Biology Reference
In-Depth Information
of methods to resolve many biological questions. For example, once whole-
genome sequences are available, microarrays can be produced to analyze gene
expression in different tissues and life stages. Metabolic pathways can be iden-
tified, or the whole genome can be compared with other whole genomes of
other arthropods. Tiling microarray experiments can be done to assay transcrip-
tion at regular intervals of the genome, using regularly spaced probes; these
allow the discovery of genes with rare transcripts (
Johnson et al. 2005
). Finally,
as more is learned about the genome, updates of the annotation need to be
conducted so that accurate data are available for use by others.
7.14 Transposable Elements (TEs) as Agents of Genome Evolution
Our perception of the role of TEs in genome evolution has undergone a rapid
change as more complete genomes are compared (
Kidwell and Lisch 2001, Levin
and Moran 2011
). TEs now may be thought of as “natural genetic engineering
systems” that act to provide genetic variability and other functions (
Shapiro
1999
). Their designation as “selfish DNA” or “junk DNA” is “
…
either inaccurate
or misleading and
…
a more enlightened view of the transposable element-host
relationship encompasses a continuum from extreme parasitism to mutualism”
(
Kidwell and Lisch 2001
).
TEs do carry costs; they require host-cell functions to replicate and prolifer-
ate, and their activity poses a risk to the host because their integration into new
sites in the genome often results in deleterious mutations. In
D. melanogaster
,
retrotransposons are responsible for as much as 80% of all spontaneous muta-
tions (
Miller et al. 1997
). Despite these negative aspects, TEs are abundant and
ancient components of eukaryotic genomes and their long coexistence within
eukaryotic genomes suggests there has been some form of host-TE coevolution.
We know that TEs can acquire a functional role in the host genome; in
D. mela-
nogaster
retrotransposons are the telomeres (
Eickbush 1997
). TEs cause inver-
sions in
Drosophila
species (
Caceres et al. 1999
), which can tie up beneficial gene
combinations so that they are not scrambled during recombination.
The fact that TEs can be activated by environmental and population fac-
tors indicates that TEs have a positive role by creating new genetic variability
that could be useful under conditions that reduce the fitness of an organism
(
Capy et al. 2000
). One hypothesis proposes that the activation of host-defense
genes during stress and the activation of TEs are similar processes. Alternatively,
stresses could induce destabilization of the genome, leading to the malfunction
of genetic systems that would lead to the increased activity of TEs as a second-
ary, rather than a direct, effect of stress (
Capy et al. 2000
). Over evolutionary
