Evolutionary sequence analysis of complete eukaryote genomes

Despite the conservative criterion used, 753 panorthologs (proteins) were identified for evolutionary analysis with four genomes, resulting in a single alignment of 287,000 amino acids. With this data set, we estimate that the divergence between deuterostomes and arthropods took place in the Precambrian, approximately 400 million years before the first appearance of animals in the fossil record. Additional analyses were performed with seven, 12, and 15 eukaryote genomes resulting in similar divergence time estimates and phylogenies.Our results with available eukaryote genomes agree with previous results using conventional methods of sequence data assembly from genomes. They show that large sequence data sets can be generated relatively quickly and efficiently for evolutionary analyses of complete genomes.The use of complete genomes for phylogenetic analysis has greatly improved our understanding of prokaryote evolution [1-3]. However, until recently, relatively few complete genome sequences were available for such analyses in eukaryotes. As this improves, there will be a greater demand on methodology for evolutionary analysis of complete genomes. Previous whole-genome studies of eukaryotes have focused on gene and gene family presence-absence [4-7], lineage-specific gene loss [8,9], insertion-deletion markers and introns [6,10,11], and other non-sequence based information. While these approaches have their advantages, previous studies have not used complete genome sequences (nucleotides and/or amino acids) for reconstructing evolutionary relationships. At the same time, the complexity of eukaryote genomes, with numerous gene duplications and losses in different lineages, has created a challenge for sequence-based phylogeny estimation. Here, we outline a conservative approach designed to utilize the wealth of evolutionary information present in complete genome sequences by identifying orthologs in multiple eukaryotes for the purpose of evolutionary analysis.Methods f