Biology Reference
In-Depth Information
allow the design of improved vector control methods. Likewise, the
Ixodes scap-
ularis
genome project (Arthropoda: Chelicerata: Acari: Ixodidae) should provide
important data on another major vector of human disease (Lyme disease) (
Van
Zee et al. 2007
). Its genome is very large and full of repetitive elements, so a full
analysis has not yet been published.
Once
D. melanogaster
's genome was sequenced, 12 other species of
Drosophila
have had their genomes sequenced and this provided an opportunity
to compare functional elements in them (
Stark et al. 2007
).
7.13.2 What Do You Need to Do to Sequence Your Favorite Insect's Genome?
If you wish to sequence the genome of your favorite insect using NextGen
sequencing, several steps will be involved. Ideally, you will know the size of the
target species' genome. That is important to the sequencing project because it is
necessary to know how many reads will be needed to obtain the desired cover-
age of the genome. Also, if possible, it helps to have an inbred line from which
to extract DNA. Inbreeding will reduce variability in the genome, which will be
helpful in making the assembly of the short reads into scaffolds. Unfortunately,
by inbreeding you will lose some of the genetic variability in your species, but
resequencing will discover that. Next, you need an effective DNA extraction
protocol that will provide clean DNA that has a low level of fragmentation so
that the libraries can be prepared for NextGen sequencing. Once that is done,
a skilled University core facility or commercial facility will prepare the libraries,
conduct the sequencing reactions, and assemble the data using programs appro-
priate to the sequencing method.
Once the DNA has been assembled, the genome will need to be annotated,
and annotation typically is done using both automated and manual methods.
As described by
Yandell and Ence (2012)
, genome annotation is a complex and
lengthy process that can involve the use of multiple software packages and
analysis methods. The full discussion of genome annotation is beyond the scope
of this chapter, but
Yandell and Ence (2012)
provide “A beginner's guide to
eukaryotic genome annotation” that is helpful in explaining the terminology
and steps involved, as well as listing and referencing the many software sources
used for different purposes.
Chain et al. (2009)
discuss the different criteria by
which genomes can be compared for their quality (
Box 7.1
).
Analysis of the genomes of nonmodel organisms is best done if protein or
RefSeq or expressed sequence tag (EST) data are available to aid in the delim-
itation of exons, introns, and splice variants, and involves searching databases
containing related species' genomes to determine whether the sequences match
