text: Ideally, the reference set in CAI is composed of highly expressed genes, so that CAI provides an indication of gene expression level under the assumption that there is translational selection to optimize gene sequences according to their expression levels. The rationale for this is dual: highly expressed genes need to compete for resources (i.e. ribosomes) in fast-growing organisms and it makes sense for them to be also more accurately translated. Both hypotheses lead to highly expressed genes using mostly codons for tRNA species that are abundant in the cell.