Transcript Biomedical Research

Metazoan Genomes
Fruit Fly
Rice
Puffer Fish
Drosophila melanogaster
Fruit fly mutants have been studied for nearly
100 years. Fly labs have used phenotypes
and genetic crosses to characterize 2,500
genes.
The fruit fly has 2 large chromosomes that
account for 80% of the genome as well as 2
small chromosomes (including sex).
Although the fly genome is 180 Mb, 1/3 of
that is gene-poor repetitive heterochromatin
This amount of unclonable DNA made
sequencing slow.
Drosophila Chromosomes
WGS- Whole Genome Shotgun
It was this highly repetitive genome that
Craig Venter offered to use as a pilot for his
WGS method.
Started in May, 1999- the project was
finished in record time by March, 2000.
Over 3 million sequencing reactions of
about 500 bp each were performed.
A 12.8-fold coverage at 98% accuracy had
been produced.
The finished genome still had 1,299 gaps
totaling 2.1 Mb of euchromatin.
Testing the Annotation
40 experts took 2 weeks to annotate
13,601 genes from Drosophila.
They tested these annotations by
searching for the 2,783 genes that had
been discovered by Drosophila genetics.
99.8% had been identified correctly.
About 500 more mRNAs than Drosophila
has genes were found as ESTs, these
apparently arise from alternate splicing.
EST data bases were also useful for
resolving exon boundaries.
Drosophila X Chromosome
How are Flies Different?
Flies lack simple repeats at their telomeres
and also lack telomerase.
The density of transposons increases near
heterochromatin, which has 13 x lower
gene density than euchromatin.
20% of fly genes are found in us & worms.
Flies are odor restricted, they have only 57
olfactory receptors instead of the 1,000
found in mice and worms.
Flies have a greater proportion of
transcription factors than worms or yeast.
Is Fly a Good Model Organism?
Flies have many orthologs to human
disease-causing genes.
Even though flies lack kidneys, blood, or a
heart- they have orthologs to genes involved
in renal, blood & cardiovascular disease.
Flies provide insight into human disease at a
systems level (interaction of genes in vivo).
Orthologs of p53 and retinoblastoma were
found in fly, Parkinson’s and Alzheimer’s
disease genes were found as well.
23 gaps remain in version 4, compared
to the 1,300 in version 1.
History of Grass
Grass has only been around since the dinosaurs
became extinct, yet it now covers 20% of the earth.
Rice Genome
60% of the calories for a majority of people
in the developing world comes from cereal
grains, 1/3 of the world relies on rice.
The IRGSP started in 1998, but other major
players included Monsanto, Syngenta,
Myriad Genetics, and the newly established
Beijing Genomics Institute.
China published the first rice genome
sequence in 2001, followed by the IRGSP
release in 2002. Two different subspecies,
indica & japonica, were sequenced.
Comparison of Rice Genomes
subspecies:
indica
japonica
bp in draft:
361 Mb
390 Mb
bp in finished:
466 Mb
420 Mb
% finished:
92%
93%
coverage:
4.2 fold
6 fold
# of genes:
53,400-64,500 32,000-50,000
Gene Duplication
It appears that rice has undergone extensive
duplication over time.
About 58% of the genome is duplicated, with
about 20% of the duplicated genes sharing
synteny with their paralogs.
Since rice has twice the genes as
Arabidopsis, you would predict many
Arabidopsis homologs in rice but not vice
versa (85% of the former, compared to 50%
of the latter were found).
Comparison with Other Grains
Rice predates many of the other grains:
sorghum, maize, barley, and wheat.
It is expected rice genes will be syntenic
with many of these species.
About 2,000 QTL, quantitative trait loci,
that influence measurable phenotypes
have been mapped to the rice genome.
This narrows the search for candidate
genes and can help work in other grains.
Plants vs. Animals
Animals and fungi tend to reduce extra in
their genomes faster than plants.
Wheat, for instance, appears to have
duplicated its 7 chromosomes twice to 21.
Plants have many more isozymes (members
of a gene family with similar roles) than
animals or fungi, perhaps because they can’t
move if conditions change.
Animals, on the other hand, have more
transcription factors than plants. They have
different strategies for coping with change.
Rice Chromosome 10
Insertion of Genes into Rice
A number of genes in the rice genome had
their origin in mitochondria or chloroplasts.
One particular chloroplast insertion brought
with it nearly a complete genome.
These organellar genes are not expected
to produce proteins since their promoter
are more akin to that of prokaryotes.
Even if they did, they would lack targeting
signals required of nuclear genes.
Plant genomes are more dynamic and
unpredictable than we expected.
Future of Cereal Genomics
More than 1 billion people live on < 1$/day.
If the world population continues to grow at
its current rate, grain production must
increase 80% to meet the need for food.
The International Rice Research Institute
Genebank has over 100,000 varieties of
rice which could contain productionenhancing QTLs.
Genomic insights may be combined with
traditional breeding methods to increase
cereal crop production.
09_20_puffer.fish.jpg
Puffer Fish Genomes
Why puffer fish? Rice feeds millions of
people but puffer fish feeds only the daring
few that risk being poisoned if it is not
prepared right.
Puffer fish has one of the smallest genomes
of any vertebrate, not because of lack of
genes but because of high coding capacity.
Instead of looking for needles (genes) in a
haystack (large genome), puffer fish is a
box of needles.
Genome Facts
Two puffer fish have been sequencedmarine (Takifugu rubripes) in 2002 and
freshwater (Tetraodon nigroviridis) in 2004.
The Tetraodon genome is about 342 Mb.
WGS sequencing was used to get 8.3 fold
coverage. 27,918 genes were found.
Puffer fish has < 4,000 transposons,
compared to the millions found in humans
but they are more diverse and fit into 50
more groups than in humans.
Genome Duplication?
Paralogs occurred in pairs more than
expected, when the location of these were
mapped- it was found that many adjacent
genes had their paralogs on the same
chromosome.
Researchers have hypothesized that the
puffer fish genome is the consequence of a
whole genome duplication.
Puffer fish is also predicted to have
undergone more intrachromosomal
recombination than interchromosomal.
Three predictions resulted:
duplication occurred after fish diverged
from other vertebrates
comparison with a related non-duplicated
genome should give orthologs in a 2:1
ratio
human genes should have puffer fish
orthologs on interleafed chromosomes
All of these predictions were confirmed
by an examination of the genome
Puffer Fish Genes are Interleafed
Reconstructing a Common Ancestor
Working backwards from the Tetraodon
chromosome map, researchers were able
to recreate the karyotype for a common
ancestor of fish and mammals.
Using Occam’s razor to produce the most
parsimonious karyotype, 12 original
chromosomes are predicted.
These same 12 chromosomes can be
rearranged differently to produce our
karyotype, after their size is expanded by
the addition of many transposons.
Building the Tetraodon Genome
Building
the
Human
Genome