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Efficient Comparative Genomics With Low Coverage Data Using Paladin, Rachel Cates

Master's Theses and Capstones

Comparative genomics focuses on comparing the catalog of genomic elements of whole genome sequences to determine the functional relationship between genes. One of the first steps in comparative analysis is to make genome assemblies for the organisms of interest. However, due to the cost and time required to create these assemblies, only a limited number of organisms can be analyzed simultaneously. A new software package, PALADIN, maps nucleotide reads in protein space using a modified version of the Burrows-Wheeler Aligner (BWA). We demonstrate that PALADIN can accurately and efficiently identify the proteins in a genome using inputs with significantly lower …

Phylogenetic Focusing Reveals The Evolution Of Eumetazoan Opsins, Curtis Provencher

Master's Theses and Capstones

Phylogenetic analyses of gene trees commonly begin by searching large molecular datasets from the taxa of interest using some known query sequence. Resulting sequences that exceed some threshold are then concatenated, aligned, and analyzed phylogenetically. This approach has revealed much about the evolutionary history of gene families, but several problems are apparent. Here we apply a new approach that we call Phylogenetic Focusing that circumvents some issues related to global search strategies. Our approach first circumscribes the largest possible orthogroup containing the gene family of interest and then proceeds to focus in on the gene family of interest based on …

The Paladin Suite: Multifaceted Characterization Of Whole Metagenome Shotgun Sequences, Anthony Stephen Westbrook

Master's Theses and Capstones

Whole metagenome shotgun sequencing is a powerful approach for assaying many aspects of microbial communities, including the functional and symbiotic potential of each contributing community member. The research community currently lacks tools that efficiently align DNA reads against protein references, the technique necessary for constructing functional profiles. This thesis details the creation of PALADIN – a novel modification of the Burrows-Wheeler Aligner that provides orders-of-magnitude improved efficiency by directly mapping in protein space. In addition to performance considerations, utilizing PALADIN and associated tools as the foundation of metagenomic pipelines also allows for novel characterization and downstream analysis.

The accuracy and …

Bacterial And Phage Interactions Influencing Vibrio Parahaemolyticus Ecology, Ashley L. Marcinkiewicz

Master's Theses and Capstones

Vibrio parahaemolyticus, a human pathogenic bacterium, is a naturally occurring member of the microbiome of the Eastern oyster. As the nature of this symbiosis in unknown, the oyster presents the opportunity to investigate how microbial communities interact with a host as part of the ecology of an emergent pathogen of importance. To define how members of the oyster bacterial microbiome correlate with V. parahaemolyticus, I performed marker-based metagenetic sequencing analyses to identify and quantify the bacterial community in individual oysters after culturally-quantifying V. parahaemolyticus abundance. I concluded that despite shared environmental exposures, individual oysters from the same collection site varied …

Establishment Of The Multicolored Asian Lady Beetle, Harmonia Axyridis, As A Model System For The Evolution Of Phenotypic Variation, Lindsay Havens

Master's Theses and Capstones

The mechanisms behind the evolution and maintenance of striking visual phenotypes are as varied as the species that display these phenotypes. Multiple study systems have been well characterized and provide critical information about the evolution of these traits. However, new study systems in which the phenotype of interest can be easily manipulated and quantified are essential to answer many questions about the functionality of core evolutionary processes. One such model is elytral spot number of the multicolored Asian lady beetle, Harmonia axyridis (Chapter 1). I describe Harmonia axyridis as a potential novel model species for examining extreme phenotypic evolution. To …

The Dynamic Host-Pathogen Interactions Of Verticillium Dahliae: Comparative Genomics Of V. Dahliae And Its Interactions In Cover Crop Species And Wild Strawberry (Fragaria Vesca), Garrett Gleeson

Master's Theses and Capstones

The evolutionary arms race between plants and their associated pathogens has created highly dynamic interactions. Understanding the mechanisms that drive these interactions and the phylogenetic history of the pathogens is key to developing effective disease management practices. Although there have been great advances in understanding the evolution of plant pathogens, they only scratch the surface of the true complexity of pathogens’ interactions with their hosts and their environment. In this study, the interactions between the fungal vascular wilt pathogen, Verticillum dahliae, and a variety of hosts including accessions of wild strawberry, Fragaria vesca, and several cover crop species are investigated. …

Genotyping On Custom Arrays Using A Parallel Data Pipeline, Brian Albere

Master's Theses and Capstones

In the past, genotyping (determining a set of alleles in an organism) has been an extremely challenging process. The time, monetary, and technology demands of the task have limited genotype data to a small variety of scientific model organisms with the capacity to conduct genetic crosses. New sequencing technology from companies such as NimbleGen, however, can generate custom organism-specific microarrays at relatively low cost. The combination of these arrays and the knowledge of species' genome-wide SNPs allow genotype experiments, such as generation maps, QTL studies, and natural population variation studies, to be conducted on virtually any organism. Although the NimbleGen …

Design And Implementation Of A Statistical Analysis Tool For Two Biological States, Gang Lu

Master's Theses and Capstones

The major goal of research in this thesis is to design and implement a software tool (Q5+) that can easily, quickly and reliably search biomarkers by statistically analyzing mass spectrometry data from two different biological states. Q5+ implements most of the Q5 algorithm, a very good algorithm that is used for classifying mass spectrometry data (Lilien et al). Compared Q5 Q5+ improves the usability of Q5 by incorporating a Graphic User interface and Matrix Library. Results show that by running the same data, Q5+ and Q5 showed the equivalent classification ability. Q5+ also implements the Peak Screening feature, which can …

Comparative Genomics Exploration Tools, Shilpa M. Kulkarni

Master's Theses and Capstones

Comparative Genomics focuses on elucidating the genetic differences between different species or different strains of the same species by the comparative analysis of DNA sequences to identify functional elements and regulatory regions. This thesis describes the design and development of two software tools to support comparative genomics research. These tools were specifically developed to support the analysis and assembly of sequence data produced from innovative new DNA sequencing technology from 454 Life Sciences using the PicoTiterPlate(TM) device. This technology will dramatically affect comparative genomics research. Currently available software tools were developed to handle traditional shotgun sequences averaging 500-1000 base pairs …

Software Tools For Comparing Genomic Sequence, Morel Henley

Master's Theses and Capstones

We describe three software tools related to research in comparative genomics, a growing research area that explores the variation within and between organisms. We developed a set of tools that explore sequence similarity and differences in genomes. Two of these tools are specifically aimed at examining DNA sequence data from two or more genomes: (1) The Magenta's OPUS tool compares genomic sequences to identify shared or unique segments between closely related species. This tool looks for functional similarities and differences in genomic data by classifying sequences into groups based on genomic categories: Orthologs, Paralogs, and Unique Sequence. (2) The DSNP …