GenomeRing: alignment visualization based on SuperGenome coordinates

Motivation: The number of completely sequenced genomes is continuously rising, allowing for comparative analyses of genomic variation. Such analyses are often based on whole-genome alignments to elucidate structural differences arising from insertions, deletions or from rearrangement events. Computational tools that can visualize genome alignments in a meaningful manner are needed to help researchers gain new insights into the underlying data. Such visualizations typically are either realized in a linear fashion as in genome browsers or by using a circular approach, where relationships between genomic regions are indicated by arcs. Both methods allow for the integration of additional information such as experimental data or annotations. However, providing a visualization that still allows for a quick and comprehensive interpretation of all important genomic variations together with various supplemental data, which may be highly heterogeneous, remains a challenge

Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity

The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transi-tions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive chal-lenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome tran-sitions, resulting in species-level separation between aquatic biomes

Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel

The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains (HdrR, HNI and HSOK). Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals. We have exploited this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We used Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allowed us to identify a much greater variety of high-quality structural variants compared with Illumina sequencing. We also present results and methods using a pan-genome graph representation of 12 individual medaka lines from the MIKK panel. This graph-based reference MIKK panel genome revealed novel differences between the MIKK panel lines compared to standard linear reference genomes. We found additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We were also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigated line-specific CpG methylation and performed differential DNA methylation analysis across the 12 lines. We thus present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel specific pan genome reference dataset allowing for the investigation of novel variation types that would be elusive using standard approaches

The computational analysis of post-translational modifications

The post-translational modification (PTMs) of proteins presents a means to increase the proteome size and diversity of an organism through the inclusion of structural elements not encoded at the sequence-level alone. Their erroneous inclusion or exclusion has been linked to a variety of diseases and disorders thus their characterisation has the potential to present viable drug targets. The proliferation of newer high-throughput methods, such as mass spectrometry, to identify such modifications has led to a rapid increase in the number of databases and tools to display and analyse such vast amounts of data effectively. This study covers the development of one such tool; PTM Browser, and the construction of the underlying database that it is based upon. This new database was initially seeded with annotations from the Swiss-Prot and Phospho.ELM resources. The initial database of PTMs was then expanded to include a large repertoire of previously unannotated proteins for a selection of topical species (e.g. Danio rerio and Tetraodon nigroviridis). Orthologue assignments have also been added to the database – to allow for queries to be performed regarding the conservation of modifications between homologous proteins. The PTM Browser tool allows for a full exploration of this new database of PTMs – with a special focus on allowing users to identify modifications that are both shared between and are specific to particular species. This tool is freely available for non-commercial use at the following URL: http://www.ptmbrowser.org. An analysis is presented on the conservation of modifications between members of the tumour suppressor family, p53, using this new tool. This tool has also been used to analysis the conservation of modifications between super-kingdoms and Eukaryote species

Collaborative Cross Graphical Genome

Reference genomes are the foundation of most bioinformatic pipelines. They are conventionally represented as a set of single-sequence assembled contigs, referred to as linear genomes. The rapid growth of sequencing technologies has driven the advent of pangenomes that integrate multiple genome assemblies in a single representation. Graphs are commonly used in pangenome models. However, there are challenges for graph-based pangenome representations and operations. This dissertation introduces methods for reference pangenome construction, genomic feature annotation, and tools for analyzing population-scale sequence data based on a graphical pangenome model. We first develop a genome registration tool for constructing a reference pangenome model by merging multiple linear genome assemblies and annotations into a graphical genome. Secondly, we develop a graph-based coordinate framework and discuss the strategies for referring to, annotating, and comparing genomic features in a graphical pangenome model. We demonstrate that the graph coordinate system simplifies assembly and annotation updates, identifying and segmenting updated sequences in a specific genomic region. Thirdly, we develop an alignment-free method to analyze population-scale sequence data based on a pangenome model. We demonstrate the application of our methods by constructing pangenome models for a mouse genetic reference population, Collaborative Cross. The pangenome framework proposed in this dissertation simplified the maintenance and management of massive genomic data and established a novel data structure for analyzing, visualizing, and comparing genomic features in an intra-specific population.Doctor of Philosoph

Mechanistic and metabolic basis of bacterial cross-feeding

In their natural habitat, microorganisms interact with a variety of micro- as well as macroorganisms. Such interactions result in either positive or negative effects on the growth and survival of involved species. Negative effects on growth, can be mostly attributed to competition for limited resources and space, while positive effects on growth are challenging to justify. Metabolite cross-feeding is one such interaction that describes the transfer of primary or secondary metabolites from one organism to another. Considering that metabolites are costly and impose a significant energetic cost to the cell producing them, it is intriguing to know how the process of cross-feeding is favourable. Bacteria employ different mechanisms to carry out the exchange of metabolic by-products, intermediates, and electrons between each other during the process of cross-feeding. Contact-dependent mechanisms of exchange (such as direct cell-cell contact, type secretion systems, and pili), provide the following advantages: (i) protection of the exchanged product from environmental degradation or modification, (ii) provision of the product in a concentrated form, and (iii) prevention of uptake of the product by unintended recipients. The role of contact-dependent mechanisms in the transfer of genetic material (bacterial conjugation) and toxins (contact-dependent inhibition or killing) has been studied for years. However, the importance of similar contact-dependent mechanisms during the cross-feeding of essential nutrients is not fully understood. This thesis aimed at identifying a contact-dependent mechanism for amino acid cross-feeding in bacteria