotrophic fungus of the phylum Chytridiomycota. It causes potato wart disease, has a world-wide quarantine status and is included on the HHS and USDA Select Agent list. S. endobioticum isolates are grouped in pathotypes based on their ability to evade host-resistance in a set of differential potato varieties. So far, thirty-nine pathotypes are reported. A single dominant gene (Sen1) governs pathotype 1 resistance and we anticipated that the underlying molecular model would involve a pathogen effector (AvrSen1) that is recognized by the host.The S. endobioticum specific secretome of fourteen isolates representing six different pathotypes was screened for effectors specifically present in pathotype 1(D1) isolates but absent in others. We discovered a single AvrSen1 candidate. Expression of this candidate in potato Sen1 plants showed a specific hypersensitive response, which co-segregated with the Sen1 resistance in potato populations. No HR was obtained with truncated genes found in pathotypes that evaded recognition by Sen1. These findings established that our candidate gene was indeed Avrsen1. AvrSen1 is a single copy gene and encodes a 376 amino acid protein without predicted function or functional domains, and is the first effector gene identified in Chytridiomycota.
    Population bottlenecks and deleterious variation in small populations
    Bortoluzzi, Chiara ; Bosse, Mirte ; Derks, Martijn ; Crooijmans, Richard ; Groenen, Martien ; Megens, Hendrik-Jan - \ 2019
    Wageningen University
    PRJEB34245 - ERP117120 - chicken breeds - whole genome sequencing - Gallus gallus
    Predictions about the consequences of a small population size on genetic and deleterious variation are fundamental to population genetics. As small populations are more affected by genetic drift, purifying selection acting against deleterious alleles is predicted to be less efficient, therefore increasing the risk of inbreeding depression. However, the extent to which small populations are subjected to genetic drift depends on the nature and time frame in which the bottleneck occurs. Domesticated species are an excellent model to investigate the consequences of population bottlenecks on genetic and deleterious variation in small populations. This is because their history is dominated by known bottlenecks associated with domestication, breed formation, and intense selective breeding. Here, we use whole-genome sequencing data from 97 chickens representing 39 traditional fancy breeds to directly examine the consequences of two types of bottlenecks on deleterious variation: the severe domestication bottleneck and the recent population decline accompanying breed formation. We find that recently bottlenecked populations have a higher proportion of deleterious variants relative to populations that have been kept at small population sizes since domestication. We also observe that long tracts of homozygous genotypes (runs of homozygosity) are proportionally more enriched in deleterious variants than the rest of the genome. This enrichment is particularly evident in recently bottlenecked populations, suggesting that homozygosity of these variants is likely to occur due to genetic drift and recent inbreeding. Our results indicate that the timing and nature of population bottlenecks can substantially shape the deleterious variation landscape in small populations.
    Whole genome sequencing of Heterandria formosa reveals information about the evolution of the placenta in the livebearing fish family Poeciliidae
    Kruistum, Henri van; Heuvel, Joost van den; Travis, Joseph ; Kraaijeveld, Ken ; Zwaan, Bas ; Groenen, Martien ; Megens, Hendrik-Jan ; Pollux, Bart - \ 2019
    Wageningen University
    PRJEB28818 - ERP111075 - Heterandria formosa - Comparative genomics - Poeciliidae
    Background: The evolution of complex organs is thought to occur via a stepwise process, each subsequent step increasing the organ’s complexity by a tiny amount. Studying this process requires closely related species that vary in the complexity of their organs. This is the case for the placenta in the livebearing fish family Poeciliidae, as members of this family vary markedly in their placental complexity. Here, we look for the genomic basis underlying this phenotypic variation in the genome of Heterandria formosa, a poeciliid fish with a highly complex placenta. We compare this genome to three published reference genomes of non-placental poeciliid fish to gain insight in which genes play a role in the evolution of the placenta in the Poeciliidae. Results: We sequenced the genome of H. formosa, providing the first whole genome sequence information of a placental poeciliid. We looked for signatures of adaptive evolution by comparing its gene sequences to those of three non-placental live-bearing relatives. We found 18 positively selected genes exclusive to H. formosa, as well as 5 gene duplications. Eight of the genes evolving under positive selection in H. formosa have a placental function in mammals, most notably endometrial tissue remodelling or endometrial cell proliferation. Conclusions: Our results show that a substantial portion of positively selected genes have a function that correlates well with the morphological changes that form the placenta of H. formosa, compared to the corresponding tissue in non-placental poeciliids. These functions are mainly endometrial tissue remodelling and endometrial cell proliferation. Therefore, we hypothesize that natural selection acting on genes involved in these functions plays a key role in the evolution of the placenta in H. formosa.
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