Biology subjects

Schaap, P. J.

Publications and source records attributed to Schaap, P. J..

25 records · Page 2Linked to original sources

bioRxiv2020

A chromosome-level assembly of the black tiger shrimp (Penaeus monodon) genome facilitates the identification of novel growth-associated genes

The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

genomics↗

bioRxiv2020

A protocol for adding knowledge to Wikidata, a case report

Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a "commons". Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modelled with entity schemas represented by Shape Expressions. As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable, is demonstrated by integrating data from NCBI Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, Human Coronavirus NL63, Human coronavirus 229E, Human coronavirus HKU1, Human coronavirus OC4).

bioinformatics↗

bioRxiv2019

A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle

Cultivation-independent surveys have shown that the recently described genus Romboutsia within the family Peptostreptococcaceae is more diverse than previously acknowledged. The majority of Romboutsia-associated 16S rRNA gene sequences have an intestinal origin, but the specific roles that Romboutsia species play in the digestive tract are largely unknown. The complete genomes of the human intestinal isolate Romboutsia hominis FRIFIT (DSM 28814) and the soil isolate Romboutsia lituseburensis A25KT (DSM 797) were sequenced. An evaluation of the common traits of this recently defined genus was done based on comparative genome analysis of the two strains together with the previously elucidated genome of the type species Romboutsia ilealis CRIBT. These analyses showed that the genus Romboutsia covers a broad range of metabolic capabilities with respect to carbohydrate utilization, fermentation of single amino acids, anaerobic respiration and metabolic end products. Main differences between strains were found in their abilities to utilize specific carbohydrates, to synthesize vitamins and other cofactors, and their nitrogen assimilation capabilities. In addition, differences were found with respect to bile metabolism and motility-related gene clusters.

microbiology↗

bioRxiv2018

Expected and observed genotype complexity in prokaryotes: correlation between 16S-rRNA phylogeny and protein domain content

BackgroundThe omnipresent 16S ribosomal RNA gene (16S-rRNA) is commonly used to identify and classify bacteria though it does not take into account the distinctive functional characteristics of taxa. We explored functional domain landscapes of over 5700 complete bacterial genomes, representing a wide coverage of the bacterial tree of life, and investigated to what extent the observed protein domain diversity correlates with the expected evolutionary diversity, using 16S-rRNA as metric for evolutionary distance.\n\nResultsAnalysis of protein domains showed that 83% of the bacterial genes code for at least one of the 9722 domain classes identified. By comparing clade specific and global persistence scores, candidate horizontal gene transfer and signifying domains could be identified. 16S-rRNA and functional domain content distances were used to evaluate and compare species divergence and overall a sigmoid curve is observed. Already at close 16S-rRNA evolutionary distances, high levels of functional diversity can be observed. At a larger 16S-rRNA distance, functional differences accumulate at a relatively lower pace.\n\nConclusionsAnalysis of 16S-rRNA sequences in the same taxa suggests that, in many cases, additional means of classification are required to obtain reliable phylogenetic relationships. Whole genome protein domain class phylogenies correlate with, and complement 16S-rRNA sequence-based phylogenies. Moreover, domain-based phylogenies can be constructed over large evolutionary distances and provide an in-depth insight of the functional diversity within and among species and enables large scale functional comparisons. The increased granularity obtained paves way for new applications to better predict the relationships between genotype, physiology and ecology.

genomics↗

bioRxiv2018

Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions

Currently, there is no consensus regarding the mechanism underlying Aspergillus niger citrate biosynthesis and secretion, although it is amongst the most studied biotechnological production processes. Carbon excess relative to various other medium constituents is key, but the complex interplay between the limiting factors required for extracellular citrate accumulation remains elusive. It is thought that one of the industrial bottlenecks for citrate production is citrate export, however, no A. niger citrate exporter has yet been identified. Here, we show that the phenotype of increased extracellular citrate accumulation can have fundamentally different underlying mechanisms, depending on how this response is triggered, and that combining gene expression analyses of the different conditions can lead to the compilation of a shortlist of the most promising citrate exporter candidates. Specifically, we found that varying the amount and type of supplement of an arginine auxotrophic A. niger strain shows down-regulation of citrate metabolising enzymes in the condition in which more citrate is accumulated extracellularly. This contrasts with the transcriptional adaptations triggered by iron limitation, which also induces increased A. niger citrate production. By combining data obtained from these two manners of inducing comparatively high extracellular citrate accumulation, we were able to compile a shortlist of the most likely citrate transporter candidates. Two of the most promising candidates were tested in the yeast Saccharomyces cerevisiae, one of which showed the ability to secrete citrate. Deletion of the endogenous A. niger gene encoding the corresponding transporter abolished the ability of this fungus to secrete citrate. Instead, under conditions that usually favour A. niger citrate production, we found increased accumulation of extracellular oxalate. Our findings provide steps in untangling the complex interplay of different mechanisms underlying A. niger citrate accumulation, and we identify, for the first time, a fungal citrate exporter, offering a valuable tool for improvement of A. niger as biotechnological cell-factory for organic acid production.\n\nAuthor SummaryCitrate is widely applied as acidifier, flavouring and chelating agent. Industrial citrate production currently relies on the filamentous fungus Aspergillus niger. Although the industrial production process using A. niger has vastly improved since initiated almost 100 years ago, citrate export remains a bottleneck. Here, we studied the gene expression pattern of A. niger under various citrate producing conditions. Using these expression patterns and different computational approaches, we compiled a shortlist of putative citrate exporter candidates. In this way, we were able to identify a gene encoding a transporter protein capable of citrate export. We show that the yeast Saccharomyces cerevisiae, normally a citrate non-producer, secretes detectable amounts of citrate when harbouring this gene. In addition, we verify the biological function of this gene in A. niger itself, as removing this gene resulted in a citrate non-producing phenotype, which is atypical for this fungus. This finding is particularly exciting, as it is the first identification of a eukaryotic citrate exporter. With this, we not only provide a tool for improvement of industrial citrate production, but knowledge of this gene should help develop new methods for improvement of A. niger as biotechnological cell-factory for the production of other organic acids.

molecular biology↗

bioRxiv2018

The Rumen Metatranscriptome Landscape Reflects Dietary Adaptation and Methanogenesis in Lactating Dairy Cows

Methane eructed by ruminant animals is a main contributor to greenhouse gas emissions and is solely produced by members of the phylum Euryarchaeota within the domain Archaea. Methanogenesis depends on the availability of hydrogen, carbon dioxide, methanol and acetate produced, which are metabolic products of anaerobic microbial degradation of feed-derived fibers. Changing the feed composition of the ruminants has been proposed as a strategy to mitigate methanogenesis of the rumen microbiota.\n\nWe investigated the impact of corn silage enhanced diets on the rumen microbiota of rumen-fistulated dairy cows, with a special focus on carbohydrate breakdown and methanogenesis. Metatranscriptome analysis of rumen samples taken from animals fed corn silage enhanced diets revealed that genes involved in starch metabolism were significantly more expressed while archaeal genes involved in methanogenesis showed lower expression values. The nutritional intervention also influenced the cross-feeding between Archaea and Bacteria.\n\nThe results indicate that the ruminant diet is important in methanogenesis. The diet-induced changes resulted in a reduced methane emission. The metatranscriptomic analysis provided insights into key underlying mechanisms and opens the way for new rational methods to further reduce methane output of ruminant animals.

microbiology↗

bioRxiv2017

Interoperable genome annotation with GBOL, an extendable infrastructure for functional data mining

BackgroundA standard structured format is used by the public sequence databases to present genome annotations. A prerequisite for a direct functional comparison is consistent annotation of the genetic elements with evidence statements. However, the current format provides limited support for data mining, hampering comparative analyses at large scale.\n\nResultsThe provenance of a genome annotation describes the contextual details and derivation history of the process that resulted in the annotation. To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated infrastructure (GBOL stack). GBOL is provenance aware and thus provides a consistent representation of functional genome annotations linked to the provenance. GBOL is modular in design, extendible and linked to existing ontologies. The GBOL stack of supporting tools enforces consistency within and between the GBOL definitions in the ontology (OWL) and the Shape Expressions (ShEx) language describing the graph structure. Modules have been developed to serialize the linked data (RDF) and to generate a plain text format files.\n\nConclusionThe main rationale for applying formalized information models is to improve the exchange of information. GBOL uses and extends current ontologies to provide a formal representation of genomic entities, along with their properties and relations. The deliberate integration of data provenance in the ontology enables review of automatically obtained genome annotations at a large scale. The GBOL stack facilitates consistent usage of the ontology.

genomics↗