Description of the genome query for

Genetic mosaicism

For each ORF in the chosen genome, or for each ORF in the "Results from my last query,"
From the ORF's matches to the database that are better than the specified BLASTP cutoff e-value,
If the best match outside of the chosen genome's own lineage (at the selected taxonomic level) is to an ORF from an organism within the specified outside lineage, the ORF and its match are reported to the user.

Examples:

1. It might be interesting to look for yeast genes whose best prokaryotic match is to the alpha proteobacteria. These genes may have had a mitochondrial origin, whether or not they continue to serve the mitochondrion. In order to find out if this hypothesis merits further exploration, the "Genetic mosaicism" query can be run to get a good idea of what genes may have been established in the yeast genome thanks to the mitochondrial endosymbiont. Choosing 1.0e-5 as a low-stringency match criterion for the search, one selects Saccharomyces cerevisiae from the pop-up menu, one selects the top taxonomic category (matches outside the Eukaryota), and one types Bacteria; Proteobacteria; alpha subdivision in the text input box. Performing this query on May 16, 2002, one retrieves 273 of yeast's 6334 loci. Many of these are obvious (e.g., cytochrome c) but there are a few surprises too.
2. Sticking with yeast, as in example 1 above, what about the hypothesis that the fungal ancestor possessed a chloroplast? Many eukaryotic lineages have these cyanobacterial endosymbionts. Did the line leading to fungi and animals lose its chloroplast, or might it never have possessed one? This "Genetic mosaicism" query can help us begin to answer this question, by assuming that if a chloroplast were ancestrally present, some of its genes would have become incorporated in the yeast nuclear genome. In order to run the test, to find out if this hypothesis might merit further consideration, one selects a low-stringency cutoff as before (1.0e-5), Saccharomyces cerevisiae, looking for matches outside taxonomy level 1 (matches outside the Eukaryota). In the text input box, one enters Bacteria; Cyanobacteria. GenBank is still far from saturated for cyanobacterial sequences, but the May 16, 2002 result of running this query yielded 253 ORFs, nearly as many as matched best with alpha proteobacteria.
3. Does yeast have any appreciable spirochaete content? The answer is 47. Chlamydial content? 23. High-G+C Firmicutes? 61. What about non-alpha proteobacteria? 392. Low-G+C Gram-positives? 603. Thermus/Deinococcus group? 30. Fusobacteria? 31. Archaea? 618. Clearly, the picture becomes more confusing as we explore further. What about some negative controls, using lineages that should never (?) have interacted (via lateral genetic transfer or treelike descent) with the fungi or their ancestors? Aquificales: 72; Thermotogales: 36.

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