Transcript Tigger/pogo transposons in the Fugu genome

IB 404
Comparative Genomics of Eukaryotes
1. Introduce myself
2. Survey class
3. Course objectives
4. Outline syllabus
5. Themes for the semester - gene duplication and
genome size
6. Preview quiz
One theme we will see repeatedly is the role of gene duplication. For a
long time we’ve realized that this is the primary raw material for
evolution, but it occurs in a remarkable variety of ways:
A. Tandem duplications of single genes.
B. Duplications to other locations in a genome.
C. Duplications of large blocks of genes, also known as segmental
duplications.
D. Whole genome duplications or polyploidization.
In each case the newly duplicated genes can have any of several fates.
The most obvious and simple is for one copy to become a
pseudogene through acquiring critical amino acid changes (missense
mutations), or stop codons (nonsense mutations), or frameshifting
insertions/deletions (indels), or intron boundary changes, or promoter
mutations, or major indels. Eventually such pseudogenes will be lost
from most genomes by large deletions removing part or all of them.
Alternatively one copy might evolve a new function, or each copy might
diverge to slightly different functions, then they will be retained.
Another theme will be genome size, which involves a variety of effects.
But we can think of two levels of analysis.
First, there is the mechanistic question of why genomes get bigger or
smaller. For example, they generally get bigger by accumulating many
copies of pseudogenes or transposable elements (jumping genes) or other
kinds of junk DNA. Some seem to get smaller by deleting this junk DNA
through large deletions. The balance of these two processes leads to
remarkably different genome sizes and architectures.
Second, there is the ultimate question of why all of this happens
differently in different organisms, resulting in genomes that range across
about 5 orders of magnitude (several million bp to 100 billion bp). We
don’t have a firm answer, but the best one to date depends on the details
of genetic drift in small versus large populations. The bottom line seems
to be that large organisms with small populations suffer lots of genetic
drift, which reduces the effectiveness of the slightly deleterious selection
effects of additional transposons or longer introns, hence larger genomes.