Gene pairs share greater than 80% amino acid sequence identity. Consistent with

Gene pairs share greater than 80% amino acid sequence identity. Consistent with the foreign DNA hypothesis, we do not see such signs of suppression of gene family diversification in T. thermophila. Large INK-128 manufacturer numbers of paralogous genes are found in the genome . The fraction of genes in such families in T. thermophila is much order BKM 120 higher than that seen in N. crassa. Although this fraction is not as high as would be predicted from the observed correlation between total number of genes and the fraction found in paralogous families, the fraction of gene pairs sharing greater than 80% amino acid identity is much higher than in N. crassa and similar to that found in other sequenced eukaryotes. Since it is possible some of the 1,970 gene families could have originated by duplications that occurred prior to the origin of the IES excision process, it is more useful to examine recent duplications. We searched for such duplications in multiple ways, including the identification of genes duplicated in the T. thermophila lineage relative to other lineages for which genomes are available and by searching for pairs of paralogs with very similar sequences. Both of these classes are abundant in T. thermophila, further indicating that the IES excision does not significantly affect expansion of gene families of “native”genes. We searched for but did not find evidence for either whole genome or segmental duplications. We do find extensive numbers of tandemly duplicated genes. In total, 1,603 tandem clusters of between two and 15 genes were found, comprising 4,276 total genes; 67% of these clusters are simple gene pairs and 96% contain five or fewer genes. Thus it appears many of the paralogous genes in T. thermophila are the results of separate small duplication events. The high gene count in T. thermophila relative to some other single-celled eukaryotes is not simply a reflection of gene family expansions. For example, when recent gene expansions are collapsed into ortholog sets, we find that humans and T. thermophila share more orthologs with each other than are shared between humans and the yeast S. cerevisiae or T. thermophila and P. falciparum , despite the sister phyla relationships of animals and fungi on the one hand and ciliates and apicomplexans on the other. We note that this does not mean that humans and T. thermophila are overall more similar to each other than either is to species in sister phyla. For example, humans and S. cerevisiae do share some processes that evolved in the common ancestor of fungi and animals. In addition, for orthologs found in all eukaryotes, the human and S. cerevisiae genes are more similar in sequence to each other than either is to genes from T. thermophila. The higher number of orthologs shared between humans and T. thermophila is a reflection of both the loss of genes in other eukaryotic lineages and the retention of a variety of ancestral eukaryotic functions by T. thermophila. Consistent with this conclusion, there are 874 human genes with orthologs in T. thermophila but not PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19860992 S. cerevisiae, 58 of which correspond to loci associated with human diseases. Thus genome analysis reveals many cases where T. thermophila can continue to complement experimental studies of yeast as a model system for eukaryotic cell biology. Gene Duplication as an Indicator of Important Biological Processes One motivation for obtaining the genome sequence of an organism is to advance the study of processes already under investigation. Many researc.Gene pairs share greater than 80% amino acid sequence identity. Consistent with the foreign DNA hypothesis, we do not see such signs of suppression of gene family diversification in T. thermophila. Large numbers of paralogous genes are found in the genome . The fraction of genes in such families in T. thermophila is much higher than that seen in N. crassa. Although this fraction is not as high as would be predicted from the observed correlation between total number of genes and the fraction found in paralogous families, the fraction of gene pairs sharing greater than 80% amino acid identity is much higher than in N. crassa and similar to that found in other sequenced eukaryotes. Since it is possible some of the 1,970 gene families could have originated by duplications that occurred prior to the origin of the IES excision process, it is more useful to examine recent duplications. We searched for such duplications in multiple ways, including the identification of genes duplicated in the T. thermophila lineage relative to other lineages for which genomes are available and by searching for pairs of paralogs with very similar sequences. Both of these classes are abundant in T. thermophila, further indicating that the IES excision does not significantly affect expansion of gene families of “native”genes. We searched for but did not find evidence for either whole genome or segmental duplications. We do find extensive numbers of tandemly duplicated genes. In total, 1,603 tandem clusters of between two and 15 genes were found, comprising 4,276 total genes; 67% of these clusters are simple gene pairs and 96% contain five or fewer genes. Thus it appears many of the paralogous genes in T. thermophila are the results of separate small duplication events. The high gene count in T. thermophila relative to some other single-celled eukaryotes is not simply a reflection of gene family expansions. For example, when recent gene expansions are collapsed into ortholog sets, we find that humans and T. thermophila share more orthologs with each other than are shared between humans and the yeast S. cerevisiae or T. thermophila and P. falciparum , despite the sister phyla relationships of animals and fungi on the one hand and ciliates and apicomplexans on the other. We note that this does not mean that humans and T. thermophila are overall more similar to each other than either is to species in sister phyla. For example, humans and S. cerevisiae do share some processes that evolved in the common ancestor of fungi and animals. In addition, for orthologs found in all eukaryotes, the human and S. cerevisiae genes are more similar in sequence to each other than either is to genes from T. thermophila. The higher number of orthologs shared between humans and T. thermophila is a reflection of both the loss of genes in other eukaryotic lineages and the retention of a variety of ancestral eukaryotic functions by T. thermophila. Consistent with this conclusion, there are 874 human genes with orthologs in T. thermophila but not PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19860992 S. cerevisiae, 58 of which correspond to loci associated with human diseases. Thus genome analysis reveals many cases where T. thermophila can continue to complement experimental studies of yeast as a model system for eukaryotic cell biology. Gene Duplication as an Indicator of Important Biological Processes One motivation for obtaining the genome sequence of an organism is to advance the study of processes already under investigation. Many researc.