(Correction to last part of the article on COD GENOME ASSEMBLY:) We are currently trying to make use of all
the data we have in the best possible
way,” he says.
Layering these reads together, and
using the highly accurate consensus,
the team generated very long reads,
error-corrected them using the short
read data, and ran them through
Celera® Assembler. “We’ve never seen
a faster assembly,” Nederbragt says;
it came together in just 36 hours.
As Nederbragt and his colleagues
sifted through the new assembly,
they realized that the assembler
was splitting haplotypes rather than
merging them, so the heterozygous
regions were being run as linear
sections of the genome, rather than
alternates of the same section. “The
sequencing problem is now gone; it
looks like we have the whole genome
present in PacBio reads,” Nederbragt
says. “Now it has become a
bioinformatics challenge.” He and his
team are currently working to quantify
the regions they believe should be
split into haplotypes and to figure out
the differences between them.
As they determine the best
bioinformatic solution to the
assembly, they are starting to
investigate the new genome data to
see where it varies from the original
stickleback-oriented assembly.
They’ve already seen an exon in the
original annotation that potentially
does not exist in the all-cod assembly,
Nederbragt says, noting that a full
comparison of the two genome
assemblies will take place in the
future. For now, they are focused on
getting this new assembly into its
23 pseudochromosomes, which can
then be shipped off for annotation.
“The goal is to get the annotators an
assembly good enough that they don’t
need to retrofit it with information
from other organisms,” he says.
Implications for Future
Initiatives
The interest in generating an
improved cod genome assembly took
a critical turn when the Norwegian
Research Council funded a large
grant to resequence 1,000 cod. The
four-year Aqua Genome Project,
as it is known, will produce truly
meaningful and useful results if this
resequencing can be done with a
high-quality draft of the actual fish
being studied, rather than relying on
the old cod assembly with information
from other fish genes woven into it.
“The goal is to do deep cataloging of
genomic variation,” a process that will
also include studies of transcriptome,
methylation, and structural variation
data on the PacBio platform,
Nederbragt says. “Having a really
good reference genome will make a
big difference.”
The Aqua Genome Project seeks to
characterize the variation between
wild-caught and farmed fish in an
effort to increase the success of
aquaculture. This is no trivial matter:
“Sustainable aquaculture could
contribute to solving the world’s food
problems,” Nederbragt says.
As he and his colleagues get started
on that new project, they’ll be relying
on their PacBio sequencer. “If you
want to have long-range information
that you can trust, PacBio reads are
very useful,” Nederbragt says.
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