Today• Elements of complex genomes

– Protein domains and exon shuffling– Origin of novel genes– Alternative splicing– Transposable elements and genome size

Protein domains bind antigens in human immunoglobulin

Evolution and conservation of domains in diverse proteins

New domains and human cognition

Number of paralogs in complete genomes of five species of yeast

Paralog number and organismal complexity

Origin of a new Drosophila gene, jingwei

Antarctic Notothenoids - a radiation of ‘ice fish’

The evolution of AFGP genes of Antarctic notothenioid fishes

Mechanisms of creating new genes

Co-option of an ancient transposable element

Abundance of an novel transposable element in coelacanth

Identifying cases of alternative splicing

Genomic sequence (introns and exons)

Shading indicates matches of genomic sequence and ESTs(white - 1 or 2 database matches; dark - multiple database matches)

Tall boxes - humanShort boxes - mouse

Drosophila Dscam gene

Alterantive splicing in the Drosophila fruitless gene

Splice variants control sexual behavior

• fruF prevents male-specific splicing

• fruM and fru∆tra force male splicing

• FruC, control allele

Mark B. Gerstein et al. Genome Res. 2007; 17: 669-681

The ENCODE project and new view of the gene

Genome size variation

Fractions of genomic DNA

Age distribution of human retroelements

Classic genomic differences between birds and mammals

• Small genomes• Little repetitive DNA• Small introns (?)• Michrochomosomes• High gene density

• Large genomes• Abundant repeats• Large introns• Macrochromosomes• Low gene density