A nucleotide sequence level approach to detection of lateral gene transfer in eukaryotic genomes
Date of Award
Master of Science (MS)
Michael A. Muratet
Eukaryotic cells., Genomes., Genetic transformation., Gene expression., Bioinformatics., Nucleotide sequence.
Detection of lateral gene transfer (LGT) in eukaryotes has previously relied almost exclusively on phylogenetic analysis of amino acid sequences. This study developed a method for detection of eukaryotic LGT at the nucleotide sequence level. A pipeline was constructed consisting of Perl scripts that automate BLAST searches, phylogeny construction, and selection of phylogenetic trees indicating LGT. This pipeline was tested on the genomes of a bdelloid rotifer, Adineta vaga, and the pea aphid, Acyrthosiphon pisum, using known LGT events as positive controls, as well as on a soil fungus, Laccaria bicolor, and a the black cottonwood tree, Populus trichocarpa. Analysis of positive controls showed that LGT detection was possible in both A. pisum and A. vaga. Seventeen previously unknown probable LGTs from bacteria to A. vaga were detected, many of which were pseudogenes, and a known eukaryote to bacteria LGT event was seen in L. bicolor and P. trichocarpa.
Gray, David E., "A nucleotide sequence level approach to detection of lateral gene transfer in eukaryotic genomes" (2015). Theses. 112.