Papers by Peterson Cullimore
The files in this collection consist of the improved genomic sequences, gene annotations, and evi... more The files in this collection consist of the improved genomic sequences, gene annotations, and evidence tracks that were used in the analyses described in the manuscript "Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution" (doi: 10.1534/g3.114.015966). The improved genomic sequences and gene annotations were produced by students participating in the Genomics Education Partnership (GEP; http://gep.wustl.edu) during 2007–2012. This study seeks to understand the evolution of the Muller F element through the comparative analysis of Drosophila melanogaster, Drosophila erecta, Drosophila mojavensis, and Drosophila grimshawi. As part of this analysis, we have improved the genomic scaffolds from the D. mojavensis and D. grimshawi assemblies, and produced manual gene annotations for D. erecta, D. mojavensis, and D. grimshawi. The digital assets include the improved sequences and annotations in GenBank ASN.1 format, and the files required to create the UCSC Genome Browser instances for D. melanogaster, D. erecta, D. mojavensis, and D. grimshawi. The Genome Browser instances include the improved genomic sequences, gene annotations, and the results of the bioinformatics analyses described in the manuscript.
G3 (Bethesda, Md.), Jan 4, 2015
The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila mela... more The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have higher transposon density (25%-50%) than euchromatic reference regions (3%-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% versus 11%-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density ...
Plethodontidae is the largest family of salamanders, exhibiting great diversity of natural histor... more Plethodontidae is the largest family of salamanders, exhibiting great diversity of natural history, and reaching maximum species richness in the eastern United States throughout the southern Appalachian Mountains region. There is much confusion and debate regarding the status of species placed within genus Desmognathus, a common issue among plethodontid genera. Their widespread distribution and altitudinal separation have resulted in several populations that exhibit increased genetic variation. In 2004, researchers discovered an isolated population of Desmognathus fuscus at Murphy Lake State Game Area in Southeastern Michigan. As the nearest population is reported in north central Ohio, appriximately 500 km away, the origin of this population is in question. I amplified a 600-bp fragment of the cytochrome c oxidase subunit I (CO1) gene from individuals collected from the Michigan population and compared it with CO1 gene sequences from individuals collected across the species' distribution and from published data. A 387-bp sequence of cytochrome b was also sequenced to compare among collected samples. Sequence data will help us to determine if the Michigan population's origin was due to a recent human introduction, if it was the result of a dispersal event, or if it is a relic population left over from Pleistocent glaciations when the range of D. fuscus was affected by glacial advances. Generated CO1 gene phylogenies were compared to published phylogenies of the genus, and discussed in the context of the generic diversity of natural history.Master of ScienceBiologyUniversity of Michiganhttp://deepblue.lib.umich.edu/bitstream/2027.42/112027/1/Cullimore_MolecularPhylogenticsIsolatedPop.pdfDescription of Cullimore_MolecularPhylogenticsIsolatedPop.pdf : Restricted to UM users only
Uploads
Papers by Peterson Cullimore