PowerPoint for BI 520-01 Spring 2013

1. Comparative Genomics
and the Evolution of
Genes

2. Evolution of Genes and Genomes on
the Drosophila phylogeny
Based on 12 way comparison

3. Phylogenetic Tree of Drosophila

5. http://blast.ncbi.nlm.nih.gov

6. SHOTGUN SEQUENCING

7. It is named by analogy with the rapidly-
expanding, quasi-random firing pattern
of a shotgun.
The technique was developed in the
1970s by double Nobel prize laureate
Frederick Sanger.

8. Craig Venter

10. W = dN/ds
dN (non synonymous)
dS (synonymous)
Examined the ratio of non-synonymous
W=d
to synonymous divergence to explain
distribution

11. • A major question in evolutionary biology is how important tinkering with
promoter sequences is to evolutionary change, for example, the changes
that have occurred in the human lineage after separating from chimps.
Are evolution in promoter or regulatory regions more important than
changes in coding sequences over such time frames?
A key reason for the importance of promoters is the potential to incorporate
endocrine and environmental signals into changes in gene expression[1]: A
great variety of changes in the extracellular or intracellular environment[2]
may have impact on gene expression, depending on the exact configuration of
a given promoter [2]: the combination and arrangement of specific DNA
sequences that constitute the promoter defines the exact groups of proteins
that can be bound to the promoter, at a given time [3].

13. • Demonstrated the ability to place every one of these
genomic comparisons on a phylogeny with a taxon
separation that is ideal for asking a wealth of questions
about evolutionary patterns and processes.
• The use of multi-species orthology “provides” especially
convincing evidence in support of particular gene
models, not only for protein-coding genes, but also for
miRNA and other ncRNA genes.

14. The methodology and principles are absolutely
general and they are applicable to any genome.
The genomes of these species provide an
excellent model for studying how conserved
functions are maintained in the face of
sequence divergence. These genome sequences
provide an unprecedented dataset to contrast
genome structure, genome content, and
evolutionary dynamics across the well-defined
phylogeny of the sequenced species

15. • Species D. willistoni doesn’t appear to have genes to make proteins
containing selenium – proteins that researches had thought were
common to all animals.
• analysis suggests that “some” gene families expand of contract at a
rate of 0.0012 gains and losses per gene per million years or roughly
one fixed gene gain/ loss across the genome every 60,000 yr.
• Number of structural changes and rearrangements is much larger, for
example, there are several different rearrangements of genes in the
Hox cluster found in these Drosophila species

16. Brosius J, Erfle M, et al. (1985). "Spacing of the -10 and -35 regions in the TAC promoter -
effect on its in vivo activity". Journal of Biological Chemistry 260 (6): 3539 –3541.
Celniker SE, Drewell RA (2007). "Chromatin looping mediates boundary element promoter
interactions". Bioessays 29 (1): 7–10
Vlahopoulos S, Zoumpourlis VC (2004). "JNK: a key modulator of intracellular signaling".
Biochemistry (Mosc) 69 (8): 844–54.
http://en.wikipedia.org/wiki/Promoter_%28biology%29
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