Biology Reference
In-Depth Information
time, TEs have provided novel regulatory regions to preexisting host genes and
TE-derived components have undergone a molecular transition into novel host
genes through a process called “molecular domestication” (
Miller et al. 1997
).
TEs may be more than just agents for local mutations; TEs might provide coor-
dinated changes in the genome by inserting into a series of genes whose prod-
ucts already function together (
Shapiro 1999
). Under this scenario, different
insertions could recruit new proteins into the system. During periods of exten-
sive genome reorganization, TEs could interact with cell signals to confer a far
higher probability of evolving useful new multilocus systems. Thus, the rela-
tionship of TEs to their host could resemble “more symbiosis than parasitiasis”
(
Brosius 1999
).
The association of TEs with their hosts over evolutionary time could lead to
three different outcomes: 1) the coevolution of TE-derived mechanisms to min-
imize the negative effects of TEs on their hosts (such as transposon self-regu-
lation, tissue specificity, targeting and genome partitioning); 2) the evolution
of host-defense mechanisms, which include host suppressors; and 3) the evolu-
tion of new and altered functions of TEs in hosts (regulatory functions, struc-
tural functions, enzymatic functions, and new coding sequences) (
Kidwell
and Lisch 2001
). Thus, TEs could enable genomes to enhance their own evolu-
tion and serve as a major source of tools for generating the necessary diver-
sity to respond to changes in the environment. Analysis of the
D. melanogaster
genome yielded an estimate of approximately one horizontal transfer event
per
TE family
every 20 million years (
Schaack et al. 2010
).
7.15 Transcriptomics
Transcriptome analysis is often done to discover genes and to annotate both
coding and noncoding regions of a sequenced genome. Sequencing of tran-
scriptomes of arthropods also is often done
before
sequencing the genomes of
nonmodel organisms because it provides important information as to “what is a
gene” (
Iyer and Chinnaiyan 2011
). For example,
Mita et al. (2003)
analyzed the
cDNAs from multiple life stages and tissues to discover as many genes as pos-
sible of the silk moth
Bombyx mori
, and
Nunes et al. (2004)
developed expressed
sequence tags (ESTs) from the honey bee
Apis mellifera
before the sequencing
of their genomes. Transcriptomic analyses also allow scientists to determine
what genes are being transcribed in what tissues and in which developmental
stage. A
transcriptome
is an analysis of the transcripts of genes, including large
and small RNAs. It can provide information on novel transcripts from unanno-
tated genes, and information on splicing variants.
