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Open Access Publications from the University of California

Scholarly Works (7 results)

  • Thesis
  • Peer Reviewed
UC Santa Cruz Electronic Theses and Dissertations (2014)

In the fourteen years since the announcement of the rough draft of the human genome there has been a precipitous drop in the cost of genome sequencing, from several billions of dollars down to a few thousand. This has lead to a new age of data prosperity in biological sciences and to a large growth in the field of Bioinformatics. The extremely low cost of sequencing means that multitudes of species can now be sequenced and those data can be added to the ever-expanding library. This sudden wealth of raw data at a low level in the analysis hierarchy has given an urgency to important methodological questions. What is the best method to assemble a new genome? Given that you have several assembled genomes and you want to know how they're related to one another, what is the best way to align these genomes? And finally, once in possession of an alignment of genomes, how can we best use that information to annotate genes and other biologically interesting regions upon those genomes?

The work presented herein is an attempt to quantify and compare the methods for carrying out these fundamental research tasks. In the first chapter (on the Assem- blathon, a collaborative competition that brought together the world's genome assembly expects), I investigate the problem of short read whole genome de novo assembly. In the second chapter (on the Alignathon, a collaborative competition that brought together the world's whole genome alignment experts) I investigate the problem of whole genome alignment. Finally I address the problem of comparative annotation by using a dataset comprised of the genomes of 17 strains of inbred mouse and the rat in order to establish a quick method of annotating multiple genomes using a combination of evolutionary homology information, existing annotations and extrinsic data (e.g. RNAseq) using off the shelf software components for the majority of the work.

    Cover page: Evaluation And Application Of The Three A's Of Genomics: Assembly, Alignment, Annotation.Creative Commons 'BY' version 4.0 license
    • Article
    • Peer Reviewed
    UC Santa Cruz Previously Published Works (2013)
    Abstract Background Retroposed processed gene transcripts are an important source of material for new gene formation on evolutionary timescales. Most prior work on gene retrocopy discovery compared copies in reference genome assemblies to their source genes. Here, we explore gene retrocopy insertion polymorphisms (GRIPs) that are present in the germlines of individual humans, mice, and chimpanzees, and we identify novel gene retrocopy insertions in cancerous somatic tissues that are absent from patient-matched non-cancer genomes. Results Through analysis of whole-genome sequence data, we found evidence for 48 GRIPs in the genomes of one or more humans sequenced as part of the 1,000 Genomes Project and The Cancer Genome Atlas, but which were not in the human reference assembly. Similarly, we found evidence for 755 GRIPs at distinct locations in one or more of 17 inbred mouse strains but which were not in the mouse reference assembly, and 19 GRIPs across a cohort of 10 chimpanzee genomes, which were not in the chimpanzee reference genome assembly. Many of these insertions are new members of existing gene families whose source genes are highly and widely expressed, and the majority have detectable hallmarks of processed gene retrocopy formation. We estimate the rate of novel gene retrocopy insertions in humans and chimps at roughly one new gene retrocopy insertion for every 6,000 individuals. Conclusions We find that gene retrocopy polymorphisms are a widespread phenomenon, present a multi-species analysis of these events, and provide a method for their ascertainment.
    • 2 supplemental files
    Cover page: Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
    • Article
    • Peer Reviewed
    UC Santa Cruz Previously Published Works (2015)
    A reference genome is a high quality individual genome that is used as a coordinate system for the genomes of a population, or genomes of closely related subspecies. Given a set of genomes partitioned by homology into alignment blocks we formalize the problem of ordering and orienting the blocks such that the resulting ordering maximally agrees with the underlying genomes' ordering and orientation, creating a pan-genome reference ordering. We show this problem is NP-hard, but also demonstrate, empirically and within simulations, the performance of heuristic algorithms based upon a cactus graph decomposition to find locally maximal solutions. We describe an extension of our Cactus software to create a pan-genome reference for whole genome alignments, and demonstrate how it can be used to create novel genome browser visualizations using human variation data as a test. In addition, we test the use of a pan-genome for describing variations and as a reference for read mapping.
      Cover page: Building a Pan-Genome Reference for a Population
      • Article
      • Peer Reviewed
      UC Santa Cruz Previously Published Works (2014)
      Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.
        Cover page: Alignathon: a competitive assessment of whole-genome alignment methods
        • Article
        • Peer Reviewed
        UC Santa Cruz Previously Published Works (2014)
        To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.
          Cover page: Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
          • Article
          • Peer Reviewed
          UCLA Previously Published Works (2018)
          We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immunity and exhibit enrichment of transposable elements and signatures of recent retrotransposition events. Combinations of alleles and genes unique to an individual strain are commonly observed at these loci, reflecting distinct strain phenotypes. We used these genomes to improve the mouse reference genome, resulting in the completion of 10 new gene structures. Also, 62 new coding loci were added to the reference genome annotation. These genomes identified a large, previously unannotated, gene (Efcab3-like) encoding 5,874 amino acids. Mutant Efcab3-like mice display anomalies in multiple brain regions, suggesting a possible role for this gene in the regulation of brain development.
            Cover page: Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2013)
            Abstract Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
            • 1 supplemental file
            Cover page: Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
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