Biology Reference
In-Depth Information
Transcriptome analysis also can be done to compare the activity of genes of
insects under different physiological conditions. For example,
Doroszuk et al.
(2012)
compared transcriptomes of a long-lived strain of
Drosophila
with flies
with a normal life span and discovered significant differences in stress-related
genes and in reproduction. Long-lived flies expressed reproduction genes at a
lower level and did not down-regulate them with age, and several candidate
markers of aging and life span extension were identified.
7.15.1 Tiling Microarrays
Tiling microarrays
can be used to analyze and measure gene expression levels
(
Mockler and Eckler 2005, Oliver 2006, Liu 2007
). These microarrays incorporate
sequences from the whole genome and can be used to analyze DNA methyla-
tion status, genome-wide-binding locations of transcriptions factors and other
DNA-binding proteins (this is called ChIP-chip, in which
ch
romatin
i
mmuno
p
re-
cipitation is detected on a chip). In addition, it is possible to localize nucleo-
somes, which determines which genes are able to function in the genome.
7.16 Metagenomics
Metagenomics involves sampling the genome sequences of a community of
microorganisms inhabiting a common environment (
Marco 2011
). It may be
defined as any type of analysis of DNA obtained directly from the environment
and typically involves analysis of microbial genomes (
Hugenholtz and Tyson
2008
). It is a culture-independent method of identifying microbes (or their
genes) in a specific environment. Because so few (probably
<
5%) microorgan-
isms can be cultured, it is the only way to investigate the activity of microor-
ganisms in many environments, including the guts of termites or other insects.
Obviously, analysis of the data is easier if the environment sampled is relatively
simple, but metagenomic studies have been applied to complex environments
such as the human microbiome, the enormous complex of microorganisms
associated with the human body. Sometimes whole microbial genomes can be
reconstructed from an environmental sample, especially if the environment
is relatively simple. Often only genes or physiological pathways can be identi-
fied. So far, analysis of insect microbial communities attempts to eliminate the
genome of the insect to reduce sequencing costs, but if sequencing costs are
reduced significantly further, it could be tractable to sequence and analyze both
insect and symbiont genomes. Metagenomics could answer some interesting
pest-management problems. For example,
Cox-Foster et al. (2007)
conducted a
metagenomic survey of microorganisms in bee colonies affected and unaffected
by colony collapse disorder. Metagenomics also can be conducted to determine
what genes are involved in digestion in termite guts.
