The animal in the genome: comparative genomics and evolution

Abstract

Comparisons between completely sequenced metazoan genomes have generally emphasized how similar their encoded protein content is, even when the comparison is between phyla. Given the manifest differences between phyla and, in particular, intuitive notions that some animals are more complex than others, this creates something of a paradox. Simplistic explanations have included arguments such as increased numbers of genes; greater numbers of protein products produced through alternative splicing; increased numbers of regulatory non-coding RNAs and increased complexity of the cis-regulatory code. An obvious value of complete genome sequences lies in their ability to provide us with inventories of such components. I examine progress being made in linking genome content to the pattern of animal evolution, and argue that the gap between genomic and phenotypic complexity can only be understood through the totality of interacting components.

Figure 1

The DNA-binding domain of brinker is conserved within insects, but has no significantly similar sequences in other taxa. (a) The alignment shows the conserved core from selection of insect species. Drosophila species sequences were taken from the UCSC web browser (http://genome.ucsc.edu), Anopheles and Aedes from ENSEMBL (http://www.ensembl.org), other predictions were made from sequences at the NCBI. GI Accessions: N.vit 146253130, T.cas 73486274, C.pip 145464888, P.hum 145365328, A.mel 63051942, B.mor 91842977 and A.pis 47522326. (b) The three-dimensional structure of the aligned region when binding DNA. The structure was taken from the PDB file 2glo.

Figure 2

Adjacent TFBSs cause extended regions of DNA sequence conservation. Structure of CEBPβ homodimer and Runx-1 (Tahirov et al. 2001). Three transcription factors (2xCEBPB and RUNX1) bind in a region of 25 nucleotides conserved throughout placental mammals. The DNA-binding domains represented as three-dimensional structures are boxed and colour coded in the schematic of the proteins. In each case, the majority of the protein is not represented in the structure; these regions could interact with other transcription factors, activators and repressors. The human sequence coordinates are chromosome 5, bases 149 446 373–149 446 396 of the NCBI build 36. The alignment is taken from the UCSC web browser http://genome.ucsc.edu.