Mechanisms of vegetative propagation in bulbs : a molecular approach
Moreno-Pachón, Natalia - \ 2017
Wageningen University. Promotor(en): R.G.H. Immink, co-promotor(en): H.W.M. Hilhorst. - Wageningen : Wageningen University - ISBN 9789463437011 - 178
ornamental bulbs - tulipa - lilium - vegetative propagation - flowering date - gene regulation - genes - transcriptomes - dna sequencing - regeneration - shoot apices - bloembollen - tulipa - lilium - vegetatieve vermeerdering - bloeidatum - genregulatie - genen - transcriptomen - dna-sequencing - verjonging - scheuttoppen
Vegetative propagation is very important for the survival of species with long juvenile and adult vegetative phases, as it is the case for bulbous plants. Bulbous plants are ornamental geophytes with a bulb as an underground storage organ. Among flower bulbs, tulip and lily are the two commercially leading plants in The Netherlands. Tulip propagates vegetatively via axillary bud outgrowth, while lily propagates via adventitious bulblet formation. The vegetative propagation rate in tulip is very low due to the limited amount of axillary buds that will grow successfully. Moreover, tulip is very recalcitrant to in vitro regeneration. On the other hand, lily propagates efficiently via adventitious bulblet formation, either naturally from the underground portion of the stem of the apical bud, or artificially from detached bulb scales.
This thesis study aimed to understand how axillary bud outgrowth is controlled in tulip bulbs and how regeneration capacity is established in lily bulb scales. As a first step towards these goals, the state of the art of the molecular control of sexual and vegetative reproduction was reviewed for model species. Moreover, two approaches, “bottom-up” and “top-down”, to transfer the knowledge from model to non-model species were described (Chapter 2). In short, the “bottom-up” approach usually goes from individual genes to systems, assuming conservation of molecular pathways and using sequence homology searches to identify candidate genes. ”Top-down” methodologies go from systems to genes, and are based on large scale transcriptome profiling via e.g. microarrays or RNA sequencing, followed by the identification of associations between phenotypes, genes, and gene expression patterns and levels.
Next (Chapter 3), two sets of high quality transcriptomes, one for tulip and one for lily were generated from a collection of several tissues using the Illumina HiSeq 2000 platform. Several assembly filtering parameters were applied, to highlight the limitations of stringent but routinely used filtering in de novo transcriptome assembly. The final created transcriptomes were made publicly available via a user friendly Transcriptome browser (http://www.bioinformatics.nl/bulbs/db/species/index) and their usefulness was exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family.
One TCP member was of special interest because it has proven to integrate several pathways that control axillary bud outgrowth in a wide range of species. It is called TEOSINTE BRANCHED 1 (TB1) in monocots and BRNACHED 1 (BRC1) in dicots. A Tulipa gesneriana TB1 transcript was identified from the generated transcriptome and subsequently, tulip axillary bud outgrowth was studied through a “bottom-up” approach (Chapter 4). The degree of axillary bud outgrowth in tulip determines the success of their vegetative propagation. However the number of axillary meristems in one bulb is low –six on average– and not all of them seem to have the same growth capacity. The combination of physiological and targeted molecular experiments indicated that the first two inner located buds do not seem to experience dormancy (assessed by weight increase and TgTB1expression) at any point of the growth cycle, while mid-located buds enter dormancy by the end of the growing season. Moreover it was shown that TgTB1 expression in tulip bulbs can be modulated by sucrose, cytokinin and strigolactone, just as it has been reported for other species. However, the limited growth of mid-located buds even when their TgTB1 expression was naturally or artificially downregulated, pointed at other factors, probably physical, inhibiting their growth.
Next, the remarkable regeneration capacity of lily by initiating de novo shoot meristems from excised bulb scales without the addition of exogenous hormones or growth regulators was studied using a “top-down” approach (Chapter 5). An extensive and comprehensive transcriptome set was generated from lily bulb scales in a time-series using two cultivars and two explant types, all differing in regeneration capacity. This set up provided first insight in the key molecular process underlying pro-meristem induction and meristem initiation in lily. We found that wounding activates a very fast regeneration response, probably mediated by APETALA2/ETHYLENE RESPONSIVE FACTORS (AP2/ERF,) such as LoERF115 and WOUND INDUCED DEDIFFERENTIATION 2 (LoWIND2), which in turn might mediate polar auxin re-distribution, cell proliferation and de-differentiation. Moreover, the timing and level of induction of shoot meristem regulators, such as ENHANCER OF SHOOT REGENERATION 2 (LoESR2) and SHOOT MERISTEMLESS (LoSTM) correlated with the regeneration capacity of the scale.
Regardless the regeneration capacity of the different explants e.g. cultivar or position within the scale, regeneration occurs at the proximal-adaxial side of the bulb scale, right on top of the excision line. Thus the possible cellular and physiological factors granting lily bulb scales their competence to regenerate was investigated (Chapter 6). We found that the adaxial parenchyma tissue seems to be more competent than the abaxial tissue, partially because of higher number of secondary veins and larger cell population than the abaxial parenchyma region. It was proposed that upon explant excision, the polar auxin transport is disrupted, creating an auxin maximum at the excision line, which might create a gradient of cell divisions favouring the adaxial parenchyma tissue. The direction of this cell division gradient proved to be negatively affected by the absence of the adaxial epidermis. Moreover, explants without epidermis reduced dramatically their regeneration capacity, and lost the typical proximal-adaxial orientation of regeneration. Thus, a better understanding of the composition and physiology of the epidermis in lily bulb scales is essential to identify the regeneration stimulating signals originating from this tissue layer in Lilium sp.
Finally in Chapter 7, integration of all the results was done and I addressed how this may contributes to the fundamental and applied understanding of vegetative propagation in bulbous plants. Also, some challenges are discussed, for example, the complexity in the architecture of tulip bulbs and how this influences ways for improving its rate of axillary bud outgrowth. The challenge to prove the findings of this thesis through functional analysis is also discussed and the possibility of using transient virus-induced gene silencing is highlighted. Moreover, the potential of lily bulb scales as a model system to study some aspects of de novo regeneration, as well as to study the recalcitrance of in vitro propagation is highlighted, supporting the idea that more “omics” data and biotechnological tools for bulbous plant research are necessary.
Prospects of whole-genome sequence data in animal and plant breeding
Binsbergen, Rianne van - \ 2017
Wageningen University. Promotor(en): R.F. Veerkamp; F.A. Eeuwijk, co-promotor(en): M.P.L. Calus. - Wageningen : Wageningen University - ISBN 9789463431903 - 220
next generation sequencing - dna sequencing - quantitative trait loci - cattle - genomics - solanum lycopersicum - animal breeding - plant breeding - next generation sequencing - dna-sequencing - loci voor kwantitatief kenmerk - rundvee - genomica - solanum lycopersicum - dierveredeling - plantenveredeling
The rapid decrease in costs of DNA sequencing implies that whole-genome sequence data will be widely available in the coming few years. Whole-genome sequence data includes all base-pairs on the genome that show variation in the sequenced population. Consequently, it is assumed that the causal mutations (e.g. quantitative trait loci; QTL) are included, which allows testing a given trait directly for association with a QTL, and might lead to discovery of new QTL or higher accuracies in genomic predictions compared to currently available marker panels. The main aim of this thesis was to investigate the benefits of using whole-genome sequence data in breeding of animals and plants compared to currently available marker panels. First the potential and benefits of using whole-genome sequence data were studied in (dairy) cattle. Accuracy of genotype imputation to whole-genome sequence data was generally high, depending on the used marker panel. In contrast to the expectations, genomic prediction showed no advantage of using whole-genome sequence data compared to a high density marker panel. Thereafter, the use of whole-genome sequence data for QTL detection in tomato (S. Lycopersicum) was studied. In a recombinant inbred line (RIL) population, more QTL were found when using sequence data compared to a marker panel, while increasing marker density was not expected to provide additional power to detect QTL. Next to the RIL population, also in an association panel it was shown that, even with limited imputation accuracy, the power of a genome-wide association study can be improved by using whole-genome sequence data. For successful application of whole-genome sequence data in animals or plants, genotype imputation will remain important to obtain accurate sequence data for all individuals in a cost effective way. Sequence data will increase the power of QTL detection in RIL populations, association panels or outbred populations. Added value of whole-genome sequence data in genomic prediction will be limited, unless more information is known about the biological background of traits and functional annotations of DNA. Also statistical models that incorporate this information and that can efficiently handle large datasets have to be developed.
Characterization of Coxiella burnetii outbreak strains
Kuley, Runa - \ 2017
Wageningen University. Promotor(en): M.A. Smits; J.M. Wells, co-promotor(en): A. Bossers. - Wageningen : Wageningen University - ISBN 9789463431514 - 226
coxiella burnetii - q fever - outbreaks - strains - characterization - pathogenesis - zoonoses - virulence - dna sequencing - polymerase chain reaction - livestock farming - netherlands - coxiella burnetii - q-koorts - uitbraken (ziekten) - stammen (biologisch) - karakterisering - pathogenese - zoönosen - virulentie - dna-sequencing - polymerase-kettingreactie - veehouderij - nederland
Q fever is a worldwide zoonotic infectious disease caused by the bacterium Coxiella burnetii. During 2007-2010, the largest Q fever outbreak was reported in The Netherlands, where more than 4000 human cases were registered showing a serious burden of the disease. During this outbreak, goats harboring predominantly the CbNL01 genotype strain were identified as the major source of disease in humans and drastic measures such as mass culling of infected goats were implemented to reduce the spread of the pathogen and control the disease. In order to minimize such complications in the future, it is crucial to have a thorough understanding of the disease causing pathogen and to develop effective Q fever vaccines. The causes of the large Dutch outbreak are not well-understood and one of the main reasons speculated were the hyper-virulent behavior of the circulating C. burnetii isolates. The research described in this thesis focuses on the characterization of C. burnetii outbreak strains isolated from infected goats, cattle, sheep and human clinical materials. Our studies were initiated to better understand the bacterial pathogenesis, virulence, evolution, adaptations in various environments, host immune responses and to identify pathogen related factors that have modulated the disease outbreak. We specifically aimed to identify the virulence factors and mechanisms that contributed to the increased zoonotic potential of the strain associated with the Dutch Q fever outbreak.
The studies presented in this thesis majorly applied Pathogenomic approaches at the genome and transcriptome level to decipher host-pathogen interactions and to develop new tools to study C. burnetii infections. A transcriptome analysis of the outbreak C. burnetii strain of the CbNL01 genotype grown under in vivo and in vitro conditions resulted in the identification of distinct metabolic adaptations and virulence mechanisms of the bacterium. Detailed comparative analysis of complete genome sequences of C. burnetii strains showed a high similarity between strains of the same genotype. Genome sequences of the Dutch outbreak CbNL01 genotype strains were more divergent than the genome sequences of the less prevalent CbNL12 genotype strains and the NM reference strain. The analysis also showed that the high virulence of the outbreak strains was not associated with acquiring novel virulence-related genes arguing against the idea that the Dutch outbreak was due to emergence of hyper-virulent strains though horizontal gene transfer. Among the prominent genetic differences in the CbNL01 outbreak strains compared to CbNL12 and NM, were the presence of several point mutations and increased transposon mediated genome plasticity, which might have contributed to its epidemic potential. Point mutations, especially in a large number of membrane proteins, could also have contributed to the increased zoonotic potential of CbNL01 strains allowing this clone to escape the host immune responses in goats and humans. In addition, mutations in critical genes involved in virulence and evasion of the host immune system could be potentially involved in the increased virulence of the CbNL01 outbreak strains. On the contrary, studies on host immune responses in an in vivo (experimental infections in mice) and an in vitro (human PBMC’s stimulation) model did not show any difference associated with the strain genotype. However, differences in immune responses were found to be associated with the host-origin of the C. burnetii strains. Among different host-origin strains, strains derived from goats and humans generated significantly lower innate and adaptive immune responses than strains derived from cattle, whereas no differences in immune responses were observed when strains were grouped based upon their genotype. These observations support immune evasions as a major virulence strategy of goat and human strains in hosts and further suggest that bacteria originating from goats have a greater potential to cause outbreaks in humans. This indicates that for Q fever prevention purposes goats should be efficiently monitored for the presence of C. burnetii. Taken together, the results described in this thesis suggest that the virulence potential of C. burnetii strains is not only based on genetic differences, but also on other host-adaptation mechanisms such as transposition of genomic elements and/or differential regulation of gene expression. Finally, the results from this thesis provide a framework for future studies in the development of vaccines and diagnostic tools for Q fever.
Mining the human intestinal microbiota for biomarkers associated with metabolic disorders
Hermes, Gerben - \ 2016
Wageningen University. Promotor(en): Hauke Smidt; Erwin Zoetendal. - Wageningen : Wageningen University - ISBN 9789462579514 - 205
gastrointestinal microbiota - metabolic disorders - biomarkers - obesity - intestinal microorganisms - antibiotics - dna sequencing - rna - ribosomal rna - microbiota van het spijsverteringskanaal - stofwisselingsstoornissen - biomarkers - obesitas - darmmicro-organismen - antibiotica - dna-sequencing - rna - ribosomaal rna
After birth, our gastrointestinal (GI) tract is colonized by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develop intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or even new therapeutic target. Nevertheless, it is currently still unclear which bacterial groups play a role in the development of the metabolic syndrome in humans. This might partly be explained by: 1. Biological factors such as the heterogeneity in genotype, lifestyle, diet; and the often complex aetiology of human disease of which the metabolic syndrome is no exception. 2. Technological factors, such as the use of miscellaneous incompatible methods to assess the gut microbiota, often enumerating specific groups rather than using broad 16S rRNA gene surveys or metagenomics. 3. Studies vary greatly in the populations considered, their designs, and the degree of control for potential confounding factors such as lifestyle and diet. Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, based on stricter control over variables such age range or through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define groups.
Perturbations in microbial diversity and community structure in adults with overweight and obesity may be partly due to long-term dietary habits or physiological changes in these subjects. As such, exploring the association between the gut microbiota and variation in BMI and weight in early life, prior to or close to the onset of overweight, might provide additional insights into these processes. Therefore, we studied the fecal microbiota of 295 six-seven year old children from the KOALA Birth Cohort, living in the south of the Netherlands. This age range is relatively uncharted microbiota territory. We found that its composition seems to conform to tot same ecosystem rules as that of adults. The bimodal distribution pattern of several bacterial groups as well as their co-correlating groups that were reported previously, including Uncultured Clostridiales II (UCII), Prevotella spp. and Dialister were confirmed. Furthermore, one of the previously described bimodal groups (Uncultured Clostridiales I) was shown before to exhibit very clear shifting state probabilities associated with ageing, where the high abundance state was mainly observed above 40 years of age. This was corroborated as no support for bimodality of this group was observed in the children included in the study described here. A large part of the variation in microbiota composition was explained by the abundance of aforementioned groups in contrast to the anthropometric outcomes, suggesting that in this group of healthy children within a relatively normal weight range, weight and associated parameters were not major drivers of overall genus-level microbial composition or vice versa. Hereafter, multiple linear and logistic regression models with rigorous adjustment for confounders were applied to investigate individual microbiota features association with weight related anthropometric outcomes. Previously reported parameters such as diversity, richness and Bacteroidetes to Firmicutes ratio, were not significantly associated with any of the outcomes. Nevertheless, the abundance of several specific bacterial taxa; Akkermansia, Sutterella wadsworthia et rel. and Bryantella formatexigens et rel. and the dichotomous abundance state of the bi-modally distributed UCII was consistently associated with weight-related outcomes.
Other biochemical features of the metabolic syndrome have been associated with the gut microbiome. Mainly rodent studies have indicated that antibiotic treatment may improve glucose homeostasis and metabolic impairments. Therefore, the effects of gut microbiota manipulation by antibiotics (7d administration of amoxicillin, vancomycin or a placebo) on tissue-specific insulin sensitivity, energy metabolism, gut permeability and inflammation in 57 obese, pre-diabetic men from the same geographical region, were investigated. Vancomycin decreased bacterial diversity and significantly reduced well known butyrate- producing Firmicutes from Clostridium clusters IV and XIVa and bacterial groups involved in bile acid metabolism. These changes occurred concomitantly with altered plasma and fecal concentrations of these metabolites. In adipose tissue, gene expression of oxidative pathways was upregulated by antibiotics, whereas immune-related pathways were downregulated by vancomycin. However, antibiotic treatment had no significant effects on tissue-specific insulin sensitivity, energy/substrate metabolism, postprandial hormones and metabolites, systemic inflammation, gut permeability and adipocyte size. Importantly, despite a still considerably altered microbial composition at eight weeks follow-up, energy harvesting, adipocyte size and whole-body insulin sensitivity (HOMA-IR) remained unaltered. Overall these data indicate that interference with adult microbiota by antibiotic treatment for 7 days had no clinically relevant impact on metabolic health in obese humans. These data are in contrast with several rodent studies as well as a human intervention. The present study, which was well-powered and placebo-controlled, indicates that the previously reported vancomycin-induced effects on human peripheral insulin sensitivity are probably of minor physiological significance.
The aforementioned group that was relatively homogeneous with regards to phenotype was combined with another cohort with similar phenotypical characteristics (obese, male and pre-diabetic) from another region of the Netherlands, to investigate whether tissue specific insulin sensitivity, as measured by the golden standard hyperinsulinemic-euglycemic clamp technique, is related to a specific microbial pattern. Remarkably, despite the fact that both cohorts were constructed based on comparable recruitment strategies, the average microbiota composition in both cohorts showed pronounced differences. Firstly, we found no consistent and significant association between liver, adipose tissue or skeletal muscle insulin sensitivity and the microbiota in both cohorts. Nevertheless, Random Forests classifiers using microbiota composition as predictors revealed taxa associated with fasting glucose concentrations and HbAc1 but only in one cohort. The top microbial features distinguishing classes were different Proteobacteria and groups involved in butyrogenesis, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Eubacterium rectale and related species, for fasting glucose levels. For HbAc1 these taxa were Oscillospira guillermondii, Sporobacter termitidis, Lactobacillus gasseri and Peptococcus niger and related species. The striking cohort-specific observations suggest that the relation between microbiota composition and type 2 diabetes mellitus as well as other characteristics of the metabolic syndrome is very dependent on the selected cohort of patients and their respective baseline microbiota composition. Similar observations have been made by other researchers as well. It could be that differences in microbiota composition are not associated with the insulin resistance phenotype when the overweight and/or obese state of the patient is already established, as is the case for our metabolic syndrome patients. In the latter case we cannot exclude that the composition of the fecal microbiota may play a role in the worsening of insulin sensitivity in an early stage in the development from a lean towards an overweight/obese phenotype. Furthermore, the observation of a subgroup- specific microbiota only observed in one of the cohorts might indicate an alternative state of microbiota composition driven by yet unknown forces. Nevertheless, this study clearly demonstrated that cohort-specific microbiota differences hamper finding a consensus biological interpretation between cross-sectional studies. This, combined with the complexity of individual disease pathogenesis, as well as the individual-specific differences in microbiota composition, may explain the inconsistency in observations between different studies concerning the identification of signature microbes for obesity, irritable bowel syndrome and other diseases.
Besides the biological drivers for cohort specific inconsistencies in identified microbial biomarkers, there are also technological factors. Although high-throughput sequencing of short, hypervariable segments of the 16S ribosomal RNA (rRNA) gene has transformed the methodological landscape describing microbial diversity within and across complex biomes, evidence is increasing that methodology rather than the biological variation is responsible for observed sample composition and distribution. Large meta-analyses would aid in elucidating whether the basis for these observed inconsistencies is biological, technical or maybe a combination of both. To facilitate these meta-analyses of microbiota studies we developed NG-Tax, a pipeline for 16S rRNA gene amplicon sequence analysis that was validated with different Mock Communities (MC). NG-Tax demonstrated high robustness against choice of region and other technical biases associated with 16S rRNA gene amplicon sequencing studies. The analysis of α- and β-diversity of these MC confirmed conclusions guided by biology rather than the methodological aspects. This pipeline was applied to biological samples to monitor the developing communities an in vitro gut model (TIM-2) fed either with a normal diet, or modified versions from which the carbohydrate (MPLC) or protein fraction was diluted (LPMC) for 72h. In combination with global metatranscriptomics and metabolomics this revealed that each diet produced distinct microbial communities and temporal patterns and ratios of metabolites. The microbiota in reactors fed diets containing normal carbohydrate levels were enriched in members of the genera Prevotella, Subdoligranulum, Blautia and Bifidobacterium, all associated with carbohydrate fermentation. In turn, the microbiota in the reactors fed the MPLC diet, containing ten-fold less carbohydrates, was enriched in the genus Bacteroides, which is associated with diets rich in protein and animal fat. This setup allows researchers to study the (trophic) interactions and task division within a community and how they are impacted by diet-related factors under controlled conditions, which may assist in defining causal links between specific diet-derived parameters microbial groups and their activities.
In conclusion, currently it seems that GI microbiota based biomarkers associated with metabolic impairments and anthropometric variables associated with the metabolic syndrome are cohort specific or possibly individual, which could partly be due to the use of incompatible analytical approaches. Nevertheless, there is growing evidence that human health is a collective property of the human body and its associated microbiome and thus requires to study the interface of two very complex systems, i.e. on one side the extraordinary coding capacity, high inter-individuality and complex dynamics of the microbiome and on the other side the multifactorial individual nature of human disease. In light of these observations the manifestation of individual dynamics of the microbiota with the host when homeostasis is lost seems plausible and likely.
Interplay between gut microbiota and antibiotics
Jesus Bello Gonzalez, Teresita de - \ 2016
Wageningen University. Promotor(en): Hauke Smidt, co-promotor(en): M.W.J. van Passel. - Wageningen : Wageningen University - ISBN 9789463430043 - 293
antibiotics - intestinal microorganisms - aminoglycoside antibiotics - enterococcus - interactions - zoo animals - man - patients - dna sequencing - polymerase chain reaction - antibiotica - darmmicro-organismen - aminoglycoside antibiotica - enterococcus - interacties - dierentuindieren - mens - patiënten - dna-sequencing - polymerase-kettingreactie
The human body is colonized by a vast number of microorganisms collectively defined as the microbiota. In the gut, the microbiota has important roles in health and disease, and can serve as a host of antibiotic resistance genes. Disturbances in the ecological balance, e.g. by antibiotics, can affect the diversity and dynamics of the microbiota. The extent of the disturbance induced by antibiotics is influenced by, among other factors, the class of antibiotic, the dose, and administration route. One of the most common consequences of excessive antibiotic use is the emergence of antibiotic resistant bacteria and the dissemination of the corresponding resistance genes to other microbial inhabitants of the gut community, in addition to affecting the colonization resistance and promoting the overgrowth of pathogens. These effects are particularly relevant for Intensive Care Unit (ICU) patients, which are frequently exposed to a high risk of hospital-acquired infections associated with antibiotic resistant bacteria.
Due to the important roles that members of the gut microbiota play in the host, including their role as potential hubs for the dissemination of antibiotic resistance, recent research has focused on determining the composition and function of gut microorganisms and the antibiotic resistance genes associated with them.
The objectives of the research described in this thesis were to study the diversity and dynamics of the gut microbiota and resistome in ICU patients receiving antibiotic prophylactic therapy, and to assess the colonization dynamics with antibiotic resistant bacteria focusing on the commensal microbiota as a reservoir of antibiotic resistance genes by using culture dependent and independent techniques. Furthermore, the genetic background involved in the subsistence phenotype was investigated to disentangle the links between resistance and subsistence.
Bacteria harbor antibiotic resistance genes that participate in a range of processes such as resisting the toxic effects of antibiotics, but could also aid in the utilization of antibiotics as sole carbon source, referred to as antibiotic subsistence phenotype. In chapter 2, the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics was investigated.
Various gut isolates of Escherichia coli and Cellulosimicrobium spp. displayed the subsistence phenotype, mainly with aminoglycosides. Although no antibiotic degradation could be detected, the number of colony forming units increased during growth in medium with only the antibiotic as a carbon source. By using different approaches to study the aminoglycoside subsistence phenotype, we observed that laboratory strains carrying the aminoglycoside 3’phosphotransferase II gene also displayed the subsistence phenotype on aminoglycosides and that glycosyl-hydrolases seem to be involved in the subsistence phenotype. As the zoo animals for which the subsistence phenotype was investigated also included a number of non-human primates, the applicability of Human Intestinal Tract Chip (HITChip) to study the gut microbiota composition of these animals was assessed, including a comparison with healthy human volunteers (Chapter 3). It was concluded that the HITChip can be successfully applied to the gut microbiota of closely related hominids, and the microbiota dynamics can therefore be quickly assessed by the HITChip.
In Chapter 4, a combination of 16S rRNA phylogenetic profiling using the HITChip and metagenomics sequencing was implemented on samples from a single ICU hospitalized patient that received antibiotic prophylactic therapy (Selective Digestive Decontamination - SDD). The different approaches showed a highly dynamic microbiota composition over time and the prevalence of aminoglycoside resistance genes harbored by a member of the commensal anaerobic microbiota, highlighting the role of the commensal microbiota as a reservoir of antibiotic resistance genes. As an extension of this study (Chapter 5), 11 ICU patients receiving SDD were followed using 10 healthy individuals as a control group to compare the diversity and dynamics of the gut microbiota and resistome by HITChip and nanolitre-scale quantitative PCRs, respectively. The microbial diversity of the healthy individuals was higher compared to ICU patients, and it was less dynamic compared to ICU patients under antibiotic treatment. Likewise, the levels of antibiotic resistance genes increased in ICU patients compared to healthy individuals, indicating that during ICU hospitalization and the SDD, gut microbiota diversity and dynamics are profoundly affected, including the selection of antibiotic resistance in anaerobic commensal bacteria.
This was further expanded in an extensive study focusing on colonization dynamics with antibiotic resistant bacteria as described in Chapter 6. This was performed in the same group of ICU-hospitalized patients receiving SDD therapy and showed that by using a range of culture media and selective conditions a variety of taxonomic groups could be isolated, including aerobic and anaerobic antibiotic resistant bacteria. The overall composition of the faecal microbiota detected by HITChip indicated mainly a decrease of Enterobacteriaceae and an increase of the enterococcal population. Since critically ill patients are susceptible to hospital-acquired infections and the control of the emergence of antibiotic resistance is crucial to improve therapeutic outcomes, an extended analysis of the Enterococcus colonization dynamics in this group of patients by cultivation and phenotypic and genotypic characterization of the isolates provided new information about carriage of antibiotic resistance and virulence factor encoding genes (Chapter 7). It also highlighted the opportunity for the exchange of resistance and virulence genes, which could increase the risk of acquiring nosocomial infections.
Next, chapter 8 described the implementation of high-throughput cultivation-based screening using the Microdish platform combined with high-throughput sequencing (MiSeq) using faecal samples from ICU patients receiving SDD. This allowed for the recovery of previously uncultivable bacteria, including a pure culture of a close relative of Sellimonas intestinalis BR72T that was isolated from media containing tobramycin, cefotaxime and polymyxin E. This strain could therefore represent a potential antibiotic resistance reservoir.
In conclusion, this thesis provides broad insight into the diversity and dynamics of the gut microbiota and resistome in ICU hospitalized patients receiving SDD therapy as well as the dynamics of colonization with antibiotic resistant bacteria. Especially our extensive study of the colonization dynamics of Enterococcus spp. during ICU stay reinforced the notion that SDD therapy does not cover this group of bacteria and highlights the importance of a critical control of the emergence of antibiotic resistance in enterococci and their spread and dissemination as known potential pathogens.
Furthermore, the extensive use of antibiotics could select for an increase in the rate of antibiotic resistance against aminoglycosides and beta-lactams, indicating that a control in the use of broad spectrum antibiotics needs to be considered. In addition, this thesis provides evidence regarding the possible genetic background involved in the subsistence phenotype, however, future studies on metabolic pathways could provide novel insight into the underlying mechanisms.
Utilization of complete chloroplast genomes for phylogenetic studies
Ramlee, Shairul Izan Binti - \ 2016
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Rene Smulders; Theo Borm. - Wageningen : Wageningen University - ISBN 9789462579354 - 186
phylogenetics - genomes - chloroplasts - models - solanum - orchidaceae - phylogenomics - dna sequencing - fylogenetica - genomen - chloroplasten - modellen - solanum - orchidaceae - phylogenomica - dna-sequencing
Chloroplast DNA sequence polymorphisms are a primary source of data in many plant phylogenetic studies. The chloroplast genome is relatively conserved in its evolution making it an ideal molecule to retain phylogenetic signals. The chloroplast genome is also largely, but not completely, free from other evolutionary processes such as gene duplication, concerted evolution, pseudogene formation and genome rearrangements. The conservation of the chloroplast genome sequence allows designing primers targeting regions conserved well beyond species boundaries, and amplification of these targets.
The small size together with their high copy number in leaf cells greatly facilitates chloroplast genome sequencing. In this thesis, chloroplast phylogenomics was conducted using complete chloroplast DNA genomes obtained by a newly developed method of de novo assembly. The method was not only cost-effective but also has the potential to extract a wealth of useful information of thousands of chloroplast genomes from Whole Genome Shotgun (WGS) data. We used k-mer frequency tables to identify and extract the chloroplast reads from the WGS reads and assemble these using a highly integrated and automated custom pipeline. This pipeline includes steps aimed at optimizing assemblies and filling gaps that are left due to coverage variation in the WGS dataset. The pipeline enabled successful de novo assembly across a range of nuclear genome sizes, from Solanum lycopersicon (tomato, 0.9 Gb) to Paphiopedilum heryanum (slipper orchid, 35 Gb).
The pipeline is suitable for studying structural variation in the chloroplast genome, as opposed to the common procedure of read mapping against a reference genome. To support the putative rearrangements, a flexible assembly quality comparison tool was created that combines and visualizes read mapping and alignment results in a two-dimensional plot. We have evaluated the ability of this tool using the de novo assemblies of S. lycopersicon and P. henryanum chloroplasts. The results show that not only we can immediately select the best of two options, but also determine the location of specific artefacts.
In order to explore and evaluate the utility of complete chloroplast phylogenomics, tomato and Paphiopedilum spp were used to conduct phylogenetic inferences based on the complete chloroplast genome. In total 84 tomato chloroplast genomes within the section Lycopersicon were assembled and phylogenetic trees produced. The analyses revealed that next to the chloroplast regions and spacers traditionally used for phylogenetics, additional regions of protein coding and non-coding DNA may be exploited for intraspecific phylogenetic studies. In particular, more than 50% of all phylogenetically relevant information could be included by just using four genes (ycf1, ndhF, ndhA, and ndhH), of which 34% in ycf1 alone. The topology of the phylogenetic tree inferred from ycf1 was the same as that of trees based on all other protein coding genes, although with lower bootstrap values. The phylogenetic analyses based on 32 complete Paphiopedilum spp. chloroplast genomes confirmed the division of the genus into three subgenera Parvisepalum, Brachypetalum and Paphiopedilum. The division of five sections of subgenus Paphiopedilum was also recovered. The de novo assemblies revealed several structural rearrangements including gene loss and inversion. In addition, the chloroplast genome of Paphiopedilum has experienced extreme IR expansion that has included part of or the entire SSC region, resulting in larger IR regions than commonly observed among monocots.
In conclusion, WGS data offer opportunities to generate partial or entire chloroplast genomes for phylogenetic studies. Species discrimination can be achieved already with partial data (subsets of genes), but evolutionarily young lineages may require more informative characters. Therefore, it is expected that many complete chloroplast genomes will be produced in the years to come. While generating these genomes, the urge for de novo assembly of chloroplast genomes rather than mapping against reference genomes is adamant in order to also uncover structural rearrangements in chloroplast genome.
Akkermansia species : phylogeny, physiology and comparative genomics
Ouwerkerk, J.P. - \ 2016
Wageningen University. Promotor(en): Willem de Vos, co-promotor(en): Clara Belzer. - Wageningen : Wageningen University - ISBN 9789462577411 - 178
akkermansia - akkermansia muciniphila - gastrointestinal microbiota - phylogeny - physiology - genomics - dna sequencing - nucleotide sequences - transcriptomes - antibiotic resistance - genome annotation - akkermansia - akkermansia muciniphila - microbiota van het spijsverteringskanaal - fylogenie - fysiologie - genomica - dna-sequencing - nucleotidenvolgordes - transcriptomen - antibioticaresistentie - genoomannotatie
The gastrointestinal tract is lined with a mucus layer, which is colonized by a distinct mucosal microbial population. The anaerobic gut bacterium Akkermansia muciniphila is a well-described member of the mucosal microbiota and has been shown to be a human gut symbiont. In the mucus layer this gut symbiont is likely exposed to the oxygen that diffuses from mucosal epithelial cells. We showed that A. muciniphila has an active detoxification system to cope with reactive oxygen species and can use oxygen for respiration at nanomolar oxygen concentrations, with cytochrome bd as terminal oxidase.
Until now, the type strain A. muciniphila MucT was the only cultured representative of this species. We isolated and characterized six new A. muciniphila strains from faecal samples of four different human subjects. These A. muciniphila strains showed minimal genomic and physiologic divergence while retaining their mucin degrading and utilisation capacities. Apart from the human gastrointestinal tract, we detected Akkermansia species in intestinal samples of numerous mammals. An additional ten new A. muciniphila strains were isolated from seven different mammalian species and showed high genomic and physiologic similarity to type strain A. muciniphila MucT. Apart from Akkermansia species, other Verrucomicrobia were identified within the gastrointestinal tract of non-human mammals. Furthermore, we obtained an Akkermansia isolate from the reticulated python, which had a similar mucin degrading capacity as the human strain A. muciniphila MucT but showed more efficient galactose utilization. On the basis of further phylogenetic, physiological, and genomic characterisations, strain PytT was found to represent a novel species within the genus Akkermansia, for which the name Akkermansia glycaniphilus sp. nov. is proposed.
Overall, A. muciniphila strains isolated from intestinal samples of human and other mammals show very limited genomic and physiologic divergence. This together with the widely-spread global presence of A. muciniphila and the dependence on mucin for optimal growth, points towards a conserved symbiosis. This conserved symbiosis might be indicative for the beneficial role of this organism in respect to the host metabolic health. This is in line with the observation that A. muciniphila has been negatively associated with obesity and its associated metabolic disorders.
In mice, treatment with viable A. muciniphila cells reversed high-fat diet-induced obesity. We described a scalable workflow for the preparation and preservation of high numbers of viable cells of A. muciniphila under strict anaerobic conditions for therapeutic interventions. Moreover, we developed various quality assessment and control procedures aimed to ensure the use of viable cells of A. muciniphila at any location in the world. These viable cells were used in a pilot study in humans in which no adverse events were observed. This is promising for future applications of A. muciniphila as a new therapeutic, leading towards the potential treatment of unhealthy states of the microbiota.
Conservation genetics of the frankincense tree
Bekele, A.A. - \ 2016
Wageningen University. Promotor(en): Frans Bongers, co-promotor(en): Rene Smulders; K. Tesfaye Geletu. - Wageningen : Wageningen University - ISBN 9789462576865 - 158
boswellia - genomes - dna sequencing - tropical forests - genetic diversity - genetic variation - genetics - forest management - plant breeding - boswellia - genomen - dna-sequencing - tropische bossen - genetische diversiteit - genetische variatie - genetica - bosbedrijfsvoering - plantenveredeling
Boswellia papyrifera is an important tree species of the extensive Combretum-Terminalia dry tropical forests and woodlands in Africa. The species produces a frankincense which is internationally traded because of its value as ingredient in cosmetic, detergent, food flavor and perfumes productions, and because of its extensive use as incense during religious and cultural ceremonies in many parts of the world. The forests in which B. papyrifera grows are increasingly overexploited at the expense of the economic benefit and the wealth of ecological services they provide. Populations of B. papyrifera have declined in size and are increasingly fragmented. Regeneration has been blocked for the last 50 years in most areas and adult productive trees are dying. Projections showed a 90% loss of B. papyrifera trees in the coming 50 years and a 50% loss of frankincense production in 15 years time.
This study addressed the conservation genetics of B. papyrifera. Forty six microsatellite (SSR) markers were developed for this species, and these genetic markers were applied to characterize the genetic diversity pattern of 12 B. papyrifera populations in Ethiopia. Next to this, also the generational change in genetic diversity and the within-population genetic structure (FSGS) of two cohort groups (adults and seedlings) were studied in two populations from Western Ethiopia. In these populations seedlings and saplings were found and natural regeneration still takes place, a discovery that is important for the conservation of the species.
Despite the threats the populations are experiencing, ample genetic variation was present in the adult trees of the populations, including the most degraded populations. Low levels of population differentiation and isolation-by-distance patterns were detected. Populations could be grouped into four genetic clusters: the North eastern (NE), Western (W), North western (NW) and Northern (N) part of Ethiopia. The clusters corresponded to environmentally different conditions in terms of temperature, rainfall and soil conditions. We detected a low FSGS and found that individuals are significantly related up to a distance of 60-130 m.
Conservation of the B. papyrifera populations is urgently needed. The regeneration bottlenecks in most existing populations are an urgent prevailing problem that needs to be solved to ensure the continuity of the genetic diversity, species survival and sustainable production of frankincense. Local communities living in and around the forests should be involved in the use and management of the forests. In situ conservation activities will promote gene flow among fragmented populations and scattered remnant trees, so that the existing level of genetic diversity may be preserved. Geographical distance among populations is the main factor to be considered in sampling for ex situ conservation. A minimum of four conservation sites for B. papyrifera is recommended, representing each of the genetic clusters. Based on the findings of FSGS analyses, seed collection for ex situ conservation and plantation programmes should come from trees at least 100 m, but preferably 150 m apart.
Quantitative and ecological aspects of Listeria monocytogenes population heterogeneity
Metselaar, K.I. - \ 2016
Wageningen University. Promotor(en): Marcel Zwietering; Tjakko Abee, co-promotor(en): Heidy den Besten. - Wageningen : Wageningen University - ISBN 9789462577664 - 173
listeria - listeria monocytogenes - stress - stress tolerance - ribosomes - proteins - lactobacillus plantarum - behaviour - ecological assessment - genome analysis - dna sequencing - resistance - heterogeneity - listeria - listeria monocytogenes - stress - stresstolerantie - ribosomen - eiwitten - lactobacillus plantarum - gedrag - ecologische beoordeling - genoomanalyse - dna-sequencing - weerstand - heterogeniteit
Bacterial stress response and heterogeneity therein is one of the biggest challenges posed by minimal processing. Heterogeneity and resulting tailing representing a more resistant fraction of the population, can have several causes and can be transient or stably in nature. Stable increased stress resistance is caused by alterations in the genome and therefore inheritable and is referred to as stable stress resistant variants. Also L. monocytogenes exhibits a heterogeneous response upon stress exposure which can be partially attributed to the presence of stable stress resistant variants. Adverse environments were shown to select for stable stress resistant variants. The objective of the research described in this thesis was to evaluate if L. monocytogenes population diversity and the presence of stable resistant variants is a general phenomenon that is observed upon different types of stress exposure, to get more insight in the mechanisms leading to increased resistance and to evaluate the ecological behaviour and potential impact on food safety of these stable resistant variants. Acid stress was chosen as it is an important hurdle both in food preservation, as well as in stomach survival.
First, the non-linear inactivation kinetics of L. monocytogenes upon acid exposure were quantitatively described. A commonly used biphasic inactivation model was reparameterized, which improved the statistical performance of the model and resulted in more accurate estimation of the resistant fraction within L. monocytogenes WT populations. The observed tailing suggested that stable stress resistant variants might also be found upon acid exposure. Indeed, 23 stable acid resistant variants of L. monocytogenes LO28 were isolated from the tail after exposure of late-exponential phase cells to pH 3.5 for 90 min, with different degrees of acid resistance amongst them. Increased acid resistance showed to be significantly correlated to reduced growth rate. Studying the growth boundaries of the WT and a representative set of variants indicated that the increased resistance of the variants was only related to survival of severe pH stress but did not allow for better growth or survival at mild pH stress.
Next, the performance in mixed species biofilms with Lactobacillus plantarum was evaluated, as well as their benzalkonium chloride (BAC) resistance in these biofilms. It was hypothesized that the acid resistant variants might also show better survival in biofilms with L. plantarum, which provide an acidic environment by lactose fermentation with pH values below the growth boundary of L. monocytogenes when biofilms mature. L. monocytogenes LO28 WT and eight acid resistant variants were capable of forming mixed biofilms with L. plantarum at 20°C and 30°C in BHI supplemented with manganese and glucose. Some of the variants were able to withstand the low pH in the mixed biofilms for a longer time than the WT and there were clear differences in survival between the variants which could not be correlated to (lactic) acid resistance alone. Adaptation to mild pH of liquid cultures during growth to stationary phase increased the acid resistance of some variants to a greater extent than of others, which could be correlated to increased survival in the mixed biofilms. There were no clear differences in BAC resistance between the wild type and variants in mixed biofilms.
Lastly, a set of robustness and fitness parameters of WT and variants was obtained and used to model their growth behaviour under combined mild stress conditions and to model their performance in a simulated food chain. This gave more insight in the trade-off between increased stress resistance and growth capacity. Predictions of performance were validated in single and mixed cultures by plate counts and by qPCR in which WT and an rpsU deletion variant were distinguished by specific primers. Growth predictions for WT and rpsU deletion variant were matching the experimental data generally well. Globally, the variants are more robust than the WT but the WT grows faster than most variants. Validation of performance in a simulated food chain consisting of subsequent growth and inactivation steps, confirmed the trend of higher growth fitness and lower stress robustness for the WT compared to the rpsU variant. This quantitative data set provides insights into the conditions which can select for stress resistant variants in industrial settings and their potential persistence in food processing environments.
In conclusion, the work presented in this thesis highlights the population diversity of L. monocytogenes and the impact of environmental conditions on the population composition, which is of great importance for minimal processing. The work of this thesis resulted in more insight in the mechanisms underlying increased resistance of stress resistant variants and quantitative data on the behaviour of stress resistant variants which can be implemented in predictive microbiology and quantitative risk assessments aiming at finding the balance between food safety and food quality.
High-throughput open source computational methods for genetics and genomics
Prins, J.C.P. - \ 2015
Wageningen University. Promotor(en): Jaap Bakker; R.C. Jansen, co-promotor(en): Geert Smant. - Wageningen : Wageningen University - ISBN 9789462574595 - 136
plantenparasitaire nematoden - dna-sequencing - next generation sequencing - verwerkingscapaciteit - computational science - genetica - genomica - plant parasitic nematodes - dna sequencing - next generation sequencing - throughput - computational science - genetics - genomics
Biology is increasingly data driven by virtue of the development of high-throughput technologies, such as DNA and RNA sequencing. Computational biology and bioinformatics are scientific disciplines that cross-over between the disciplines of biology, informatics and statistics; which is clearly reflected in this thesis. Bioinformaticians often contribute crucial insights and novelty to scientific research because they are central to data analysis and contribute concrete algorithms and software solutions. In addition, bioinformaticians have an important role to play when it comes to organising data and software and making it accessible to others. In this thesis, in addition to contributing to biological questions, I discuss issues around accessing and sharing data, with the challenges of handling large data, input/output (IO) bottlenecks and effective use of multi-core computations.
By creating software solutions together with molecular biologists, I contributed and published insights in biological processes in nematodes and plants. I published software solutions that made it easier for others to analyse data, which impacts the wider research community. I created solutions that made it easier for others to publish software solutions by themselves. The introduction of computing and the internet makes it possible to share ideas and computational methods. I am convinced it is a good idea to publish software solutions as `free and open source' software (FOSS) in the public domain so that we can continue to build on the work of others.
Chapter 2 presents a computational method for identifying gene families in a sequenced genome that may be involved in pathogenicity, i.e., those genes that code for proteins that interact with molecules of an infected host. Such nematode proteins are known to contain highly variable DNA sections that code for the biochemical properties of an interaction site. By applying phylogenetic analysis through maximum likelihood (PAML) and comparison of homologues sequences in other organisms with comparable and different life styles, we discovered 77 unique candidate sequence families in the plant pathogen Meloidogyne incognita that deserve further investigation in the laboratory.
Chapter 3 presents GenEST, a computational method for predicting which fragments captured by the cDNA-AFLP high-throughput technology matched known expressed sequence tags (ESTs). The cDNA-AFLP biochemical process was calculated in silico and fragments matching the fragment lengths as given by cDNA-AFLP were matched. Through this technique novel effectors from the nematode Globodera rostochiensis, putatively involved in pathogenicity, were identified and partly confirmed in the laboratory.
Chapter 4 presents GenFrag, a computational method that expands on GenEST for predicting which fragments captured by cDNA-AFLP matched fragments of a fully sequenced genome with its known spliced gene variants. Through this in silico technique genes were identified in the plant Arabidopsis thaliana putatively involved in maternal genomic imprinting and partly confirmed in the laboratory.
Chapter 5 presents multiple QTL mapping (MQM), a high-throughput computational method for predicting what sections of a genome correlate with, for example, gene expression. The study of finding such eQTL is challenging, not least because many of them are potentially false positives. The MQM parallelized algorithm is embedded in the R/qtl software package which makes it widely available to researchers. The impact thereof means that it is widely cited by studies on model organisms, such as mouse, rat, the nematode Caenorhabditis elegans and the plant A. thaliana.
Chapter 6 presents a theoretical framework in the form of a review for identifying plant-resistance genes (R-genes) that combines the lessons learnt in the previous chapters. Plants lack an adaptive immune system and therefore, next to having physical defences, use R-genes to code for proteins that recognise molecules and proteins from invading pathogens, with an example on A. thaliana. These R-genes can be viewed as the counterparts of effectors identified in Chapter 3 and Chapter 4. By introducing the concept of a prior the chapter discusses eQTL or broader xQTL techniques as presented in the Chapter 5 to narrow down on gene candidates involved in plant defence.
Chapter 7 and Chapter 8 present FOSS bioinformatics tools, and modules that make use the Ruby programming language. BioRuby (Chapter 7) has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports widely used data formats and provides access to databases, external programs and public web services. All Ruby software created in the context of this thesis was contributed initially to the main BioRuby project, e.g. the PAML parser of Chapter 2, and later as individual Biogems (Chapter 8), e.g. the bio-blastxmlparser, bio-alignment, bigbio and bio-rdf biogems for Chapter 2, and three Genfrag related biogems for Chapter 4. Over 16 modules were contributed by the author as Ruby FOSS projects and are listed on the http://biogems.info/ website. Because of the open nature of the BioRuby project, both BioRuby and BioGem software modules are increasingly used and cited in biomedical research, not only in genomics, but also in phylogenetics and prediction of protein structural complexes and data integration.
Chapter 9 presents sambamba, a software tool for scaling up next generation sequencing (NGS) alignment processing through the use of multiple cores on a computer. Sambamba is a replacement for samtools, a commonly used software tool for working with aligned output from sequencers. Sambamba makes use of multi-core processing and is written in the D programming language. Not only does sambamba outperform samtools, but it already comes with an improved deduplication routine and other facilities, such as easy filtering of data. The Sambamba software is now used in the large sequencing centres around the world.
Chapter 10 `Big Data, but are we ready?' gives a response to a publication on using cloud computing for large data processing. The chapter discusses computational bottlenecks and proves prescient because the number of citations of this paper increases every year.
Chapter 11 `Towards effective software solutions for big biology' discusses the need for a change of strategy with regard to bioinformatics software development in the biomedical sciences to realise big biology software projects. This includes improved scientific career tracks for bioinformaticians and dedicated funding for big data software development.
Chapter 12 discusses the computational methods and software solutions presented in this thesis, painting a picture of further challenges in bioinformatics computational solutions for the elucidation of biological processes. The chapter starts with a discussion on the merits and shortcomings of each individual software solution presented in this thesis, followed by a perspective on next generation sequencing, data integration and future research in software solutions.
Structural variations in pig genomes
Paudel, Y. - \ 2015
Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Ole Madsen; Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462572171 - 204
varkens - dierveredeling - genomen - genomica - single nucleotide polymorphism - dna-sequencing - fenotypische variatie - chromosoomafwijkingen - evolutie - soortvorming - pigs - animal breeding - genomes - genomics - single nucleotide polymorphism - dna sequencing - phenotypic variation - chromosome aberrations - evolution - speciation
Paudel, Y. (2015). Structural variations in pig genomes. PhD thesis, Wageningen University, the Netherlands
Structural variations are chromosomal rearrangements such as insertions-deletions (INDELs), duplications, inversions, translocations, and copy number variations (CNVs). It has been shown that structural variations are as important as single nucleotide polymorphisms (SNPs) in regards to phenotypic variations. The general aim of this thesis was to use next generation sequencing data to improve our understanding of the evolution of structural variations such as CNVs, and INDELs in pigs. We found that: 1) the frequency of copy number variable regions did not change during pig domestications but rather reflected the demographic history of pigs. 2) CNV of olfactory receptor genes seems to play a role in the on-going speciation of the genus Sus. 3) Variation in copy number of olfactory receptor genes in pigs (Sus scrofa) seems to be shaped by a combination of selection and genetic drift, where the clustering of ORs in the genome is the major source of variation in copy number. 4) Analysis on short INDELs in the pig genome shows that the level of purifying selection of INDELs positively correlates with the functional importance of a genomic region, i.e. strongest purifying selection was observed in gene coding regions. This thesis provides a highly valuable resource for copy number variable regions, INDELs, and SNPs, for future pig genetics and breeding research. Furthermore, this thesis discusses the limitations and improvements of the available tools to conduct structural variation analysis and insights into the future trends in the detection of structural variations.
Speciation and domestication in Suiformes: a genomic perspective
Frantz, L.A.F. - \ 2015
Wageningen University. Promotor(en): Martien Groenen, co-promotor(en): Ole Madsen; Hendrik-Jan Megens. - Wageningen : Wageningen University - ISBN 9789462572546 - 227
domesticatie - suiformes - soortvorming - dierveredeling - genomica - evolutie - genenstroom - dna-sequencing - moleculaire fylogenetica - domestication - suiformes - speciation - animal breeding - genomics - evolution - gene flow - dna sequencing - molecular phylogenetics
Frantz, L.A.F. (2015). Speciation and Domestication in Suiformes: a genomic perspective. PhD thesis, Wageningen University, the Netherlands
The diversity of life on earth owes its existence to the process of speciation. The concept of speciation is primordial for evolutionary biologists because it provides a framework to understand how contemporary biodiversity came to be. Moreover, not only natural phenomena can result in the differentiation of life forms. Indeed, biodiversity can also be the result of direct and indirect human influence such as domestication. In this thesis, I investigate these evolutionary processes (speciation and domestication) in the Suiformes superfamily (pigs and related species). I use complete genome sequences to illuminate many specific aspects of the speciation and domestication in Suiformes as well as to draw general conclusions on these crucial processes. In chapter 2 I show how genomes provide an essential source of information to retrieve deep taxonomic relationships among Suiformes. This allows me to describe multiple novel aspects of their early evolutionary history such as the fact that Suiformes colonised North America at least twice. In this chapter, I further highlight and discuss novel methodological limitations that are inherent to phylogenomics. In chapters 3, 4 and 5 I use genome sequences to resolve the evolutionary history of the genus Sus (domestic pigs and wild boars species). More precisely, I show that, contrary to the expectation of simple models of speciation, the evolutionary history of these species involved alternating periods of gene-flow and genetic differentiation that are tightly linked to past climatic fluctuations that took place over the last 4 million years. In addition, these chapters also provide novel insights into the process of speciation by demonstrating that genetic differentiation between species can be achieved, even when gene-flow is strong. Lastly, in chapter 6 I tested multiple models of domestication for S. scrofa. In this chapter I show that models involving reproductive isolation between wild and domestic forms are incompatible with genomic data. Moreover, this chapter demonstrates that, while domestic pigs are morphologically homogenous, they are not genetically homogenous. Together, these findings have important implications for our understanding of the process of domestication because it shows that this process was not solely the result of captivity. Together, the results of this work not only provide a comprehensive evolutionary history for the Suiformes, but also novel insights into the complex processes (speciation and domestication) that are responsible for the diversity of life on earth.
Community and genomic analysis of the human small intestine microbiota
Bogert, B. van den - \ 2013
Wageningen University. Promotor(en): Michiel Kleerebezem, co-promotor(en): Erwin Zoetendal. - S.l. : s.n. - ISBN 9789461736628 - 214
darmmicro-organismen - dunne darm - dna microarrays - dna-sequencing - microbiële ecologie - immunomodulerende eigenschappen - intestinal microorganisms - small intestine - dna microarrays - dna sequencing - microbial ecology - immunomodulatory properties
Our intestinal tract is densely populated by different microbes, collectively called microbiota, of which the majority are bacteria. Research focusing on the intestinal microbiota often use fecal samples as a representative of the bacteria that inhabit the end of the large intestine. These studies revealed that the intestinal bacteria contribute to our health, which has stimulated the interest in understanding their dynamics and activities. However, bacterial communities in fecal samples are different compared to microbial communities at other locations in the intestinal tract, such as the small intestine. Despite that the small intestine is the first region where our food and intestinal microbiota meet, we know little about the bacteria in the small intestine and how they influence our overall well-being. This is mainly attributable to difficulties in obtaining samples with the small intestine being located between the stomach and the large intestine. Therefore, the work in this thesis aimed at providing a better understanding of the composition and dynamics of the human small intestinal microbiota and to provide insight in the metabolic potential as well as immunomodulatory properties of some of its typical commensal inhabitants. Small intestinal samples used in the work described in this thesis were collected from ileostomy subjects, individuals that had their large intestine surgically removed and the end of the small intestine connected to an abdominal stoma, providing access to luminal content of the small intestine.
Considering the importance of molecular techniques in contemporary ecological surveys of microbial communities, first of all, two technologies, barcoded pyrosequencing and phylogenetic microarray analysis were compared in terms of their capacity to determine the bacterial composition in fecal and small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, the use of different primer pairs in the amplification step was assessed in terms of its impact on the outcome of microbial profiling. The analyses revealed that the different primer pairs and the two profiling technologies provide overall similar results for samples of fecal and terminal ileum origin. In contrast, the microbial profiles obtained for small intestinal samples by barcoded pyrosequencing and phylogenetic microarray analysesdiffered considerably. This is most likely attributable to the constraints that are intrinsic to the use of the microarray to enable the detection of predefined microbiota members only, which is due to the probe design that is largely based on large intestinal microbiota communities. However, the pyrosequencing technology also allows for identification of bacteria that were not in advance known to inhabit our intestinal tract.
The pyrosequencing technology was used as the method of choice to study the total and active small intestinal communities in ileostoma effluent samples from four different subjects through sequencing the 16S ribosomal RNA gene (rDNA) and ribosomal RNA (rRNA) contentcombined with metatranscriptome analysis by Illumina sequencing of cDNA derived from enriched mRNAof the same sample set to investigate the activities of the small intestinal bacteria. The composition of the small intestinal bacterial communities as assessed from rDNA, rRNA, and mRNA patterns appeared to be similar, indicating that the dominant bacteria in the small intestine are also highly active in this ecosystem. Streptococcusspp. were among the bacterial species that were detected in each ileostoma effluent sample, albeit that their abundance varied greatly between samples from the same subject as well as samples from different subjects. Veillonellaspp. frequently co-occurred with Streptococcus spp., indicating that the Streptococcusand Veillonellapopulations play a prominent role in the human small intestine ecosystem and their co-occurrence suggests a metabolic relation between these genera.
Therefore, cultivation and molecular typing methodologies were employed to zoom-in on these groups, which revealed that the richness of the small intestinal streptococci strongly exceeded the diversity that could be estimated on basis of 16S rRNA analyses, and could be extended to the genomic lineage level (anticipated to resemble strain-level). From ileostoma samples 3 different Streptococcusspecies were recovered belonging to the S. mitisgroup, S. bovisgroup, and S. salivariusgroup, which could be further divided in 7 genomic lineages. Notably, the Streptococcuslineages that were isolated displayed distinct carbohydrate utilization capacities, which may imply that their growth and relative community composition may respond quite strongly to differences in the dietary intake of simple carbohydrates over time. This notion is in good agreement with the observation that the Streptococcuslineage populations fluctuated in time with only one Streptococcuslineage being cultivated from both ileostoma samples collected in a one-year time frame. Conversely, the cultivated Veillonellaisolates from samples during that same time-interval consistently encompassed a single lineage. Furthermore, this Veillonellalineage could be isolated from both the oral cavity as well as the ileostoma effluent. Analogously, three Streptococcuslineages that belong to a single phylotype also appeared to be present in bacterial communities from the oral cavity as well as the small intestine. These observations suggest the representatives of the Veillonellaand Streptococcusgenera that are encountered in the oral and small intestinal microbial ecosystems are closely related and indicate that the oral microbiota may serve as an inoculum for the upper GI tract.
The metabolic capacity of 6 small intestinal Streptococcus lineages, that were obtained from a single ileostoma effluent sample, was further investigated through the determination of genomic sequences of these lineages. The small-intestinal Streptococcusgenomes were found to encode different carbohydrate transporters and the necessary enzymes to metabolize different sugars, which was in excellent agreement with what carbohydrates could be used by representative strains of the Streptococcuslineages.
To further our understanding how the different streptococci as representatives of the dominant small intestinal bacterial populations may influence our immune system, human dendritic cells were stimulated with strains of the different Streptococcuslineages to study their immunomodulatory properties. The Streptococcuslineages differed significantly in their capacity to modulate cytokine responses of blood-monocyte derived immature dendritic cells. As Streptococcusand Veillonellafrequently co-occur in the small intestinal ecosystem, pair-wise combinations of strains of these two species were also tested for their combined immunomodulatory properties. This resulted in considerably different cytokine responses as those that could be predicted from the stimulations with either Streptococcusor Veillonella, indicating that it is not trivial to predict gut mucosal associated immune responses and thatthe composition of the intestinal microbiota as a whole may have a distinct influence on an individual’s immune status.
In conclusion, the work described this thesis provides an expansion to the accumulating knowledge on the human intestine microbiota. Whereas most studies focus on the microbiota present in the distal regions of the intestinal tract, this study targeted the microbiota of the poorly proximal regions of the intestine and also addressed its capacity to interact with the local mucosal tissue. The data presented here can be exploited to guide the design of future studies that aim to elucidate the interplay between diet, microbiota and the mucosal tissues in the human small intestinal tract.
Identification and characterization of novel effectors of Cladosporium fulvum
Ökmen, B. - \ 2013
Wageningen University. Promotor(en): Pierre de Wit, co-promotor(en): Jerome Collemare. - S.l. : s.n. - ISBN 9789461736383 - 190
solanum lycopersicum - tomaten - plantenziekteverwekkende schimmels - passalora fulva - plant-microbe interacties - verdedigingsmechanismen - genomica - dna-sequencing - pathogeniteit - solanum lycopersicum - tomatoes - plant pathogenic fungi - passalora fulva - plant-microbe interactions - defence mechanisms - genomics - dna sequencing - pathogenicity
In order to establish disease, plant pathogenic fungi deliver effectors in the apoplastic space surrounding host cells as well as into host cells themselves to manipulate host physiology in favour of their own growth. Cladosporium fulvum is a non-obligate biotrophic fungus causing leaf mould disease of tomato. For decades, this fungus has been a model to study the molecular basis of plant-pathogen interactions involving effector proteins. Characterization of these effectors revealed their roles in both virulence and avirulence as they facilitate colonization of the host in the absence of cognate tomato Cf resistance genes, but also trigger Cf-mediated resistance in the presence of these genes. The availability of the genome sequence of C. fulvum is a great resource allowing us to dissect and better understand the molecular interaction between this fungus and tomato, particularly with regards to identification of new effectors. Such knowledge is of important to improve current strategies not only for disease resistance breeding of tomato against C. fulvum, but also for other host plants that are attacked by pathogenic fungi with similar infection strategies and lifestyles.
In chapter 1 we give an introduction to the C. fulvum-tomato pathosystem. In a compatible interaction, C. fulvum secretes small cysteine-rich effectors that positively contribute to fungal virulence. Two of these effectors are chitin-binding proteins including Avr4, which protects fungal cell walls against hydrolysis by plant chitinases, and Ecp6, which sequesters released small chitin fragments, thereby preventing induction of basal defense responses associated with their recognition by plant receptors. Another effector, Avr2, is an inhibitor of four tomato cysteine proteases that are also important for basal plant defense. However, in an incompatible interaction, these effectors are directly or indirectly perceived by corresponding resistance proteins (encoded by Cf resistance genes that belong to the class of receptor-like proteins; RLPs) mediating race-specific plant defense responses also known as effector-triggered immunity.
In chapter 2 we exploit the availability of the genome sequence of C. fulvum to identify novel effectors involved in virulence and avirulence of this fungus. An in silico search was performed using common features of characterized C. fulvum effectors: they (i) contain a signal peptide, (ii) are small (<300 amino acids) and (iii) contain at least four cysteine residues (SSCPs). This search identified 271 SSCPs in the C. fulvum genome. A subset of 60 of these predicted effectors was heterologously expressed in tomato lines carrying different R-traits, including Cf-1, Cf-3, Cf-5, Cf-9B, Cf-11 and Cf-Ecp3 in order to identify the corresponding effectors that are recognized by the RLPs. Although the screen of this subset of SSCPs did not result in identification of a new avirulence gene, two non-specific necrosis-inducing proteins were identified. In addition, a homology search identified CfNLP1, a gene encoding a functional NEP1-like protein that triggers non-specific necrosis in plants. However, quantitative PCR showed that these three genes are lowly or not expressed during tomato infection, which was also true for the in planta expression of some of the effector candidates that were tested for recognition by Cf proteins. In contrast, all genes from C. fulvum encoding the effectors that have been reported so far are highly up-regulated during infection where they play an important role in establishing disease. Like Avr2, Avr4, Ecp2 and Ecp6, we report that Ecp4 and Ecp5 also are involved in virulence of C. fulvum on tomato. Finally, we discuss the limitations of only using bioinformatics approaches to identify novel effectors involved in virulence.
Inchapter 3 we describe the identification and characterization of a novel effector secreted by C. fulvum. CfTom1 encodes a functional tomatinase enzyme, which belongs to family 10 of glycoside hydrolases (GH10). Bacterial and fungal pathogens of tomato secrete this enzyme to detoxify the toxic saponin, α-tomatine, into the less toxic compounds tomatidine and lycotetraose. Similarly, CfTom1 is responsible for α-tomatine deoxification by C. fulvum both in vitro and during infection of tomato. Accordingly, ∆cftom1 mutants are more sensitive to α-tomatine because they can no longer detoxify α-tomatine. They are less virulent on tomato plants than wild-type as reflected by a delay in disease symptom development and reduced fungal biomass production. In addition, tomatidine appears to be more toxic to tomato cells than α-tomatine, but it does not suppress plant defense responses as previously suggested in literature. Altogether, our results clearly indicate that CfTom1, the major or possibly only tomatinase enzyme produced by C. fulvum, contributes to full virulence of this fungus on tomato by detoxifying α-tomatine.
Hardly anything is known about in planta regulation of effector genes. In chapter 4 we describe the functional characterization of CfWor1, a homologue of FoSge1, a conserved transcriptional regulator of effectors in Fusarium oxysporum f. sp. lycopersici. CfWor1 is also homologous to Wor1/Ryp1/Mit1 proteins, which are involved in morphological switches in Candida albicans, Histoplasma capsulatum and Saccharomyces cerevisiae, respectively. In contrast to FoSge1, CfWor1 is unlikely a positive regulator of effector genes because it is weakly expressed during infection of tomato. Compared to wild-type, ∆cfwor1 mutants show strong developmental and morphological defects. ∆cfwor1 mutants do not produce any conidia, but differentiate sclerotium-like structures and secrete an extracellular matrix that covers fungal hyphae.∆cfwor1 mutants are no longer virulent on tomato, likely because of developmental defects. Although constitutive expression of CfWor1 in C. fulvum did not cause any obvious developmental defects, except reduced conidia production, the transformants showed reduced virulence. Quantitative PCR on known effector and secondary metabolism genes in both ∆cfwor1 mutants and constitutive expression transformant revealed that the effect of CfWor1 on the expression of these genes is likely due to developmental defects rather than direct regulation. Complementationof a non-virulent ∆fosge1 mutant of F. oxysporum f. sp. lycopersici with full length CfWor1 or chimera of CfWor1 and FoSge1 restored expression of SIX effector genes, but not virulence, indicating that reduced virulence observed for the ∆fosge1 mutant is not solely due to loss of expression ofthese effector genes. Altogether, our study suggests that CfWor1 is a major regulator of development in C. fulvum which indirectly affects virulence.
Chapter 5 provides a general discussion of the present work on C. fulvum effectors, with particular emphasis on comparative genomics and transcriptomics approaches to identify novel effectors involved in fungal virulence and avirulence. Our findings are put in a broader perspective including a discussion on how identification of effectors will improve our understanding of molecular interactions between plants and pathogenic fungi and how we can use this knowledge to develop new strategies for sustainable disease resistance breeding.
'Intraspecific pathogen variation' Verslag KNPV/Plantum/EPS-eendagsconferentie : Wageningen, 22 januari 2013
Folkertsma, R.T. ; Goverse, A. ; Posthuma, E. ; Gilijamse, T. - \ 2013
Gewasbescherming 44 (2013)2. - ISSN 0166-6495 - p. 32 - 34.
plantenziekteverwekkers - genetische variatie - genotypische variatie - dna-sequencing - moleculaire technieken - moleculaire genetica - plantenziekten - conferenties - plant pathogens - genetic variation - genetic variance - dna sequencing - molecular techniques - molecular genetics - plant diseases - conferences
Dinsdag 22 januari 2013 werd in Wageningen een eendagsconferentie gehouden getiteld ‘Intraspecific pathogen variation - implications and opportunities’. Deze conferentie werd georganiseerd naar aanleiding van discussies over het werken met intraspecifieke variatie voor diagnostiek en veredeling binnen de Nematodenwerkgroep van de KNPV en de Isolaten-beheerwerkgroep van Plantum. Het doel van de bijeenkomst was a.) onderzoekers uit de private en de publieke sector samenbrengen om recente ontwikkelingen te bespreken in fundamentele en toegepaste aspecten van het werken met intraspecifieke variatie, en b.) het stimuleren van uitwisselen van ideeën binnen en tussen beide groepen, voor mogelijke vervolginitiatieven.
De tomatenkaart is klaar, wat nu?
Finkers, H.J. ; Visser, R.G.F. - \ 2013
Kennis Online 10 (2013)mei. - p. 3 - 5.
moleculaire genetica - plantengenetica - dna-sequencing - tomaten - rassen (planten) - plantenveredeling - genetische bronnen van plantensoorten - genomen - molecular genetics - plant genetics - dna sequencing - tomatoes - varieties - plant breeding - plant genetic resources - genomes
In 2012 publiceerde Nature de genomische sequentie van de tomaat. Maar daarmee is het werk niet af, zegt Richard Finkers. Hij bepaalde de basenvolgorde van nog eens 150 verwanten van de modeltomaat, om plantenveredelaars in staat te stellen op zoek te gaan naar nieuwe genen in oude rassen.
'Ui is een puzzel met 150 duizend stukjes'
Smulders, M.J.M. - \ 2013
Kennis Online 10 (2013)mei. - p. 12 - 12.
moleculaire genetica - dna-sequencing - genomen - plantenveredeling - onderzoek - molecular genetics - dna sequencing - genomes - plant breeding - research
Om zeer grote genomen in kaart te kunnen brengen, moeten eerst fundamentele vragen worden opgelost. Zonder hulp van de overheid komen die antwoord er niet, zegt René Smulders. Terwijl grondige sequencing veredeling aantoonbaar versnelt.
Animal breeding for food security : opportunities in the genome sequencing era
Veerkamp, R.F. - \ 2012
Wageningen : Wageningen University, Wageningen UR - ISBN 9789461733245 - 23
dierveredeling - genomica - genoomanalyse - dna-sequencing - fokkerijmethoden - animal breeding - genomics - genome analysis - dna sequencing - animal breeding methods
Inaugural lecture upon taking up the position of Special Professor of Numerical Genetics and Genomics at Wageningen University.
Discovery and genotyping of existing and induced DNA sequence variation in potato
Uitdewilligen, J.G.A.M.L. - \ 2012
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Herman van Eck; Anne-Marie Wolters. - S.l. : s.n. - ISBN 9789461732330 - 165
solanum tuberosum - aardappelen - dna-sequencing - dna - nucleotidenvolgordes - genotyping - plantenveredeling - genotypen - fenotypen - tetraploïdie - solanum tuberosum - potatoes - dna sequencing - dna - nucleotide sequences - genotyping - plant breeding - genotypes - phenotypes - tetraploidy
In this thesis natural and induced DNA sequence diversity in potato (Solanum tuberosum) for use in marker-trait analysis and potato breeding is assessed. The study addresses the challenges of reliable, high-throughput identification and genotyping of sequence variants in existing tetraploid potato cultivar panels using traditional Sanger sequencing and next-generation massively parallel sequencing (MPS), and the application of this knowledge in the form of genetic markers. Furthermore, it explores the efficiency of ethyl methanesulphonate (EMS) mutagenesis combined with high resolution melting (HRM) DNA screening to induce and discover novel sequence variants in potato genotypes.
Vliegensvlug door het DNA
Schijlen, E.G.W.M. - \ 2012
WageningenWorld 1 (2012). - ISSN 2210-7908 - 2
dna-sequencing - prestatie van apparatuur - toestellen - dna sequencing - equipment performance - appliances
Wageningse wetenschappers maken gebruik van twee nieuwe DNA-sequencers. Eén daarvan werkt 25 duizend keer sneller dan de apparatuur van vijftien jaar geleden.