Evolutionary sequence analysis of complete eukaryote genomes

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.

Results: 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.

Conclusion: 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.

Figure 1

Flowchart of multigenome intersection approach (MIA). 1) Complete genomes are reciprocally compared against themselves and all other genomes with BLAST. 2) Pairwise ortholog clusters are identified using similarity scores and imported into a local database. 3) The intersection between genomes is determined by iteratively comparing sequence identification tags and retaining those clusters showing panorthology. 4) Additional genomes are added and checked as in the previous step. 5) Sequence data files are generated for evolutionary analysis.

Figure 2

Neighbor-joining tree of nine metazoan genomes, 285 panorthologs (97,581 amino acid positions, alpha = 1.28). All nodes are supported significantly (>95%) in bootstrap analyses of neighbor-joining and maximum likelihood. The arrow indicates an alternative root [6, 18].

Figure 3

Neighbor-joining trees of complete eukaryotic genome sequence analyses. (A) The intersection of fifteen eukaryotic genomes, 10 panorthologs (5094 amino acid positions, alpha = 1.01). (B) The intersection of genomes from twelve multicellular eukaryotes, 63 panorthologs (23,571 amino acid positions, alpha = 1.15). All nodes are supported significantly (>95%) in bootstrap analyses of neighbor-joining and maximum likelihood, with the exception of node indicated by an asterisk (94% with maximum likelihood) in (A).

Figure 4

Neighbor-joining trees of genomes used to address deuterostome-arthropod divergence time. (A) The intersection of seven eukaryotic genomes, 380 panorthologs (132,190 amino acid positions, alpha = 1.38). (B) The intersection of four eukaryotic genomes, 753 panorthologs (287,000 amino acid positions, alpha = 1.46). All nodes are supported significantly (>95%) in bootstrap analyses of neighbor-joining and maximum likelihood.