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The microarray results revealed changed expression in most functional gene categories for all three strains.
Non-synonymous variants were found in most functional gene classes including genes involved in general metabolism, cytoskeletal structure, and extracellular matrix formation (Additional file 8: Table S10).
Although most functional gene transfers from organelles to the nucleus occurred shortly after their endosymbiotic origin, gene transfer is an ongoing process [ 25].
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Given the high levels of sequence conservation between the two Musa species, such variation of gene structure and exon/intron boundaries is unlikely for most functional genes.
As a result of recombination loss, mammalian Y and avian W chromosomes are specific to one sex and usually have lost most functional genes, rendering their counterpart (X and Z chromosomes) hemizygous and asymmetrically transmitted between sexes.
This problem is unlikely to be severe, as simulations of the evolution of protein sequences with the same rates and among-site heterogeneity as those estimated from real mammalian protein-coding genes demonstrated that most functional genes could be detected by Blast in comparisons of even very distantly related genomes (e.g., fungi or plants vs. mammals) (Alba and Castresana 2007).
The codon models further developed by Nielsen and Yang allow variation in ω among sites [ 11], which have an extensive capability to find evidence for adaptive evolution in most functional genes where only a small fraction of amino acid sites are subject to strong positive selective pressure [ 12].
In the previous subsections we applied 'spot-centered' gene set enrichment analysis to extract the most relevant functional gene sets in each tissue sample.
A search for annotated enrichment of the differentially expressed genes for specific biological processes (GO Biological Processes, Expression Analysis Systematic Explorer score < 0.05) indicated that 'development' and 'cell cycle/M-phase' were the most overrepresented functional gene categories.
Although great care should be exercised in the recognition of remote homologues, most functional mammalian genes can be detected in eukaryotic genomes by Blast.
Gene loss affects proteins in most functional categories including gene regulation, translation, energy production, and the biosynthesis of amino acids, cofactors, and lipids (supplementary table S3, Supplementary Material online).
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