The mechanism of protein evolution is one of the major questions in molecular
evolution. Much work has been done during early molecular evolution studies, in
genome age, we are able to test many hypothesis given by early molecular evolution
studies. Using six genomes from drosophila melanogaster group, we combine
comparative genomics and functional genomics tools to take a study about protein
evolution in drosophila.
We found gene expression’s tissue bias is one of the most important determinants in
drosophila protein evolution, although we found significant correlation between gene
expression level and protein evolution rate, this trend is weak, we can not take either
codon bias or functional importance as an indicator for the relationship between gene
expression and protein evolution, thus we guess translation robustness is the major
mechanism which given the correlation between gene expression and protein
evolution. Gene dispensability and gene functional density both significant correlate
with protein evolution, these two factors are somewhat inter-connected, but gene
functional density is more important than gene dispensability in drosophila protein
evolution. Protein length is negatively correlated with gene expression level, so highly
expressed genes’ protein length do not correlate protein evolution rate, but in
non-highly expressed genes, protein length do negatively correlated with protein
evolution rate, the mechanism for the correlation between protein length and protein
evolution rate remains to be discovered. Gene’s first intron length is highly correlated
with protein evolution rate, may be due to lots of regulatory elements locate in this
region. Complex genes tend to have more duplication, we consider subfunctionalization for complex genes as the major mechanism in gene duplication’s
retention. Recombination rates are negatively correlated with protein evolution rate,
due to much of the proteins in drosophila genome are under purify selection or nearly
neutral but undergo slightly deleterious mutations.
Our research confirm several theories in evolution genomics, and give an insight
into dorosphila protein evolution in whole genome scales.+
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