Whole-Genome Shotgun Sequencing
Also see: EST Sequencing | BAC-by-BAC Sequencing
An alternative has been the whole-genome
shotgun sequencing approach, which is not biased against rare versus abundant expression of
genes. This approach has been attractive because the actual sequencing can
be accomplished in a short period of time. It can easily be scaled because
all clones can be sequenced in parallel. The major challenge, however, is
the assembly of these sequences into contiguous sequence information and to
anchor them to the genetic map. While this approach works well for genomes
with a low content of repeat sequences, it is more challenging for genomes
with a high content of repeat sequences. Key to these genomes has been the
use of sequence mates with distances of 2-3 kb, 8-10 kb, and 150 kb, also
serving as Sequence-Tagged-Connectors (STCs) in the latter case. In
addition, the 150 kb clones (BACs) have to be anchored to the genetic map to
provide a chromosomal framework of clones (see BAC-by-BAC). Still,
STCs contain many repeat sequences of transposable elements and multigene
families that generate erroneous results unless other supporting data can
be leveraged.
The following list provides links to
whole some plant and animal whole genome shotgun projects:
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