Evolutionary sequence analysis of complete eukaryote genomes |
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Authors: | Jaime?E?Blair Prachi?Shah Email author" target="_blank">S?Blair?HedgesEmail author |
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Institution: | (1) NASA Astrobiology Institute and Department of Biology, The Pennsylvania State University, 208 Mueller Laboratory, University Park, Pennsylvania 16802-5301, USA |
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Abstract: | Background Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence
times of species. Although current methods that identify clusters of orthologous genes in complete genomes have helped to
investigate gene function and gene content, they have not been optimized for evolutionary sequence analyses requiring strict
orthology and complete gene matrices. Here we adopt a relatively simple and fast genome comparison approach designed to assemble
orthologs for evolutionary analysis. Our approach identifies single-copy genes representing only species divergences (panorthologs)
in order to minimize potential errors caused by gene duplication. We apply this approach to complete sets of proteins from
published eukaryote genomes specifically for phylogeny and time estimation. |
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