Metazoan Genomes

Fruit Fly

Rice

Puffer Fish

Drosophila melanogasterFruit 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 ShotgunIt 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 Annotation40 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 Genome60% 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 DuplicationIt 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. AnimalsAnimals 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 RiceA 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 GenomicsMore 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 production- enhancing QTLs.

Genomic insights may be combined with traditional breeding methods to increase cereal crop production.

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Puffer Fish GenomesWhy 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 sequenced- marine (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