Genome bioinformatics of tomato and potato

In the past two decades genome sequencing has developed from a laborious and costly technology employed by large international consortia to a widely used, automated and affordable tool used worldwide by many individual research groups. Genome sequences of many food animals and crop plants have been deciphered and are being exploited for fundamental research and applied to improve their breeding programs. The developments in sequencing technologies have also impacted the associated bioinformatics strategies and tools, both those that are required for data processing, management, and quality control, and those used for interpretation of the data. This thesis focuses on the application of genome sequencing, assembly and annotation to two members of the Solanaceae family, tomato and potato. Potato is the economically most important species within the Solanaceae, and its tubers contribute to dietary intake of starch, protein, antioxidants, and vitamins. Tomato fruits are the second most consumed vegetable after potato, and are a globally important dietary source of lycopene, beta-carotene, vitamin C, and fiber. The chapters in this thesis document the generation, exploitation and interpretation of genomic sequence resources for these two species and shed light on the contents, structure and evolution of their genomes. Chapter 1introduces the concepts of genome sequencing, assembly and annotation, and explains the novel genome sequencing technologies that have been developed in the past decade. These so-called Next Generation Sequencing platforms display considerable variation in chemistry and workflow, and as a consequence the throughput and data quality differs by orders of magnitude between the platforms. The currently available sequencing platforms produce a vast variety of read lengths and facilitate the generation of paired sequences with an approximately fixed distance between them. The choice of sequencing chemistry and platform combined with the type of sequencing template demands specifically adapted bioinformatics for data processing and interpretation. Irrespective of the sequencing and assembly strategy that is chosen, the resulting genome sequence, often represented by a collection of long linear strings of nucleotides, is of limited interest by itself. Interpretation of the genome can only be achieved through sequence annotation – that is, identification and classification of all functional elements in a genome sequence. Once these elements have been annotated, sequence alignments between multiple genomes of related accessions or species can be utilized to reveal the genetic variation on both the nucleotide and the structural level that underlies the difference between these species or accessions. Chapter 2describes BlastIf, a novel software tool that exploits sequence similarity searches with BLAST to provide a straightforward annotation of long nucleotide sequences. Generally, two problems are associated with the alignment of a long nucleotide sequence to a database of short gene or protein sequences: (i) the large number of similar hits that can be generated due to database redundancy; and (ii) the relationships implied between aligned segments within a hit that in fact correspond to distinct elements on the sequence such as genes. BlastIf generates a comprehensible BLAST output for long nucleotide sequences by reducing the number of similar hits while revealing most of the variation present between hits. It is a valuable tool for molecular biologists who wish to get a quick overview of the genetic elements present in a newly sequenced segment of DNA, prior to more elaborate efforts of gene structure prediction and annotation. In Chapter 3 a first genome-wide comparison between the emerging genomic sequence resources of tomato and potato is presented. Large collections of BAC end sequences from both species were annotated through repeat searches, transcript alignments and protein domain identification. In-depth comparisons of the annotated sequences revealed remarkable differences in both gene and repeat content between these closely related genomes. The tomato genome was found to be more repetitive than the potato genome, and substantial differences in the distribution of Gypsy and Copia retrotransposable elements as well as microsatellites were observed between the two genomes. A higher gene content was identified in the potato sequences, and in particular several large gene families including cytochrome P450 mono-oxygenases and serine-threonine protein kinases were significantly overrepresented in potato compared to tomato. Moreover, the cytochrome P450 gene family was found to be expanded in both tomato and potato when compared to Arabidopsis thaliana, suggesting an expanded network of secondary metabolic pathways in the Solanaceae. Together these findings present a first glimpse into the evolution of Solanaceous genomes, both within the family and relative to other plant species. Chapter 4explores the physical and genetic organization of tomato chromosome 6 through integration of BAC sequence analysis, High Information Content Fingerprinting, genetic analysis, and BAC-FISH mapping data. A collection of BACs spanning substantial parts of the short and long arm euchromatin and several dispersed regions of the pericentrometric heterochromatin were sequenced and assembled into several tiling paths spanning approximately 11 Mb. Overall, the cytogenetic order of BACs was in agreement with the order of BACs anchored to the Tomato EXPEN 2000 genetic map, although a few striking discrepancies were observed. The integration of BAC-FISH, sequence and genetic mapping data furthermore provided a clear picture of the borders between eu- and heterochromatin on chromosome 6. Annotation of the BAC sequences revealed that, although the majority of protein-coding genes were located in the euchromatin, the highly repetitive pericentromeric heterochromatin displayed an unexpectedly high gene content. Moreover, the short arm euchromatin was relatively rich in repeats, but the ratio of Gypsy and Copia retrotransposons across the different domains of the chromosome clearly distinguished euchromatin from heterochromatin. The ongoing whole-genome sequencing effort will reveal if these properties are unique for tomato chromosome 6, or a more general property of the tomato genome. Chapter 5presents the potato genome, the first genome sequence of an Asterid. To overcome the problems associated with genome assembly due tothe high level of heterozygosity that is observed in commercial tetraploid potato varieties, a homozygous doubled-monoploid potato clone was exploited to sequence and assemble 86% of the 844 Mb genome. This potato reference genome sequence was complemented with re-sequencing of aheterozygous diploid clone, revealing the form and extent of sequence polymorphism both between different genotypes and within a single heterozygous genotype. Gene presence/absence variants and other potentially deleterious mutations were found to occur frequently in potato and are a likely cause of inbreeding depression. Annotation of the genome was supported by deep transcriptome sequencing of both the doubled-monoploid and the heterozygous potato, resulting in the prediction of more than 39,000 protein coding genes. Transcriptome analysis provided evidence for the contribution of gene family expansion, tissue specific expression, and recruitment of genes to new pathways to the evolution of tuber development. The sequence of the potato genome has provided new insights into Eudicot genome evolution and has provided a solid basis for the elucidation of the evolution of tuberisation. Many traits of interest to plant breeders are quantitative in nature and the potato sequence will simplify both their characterization and deployment to generate novel cultivars. The outstanding challenges in plant genome sequencing are addressed in Chapter 6. The high concentration of repetitive elements and the heterozygosity and polyploidy of many interesting crop plant species currently pose a barrier for the efficient reconstruction of their genome sequences. Nonetheless, the completion of a large number of new genome sequences in recent years and the ongoing advances in sequencing technology provide many excitingopportunities for plant breeding and genome research. Current sequencing platforms are being continuously updated and improved, and novel technologies are being developed and implemented in third-generation sequencing platforms that sequence individual molecules without need for amplification. While these technologies create exciting opportunities for new sequencing applications, they also require robust software tools to process the data produced through them efficiently. The ever increasing amount of available genome sequences creates the need for an intuitive platform for the automated and reproducible interrogation of these data in order to formulate new biologically relevant questions on datasets spanning hundreds or thousands of genome sequences. </p

LIPIcs, Volume 248, ISAAC 2022, Complete Volume

LIPIcs, Volume 248, ISAAC 2022, Complete Volum

A systems-based approach for detecting molecular interactions across tissues.

Current high-throughput gene expression experiments have a straightforward design of examining the gene expression of one group or condition relative to that of another. The data is typically analyzed as if they represent strictly intracellular events, and often treats genes as coming from a homogeneous population. Although intracellular events are crucial to nearly all biological processes, cell-cell interactions are often just as important, especially when gene expression data is generated from heterogeneous cell populations, such as from whole tissues. Cell-cell molecular interactions are generally lost in the available analytical procedures and as a result, are not examined experimentally, at least not accurately or with efficiency. Most importantly, this imposes major limitations when studying gene expression changes in multiple samples that interact with one another. In order to addresses the limitations of current techniques, we have developed a novel systems-based approach that expands the traditional analysis of gene expression in two stages. This includes a novel sequence-based meta-analytic tool, AbsIDconvert, that allows for conversion of annotated features using an interval tree for storing and querying absolute genomic coordinates for comparison of multi-scale macro-molecule identifiers across platforms and/or organisms. In addition, a systems-based heuristic algorithm is developed to find intercellular interactions between two sets of genes, potentially from different tissues by utilizing location information of each gene along with the information available in the secondary databases in the form of interactions, pathways and signaling. AbsIDconvert is shown to provide a high accuracy in identifier conversion as compared to other available methodologies (typically at an average rate of 84%) while maintaining a higher efficiency (O(n*log(n)). Our intercellular interaction approach and underlying visualization shows promise in allowing researchers to uncover novel signaling pathways in an intercellular fashion that to this point has not been possible

Combining SOA and BPM Technologies for Cross-System Process Automation

This paper summarizes the results of an industry case study that introduced a cross-system business process automation solution based on a combination of SOA and BPM standard technologies (i.e., BPMN, BPEL, WSDL). Besides discussing major weaknesses of the existing, custom-built, solution and comparing them against experiences with the developed prototype, the paper presents a course of action for transforming the current solution into the proposed solution. This includes a general approach, consisting of four distinct steps, as well as specific action items that are to be performed for every step. The discussion also covers language and tool support and challenges arising from the transformation

Tool Support for Finding and Preventing Faults in Rule Bases

This thesis analyzes challenges for the correct creation of rule bases. Based on experiences and data from three rule base development projects, dedicated experiments and a survey of developers, ten main problem areas are identified. Four approaches in the area of Testing, Debugging, Anomaly Detection and Visualization are proposed and evaluated as remedies for these problem areas

Automated Deduction – CADE 28

This open access book constitutes the proceeding of the 28th International Conference on Automated Deduction, CADE 28, held virtually in July 2021. The 29 full papers and 7 system descriptions presented together with 2 invited papers were carefully reviewed and selected from 76 submissions. CADE is the major forum for the presentation of research in all aspects of automated deduction, including foundations, applications, implementations, and practical experience. The papers are organized in the following topics: Logical foundations; theory and principles; implementation and application; ATP and AI; and system descriptions

Exploiting Similarity Patterns to Build Generic Test Case Templates for Software Product Line Testing

Ph.DDOCTOR OF PHILOSOPH

Semantic search and composition in unstructured peer-to-peer networks

This dissertation focuses on several research questions in the area of semantic search and composition in unstructured peer-to-peer (P2P) networks. Going beyond the state of the art, the proposed semantic-based search strategy S2P2P offers a novel path-suggestion based query routing mechanism, providing a reasonable tradeoff between search performance and network traffic overhead. In addition, the first semantic-based data replication scheme DSDR is proposed. It enables peers to use semantic information to select replica numbers and target peers to address predicted future demands. With DSDR, k-random search can achieve better precision and recall than it can with a near-optimal non-semantic replication strategy. Further, this thesis introduces a functional automatic semantic service composition method, SPSC. Distinctively, it enables peers to jointly compose complex workflows with high cumulative recall but low network traffic overhead, using heuristic-based bidirectional haining and service memorization mechanisms. Its query branching method helps to handle dead-ends in a pruned search space. SPSC is proved to be sound and a lower bound of is completeness is given. Finally, this thesis presents iRep3D for semantic-index based 3D scene selection in P2P search. Its efficient retrieval scales to answer hybrid queries involving conceptual, functional and geometric aspects. iRep3D outperforms previous representative efforts in terms of search precision and efficiency.Diese Dissertation bearbeitet Forschungsfragen zur semantischen Suche und Komposition in unstrukturierten Peer-to-Peer Netzen(P2P). Die semantische Suchstrategie S2P2P verwendet eine neuartige Methode zur Anfrageweiterleitung basierend auf Pfadvorschlägen, welche den Stand der Wissenschaft übertrifft. Sie bietet angemessene Balance zwischen Suchleistung und Kommunikationsbelastung im Netzwerk. Außerdem wird das erste semantische System zur Datenreplikation genannt DSDR vorgestellt, welche semantische Informationen berücksichtigt vorhergesagten zukünftigen Bedarf optimal im P2P zu decken. Hierdurch erzielt k-random-Suche bessere Präzision und Ausbeute als mit nahezu optimaler nicht-semantischer Replikation. SPSC, ein automatisches Verfahren zur funktional korrekten Komposition semantischer Dienste, ermöglicht es Peers, gemeinsam komplexe Ablaufpläne zu komponieren. Mechanismen zur heuristischen bidirektionalen Verkettung und Rückstellung von Diensten ermöglichen hohe Ausbeute bei geringer Belastung des Netzes. Eine Methode zur Anfrageverzweigung vermeidet das Feststecken in Sackgassen im beschnittenen Suchraum. Beweise zur Korrektheit und unteren Schranke der Vollständigkeit von SPSC sind gegeben. iRep3D ist ein neuer semantischer Selektionsmechanismus für 3D-Modelle in P2P. iRep3D beantwortet effizient hybride Anfragen unter Berücksichtigung konzeptioneller, funktionaler und geometrischer Aspekte. Der Ansatz übertrifft vorherige Arbeiten bezüglich Präzision und Effizienz

Proceedings of the 21st Conference on Formal Methods in Computer-Aided Design – FMCAD 2021

The Conference on Formal Methods in Computer-Aided Design (FMCAD) is an annual conference on the theory and applications of formal methods in hardware and system verification. FMCAD provides a leading forum to researchers in academia and industry for presenting and discussing groundbreaking methods, technologies, theoretical results, and tools for reasoning formally about computing systems. FMCAD covers formal aspects of computer-aided system design including verification, specification, synthesis, and testing