Scholarly Works, Biological Sciences

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https://hdl.handle.net/10919/23830
Research articles, presentations, and other scholarship

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Browsing Scholarly Works, Biological Sciences by Subject "0604 Genetics"

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    Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome
    Perry, Blair W.; Card, Daren C.; McGlothlin, Joel W.; Pasquesi, Giulia IM M.; Adams, Richard H.; Schield, Drew R.; Hales, Nicole R.; Corbin, Andrew B.; Demuth, Jeffery P.; Hoffmann, Federico G.; Vandewege, Michael W.; Schott, Ryan K.; Bhattacharyya, Nihar; Chang, Belinda SW W.; Casewell, Nicholas R.; Whiteley, Gareth; Reyes-Velasco, Jacobo; Mackessy, Stephen P.; Gamble, Tony; Storey, Kenneth B.; Biggar, Kyle K.; Passow, Courtney N.; Kuo, Chih-Horng; McGaugh, Suzanne E.; Bronikowski, Anne M.; de Koning, AP Jason P. J.; Edwards, Scott V.; Pfrender, Michael E.; Minx, Patrick; Brodie, Edmund D.; Brodie, Edmund D.; Warren, Wesley C.; Castoe, Todd A. (Oxford University Press, 2018-08-01)
    Colubridae represents themost phenotypically diverse and speciose family of snakes, yet nowell-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genomestructure that provide insight into the evolution of amniote genomes.Analyses of the garter snake andother squamate reptile genomes highlight shifts in repeat element abundance andexpansionwithin snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z andW sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionaryorigins ina rear-fanged colubridsnake, togetherwith newgenomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes.
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    Strong Purifying Selection Is Associated with Genome Streamlining in Epipelagic Marinimicrobia
    Martinez-Gutierrez, Carolina Alejandra; Aylward, Frank O. (Oxford University Press, 2019-10-01)
    Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G + C content, short intergenic regions, and low nitrogen content in encoded amino acid residue side chains (N-ARSC), but the evolutionary drivers of these characteristics are unclear. Here, we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of nonsynonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis reveals that epipelagic Marinimicrobia that exhibit features consistent with genome streamlining have significantly lower dN/dS values when compared with their mesopelagic counterparts. We also found a significant positive correlation between median dN/dS values and % G + C content, N-ARSC, and intergenic region length. We did not identify a significant correlation between dN/dS ratios and estimated genome size, suggesting the strength of selection is not a primary factor shaping genome size in this group. Our findings are generally consistent with genome streamlining theory, which postulates that many genomic features of abundant epipelagic bacteria are the result of adaptation to oligotrophic nutrient conditions. Our results are also in agreement with previous findings that genome streamlining is common in epipelagic waters, suggesting that microbes inhabiting this region of the ocean have been shaped by strong selection together with prevalent nutritional constraints characteristic of this environment.