Recent studies of the human genome have revealed that genes with TATA-type promoters have more compact gene structures than the ones with TATA-less promoters with respect to exon number, intron length, and mRNA length.
However, when examining the equivalent intron in Dre-NILT1 predicted from zebrafish, it was shown to be only 362 bp long [ 24] indicating a more compact gene structure of NILT genes in cyprinids compared to salmonids.
In mammals, gene compactness, measured by average length of introns or length of UTRs, has a stronger influence on protein evolutionary rates than does gene expression level, as mammalian proteins encoded by a more compact gene evolve more rapidly (Liao et al. 2006).
Only the 71.7-kb cpDNA of the prasinophycean Ostreococcus tauri [ 40] and the 37.5-kb plastid DNA of the parasitic trebouxiophycean Helicosporidium sp. [ 41], two genomes highly reduced in gene content, have been reported to have a more compact gene organization than the Oedogonium genome.
Thus, the results of the present analysis favor the selection hypothesis as the principal explanation why highly expressed genes are more compact than genes expressed at a lower level (the C↑E trend).
However, Li et al [ 6] found that housekeeping genes are no more compact than genes that are narrowly expressed in somatic tissues with similar average expression levels.
Highly expressed human housekeeping genes are generally shorter and more compact than genes that are expressed at lower levels, which has been explained by selection pressure to reduce metabolic costs of transcription [24], [34].
However, the energy-cost hypothesis could not be reconciled with the fact that mammalian genes expressed in large organs are not more compact than genes expressed in small organs, given expression level controlled [ 31].
The A. gossypii genome is more compact and gene density is <1.9 kb/gene.
