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Full-Text Articles in Life Sciences
Simple Sequence Repeat Variation In The Daphnia Pulex Genome, Way Sung, Abraham Tucker, R. Daniel Bergeron, Michael Lynch, W. Kelley Thomas
Simple Sequence Repeat Variation In The Daphnia Pulex Genome, Way Sung, Abraham Tucker, R. Daniel Bergeron, Michael Lynch, W. Kelley Thomas
Molecular, Cellular & Biomedical Sciences
Background: Simple sequence repeats (SSRs) are highly variable features of all genomes. Their rapid evolution makes them useful for tracing the evolutionary history of populations and investigating patterns of selection and mutation across gnomes. The recently sequenced Daphnia pulex genome provides us with a valuable data set to study the mode and tempo of SSR evolution, without the inherent biases that accompany marker selection. Results: Here we catalogue SSR loci in the Daphnia pulex genome with repeated motif sizes of 1-100 nucleotides with a minimum of 3 perfect repeats. We then used whole genome shotgun reads to determine the average …
Evolutionary Rates And Gene Dispensability Associate With Replication Timing In The Archaeon Sulfolobus Islandicus, Kenneth M. Flynn, Samuel H. Vohr, Philip J. Hatcher, Vaughn S. Cooper
Evolutionary Rates And Gene Dispensability Associate With Replication Timing In The Archaeon Sulfolobus Islandicus, Kenneth M. Flynn, Samuel H. Vohr, Philip J. Hatcher, Vaughn S. Cooper
Molecular, Cellular & Biomedical Sciences
In bacterial chromosomes, the position of a gene relative to the single origin of replication generally reflects its replication timing, how often it is expressed, and consequently, its rate of evolution. However, because some archaeal genomes contain multiple origins of replication, bias in gene dosage caused by delayed replication should be minimized and hence the substitution rate of genes should associate less with chromosome position. To test this hypothesis, six archaeal genomes from the genus Sulfolobus containing three origins of replication were selected, conserved orthologs were identified, and the evolutionary rates (dN and dS) of these orthologs were quantified. Ortholog …
Why Genes Evolve Faster On Secondary Chromosomes In Bacteria, Vaughn S. Cooper, Samuel H. Vohr, Sarah C. Wrocklage, Philip J. Hatcher
Why Genes Evolve Faster On Secondary Chromosomes In Bacteria, Vaughn S. Cooper, Samuel H. Vohr, Sarah C. Wrocklage, Philip J. Hatcher
Molecular, Cellular & Biomedical Sciences
In bacterial genomes composed of more than one chromosome, one replicon is typically larger, harbors more essential genes than the others, and is considered primary. The greater variability of secondary chromosomes among related taxa has led to the theory that they serve as an accessory genome for specific niches or conditions. By this rationale, purifying selection should be weaker on genes on secondary chromosomes because of their reduced necessity or usage. To test this hypothesis we selected bacterial genomes composed of multiple chromosomes from two genera, Burkholderia and Vibrio, and quantified the evolutionary rates (dN and dS) of all orthologs …