Population Genomics of LINE Retrotransposons in Vertebrates

Queens College, Flushing NY

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Abstract

DESCRIPTION (provided by applicant): The complete sequencing of more than 20 vertebrate genomes has been an extraordinary source of information for biomedical scientists thereby revolutionizing the field of genetics, development biology and evolutionary biology. These genomes vary considerably in size and structure, yet the mechanisms shaping genomic architecture in vertebrates are not well understood. LINEs are autonomously replicating transposable elements that have played a defining role in shaping the size, structure and function of vertebrate genomes, therefore a thorough understanding of the regulation of their activity and abundance is necessary for our comprehension of genomic evolution. The diversity and copy number of LINEs varies considerably among vertebrate classes suggesting some fundamental differences in the way vertebrates cope with their intra- genomic parasites. These differences are still unexplained and may involve differences in the rate of transposition, the intensity of selection against new inserts and the demographic history of populations. The respective roles of these factors are unresolved because studies on LINEs in natural populations are scarce and limited to a small number of taxa. It is our long-term goal to determine what controls the diversity and copy number of LINE insertions in vertebrate genomes. We propose to address this question by performing a comprehensive investigation of LINE insertions frequency in natural populations of non-mammalian vertebrates, using as models a fish, the three spine stickleback (Gasterosteus aculeatus), and a lizard, the green anole (Anolis carolinensis). In both the stickleback and the anole, LINEs do not accumulate and their copy number seems tightly regulated, yet these two species differ dramatically in their profile of LINE abundance and diversity. We will first determine the frequency of LINE insertions across anole and stickleback populations (Aim 1). Because the fate of insertions can be affected by selection and drift, it is essential to accurately reconstruct the demographic history of the host (Aim 2). To determine the relative importance of selection and drift in controlling LINE copy number in non-mammalian vertebrates, we will compare the observed frequency spectrum of LINE insertions with the distribution of their expected values under a pure drift model simulated from their estimated demographic histories (Aim 3). PUBLIC HEALTH RELEVANCE: Analyses of complete vertebrate genome have been an extraordinary source of information, providing considerable advances in the field of biomedical research, genetics, developmental biology, and evolutionary biology. However, it is essential to understand processes underlying the evolution of these genomes to meaningfully interpret the informative patterns they provide. The aims included in this application will improve our understanding of the evolutionary forces that have shaped the architecture of vertebrate genomes.