Biology Reference
In-Depth Information
Liu et al. (2012) found that the microRNA miR-34 is important in aging and
neurodegeneration in
Drosophila
. This microRNA is highly conserved, with
orthologs in
C. elegans
, mouse, and humans. miR-34 shortened life span and
resulted in late-onset brain deterioration. The ortholog in humans is highly
expressed in the brains of adults; expression can increase in age and can be mis-
regulated in humans with degenerative disease.
There is now a
D. melanogaster
genetic reference panel, based on the
sequencing of 168 highly inbred lines derived from a wild population using
next-generation (Illumina and 454) sequencing methods (
Mackay et al. 2012
).
The sequences obtained were compared with the
D. melanogaster
reference
genome to compare molecular-genetic variation and variation in quantitative
traits. The new genome data can be used to map quantitative trait loci (QTLs)
and to conduct systems-genetics analyses of the relationship between molecular
variation and genetic variation for complex traits.
7.11 Next-Generation Sequencing Methods and Beyond
The development of newer sequencing technology has revolutionized all of
genetics (
Janitz 2008; Mardis 2008a,b; Shendure and Ji 2008; Metzker 2010;
Pareek et al. 2011
). The second generation of sequencing platforms produces
millions of DNA sequence reads in a single run and provides inexpensive,
genome-wide sequence data for many uses, including mutation mapping, poly-
morphism discovery, and discovery of noncoding RNAs. These new methods
allow high-throughput functional genomics research, including gene-expres-
sion profiling, genome annotation, small-noncoding RNA discovery, and profil-
ing and detection of aberrant transcriptions that previously were available only
through analysis by microarrays (
Morozova and Marra 2008
). Other applications
include study of DNA methylation, posttranslational modification of histones,
and nucleosome position on a genome-wide scale. Sanger sequencing remains
useful for certain projects, especially those in the kilobase-to-megabase range,
but genome sequencing by next-generation methods (NextGen) has revolution-
ized genome analysis of arthropods (
Bentley 2006
).
7.11.1 Next-Generation (NextGen or Second-Generation) Sequencing
The general process of sequencing DNA using NextGen methods includes sev-
eral steps. First DNA is extracted and fragmented. The fragments are then
ligated to adaptors. The ligated fragments are then processed in specific pro-
tocols, depending on the specific platform used, to develop an array of millions
of immobilized PCR colonies (also known as
polonies
). Each polony consists of
