Freethought & Rationalism Archive

lpetrich · 05-28-2003, 11:26 PM

According to the latest article from NHGRI, work on the chimpanzee and honeybee genomes is coming along at an impressive pace.

The chimp genome will be sequenced to 4X coverage in June and assembled into a rough draft with the help of the human genome. Someone involved in this sequencing work has reported in Slashdot that human and chimp genomes are impressively similar -- 97% to 99% depending on the region.

Joining the already-draft-sequenced mouse and rat will be the rhesus monkey and the dog, whose sequencing will start this summer, but the cow genome is being held up by $15 million in unpledged money (the cow and dog genome efforts are estimated to cost $50 million each; mammalian genomes are typically 3 billion base pairs).

The dog breed to be sequenced is the boxer, which is rather inbred, meaning that it has relatively low genetic variety. But after that, about 10 to 20 breeds will have some sequencing done -- it will be interesting to look for the genes responsible for dogs' great variability.

Looking a bit further afield, the chicken genome is being worked on, and a rough draft should be done by early next year.

No news on fish genomes, though the pufferfish genome has been useful in identifying many human genes. About 75% of genes match, and the number is about 99% for mice and our species.

Going a bit further, the amphioxus, which is an almost-vertebrate, is on the proposal list, and the sea squirt Ciona intestinalis has now been sequenced. It has a lifecycle much like the career of a tenured professor: it has a tadpole-ish larva that searches for a place to settle down, and when it does, it resorbs its brain. And that tadpole has a notochord, just like an amphioxus or a juvenile vertebrate (sometimes very juvenile, as in embryonic).

In an intermediate stage, that of being sequenced, are some sea urchin species; echinoderms and hemichordates are the closest invertebrates to the chordates. Some sea urchins have long been used as model systems, because their eggs are easily accessible and easy to watch.

Turning to honeybees, a rough draft of their sequence will be available by mid-July. It will be interesting to see how a female bee is made to grow up as either a worker or a queen; what genes get switched on and off?

Other sequenced insects are the malaria mosquito Anopheles gambiae and the fruit fly Drosophila melanogaster. A closely-related one, Drosophila pseudoobscura is now being sequenced, and there are proposals for sequencing some additional species, D. yakuba and D. simulans. This should provide some clues as to speciation -- what makes closely-related species distinct? Is it some sperm/egg recognition mechanisms? Mating behavior? Pheromones and their production and detection?

The remaining animal genome sequenced is that of the nematode / roundworm Caenorhabditis elegans; the sequence of a closely-related one, C. briggsae is coming along, and there's a proposal to sequence a third one. These are tiny worms about a millimeter long, and they are studied in hopes of providing clues on development mechanisms.

Looking further, the closest relatives to the animal kingdom to be sequenced are the fungi. And of these, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have now been joined by the bread mold Neurospora crassa and the rice blast Magnaporthe grisea, and they will soon be joined by several other fungi.

Only a few plant genomes have been sequenced -- the small mustard weed Arabidopsis thaliana and rice. But they may soon be joined by the genome of the poplar tree. Also at the Joint Genome Institude is work on the one-celled green alga Chlamydomonas reinhardtii and the diatom Thalassiosira pseudonana.

Not many other eukaryotic organisms are being sequenced, though the malaria parasite Plasmodium falciparum and some other Plasmodium species have been sequenced, and work is underway on the slime mold Dictyostelium discoideum.

But there are over a hundred genome sequences of prokaryotic organisms now available, and these have enough coverage of their diversity to make possible the reconstruction of some features of the common ancestor of all existing life on Earth.

Wounded King · 05-29-2003, 01:20 AM

Dont forget the frogs!

lpetrich · 05-29-2003, 07:45 AM

Yes, a frog is on its way, with a 6X-8X draft sequence to be done in 2005.

05-28-2003, 11:26 PM	#1
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	Genomes on the Way -- Chimps, Bees, etc. According to the latest article from NHGRI, work on the chimpanzee and honeybee genomes is coming along at an impressive pace. The chimp genome will be sequenced to 4X coverage in June and assembled into a rough draft with the help of the human genome. Someone involved in this sequencing work has reported in Slashdot that human and chimp genomes are impressively similar -- 97% to 99% depending on the region. Joining the already-draft-sequenced mouse and rat will be the rhesus monkey and the dog, whose sequencing will start this summer, but the cow genome is being held up by $15 million in unpledged money (the cow and dog genome efforts are estimated to cost $50 million each; mammalian genomes are typically 3 billion base pairs). The dog breed to be sequenced is the boxer, which is rather inbred, meaning that it has relatively low genetic variety. But after that, about 10 to 20 breeds will have some sequencing done -- it will be interesting to look for the genes responsible for dogs' great variability. Looking a bit further afield, the chicken genome is being worked on, and a rough draft should be done by early next year. No news on fish genomes, though the pufferfish genome has been useful in identifying many human genes. About 75% of genes match, and the number is about 99% for mice and our species. Going a bit further, the amphioxus, which is an almost-vertebrate, is on the proposal list, and the sea squirt Ciona intestinalis has now been sequenced. It has a lifecycle much like the career of a tenured professor: it has a tadpole-ish larva that searches for a place to settle down, and when it does, it resorbs its brain. And that tadpole has a notochord, just like an amphioxus or a juvenile vertebrate (sometimes very juvenile, as in embryonic). In an intermediate stage, that of being sequenced, are some sea urchin species; echinoderms and hemichordates are the closest invertebrates to the chordates. Some sea urchins have long been used as model systems, because their eggs are easily accessible and easy to watch. Turning to honeybees, a rough draft of their sequence will be available by mid-July. It will be interesting to see how a female bee is made to grow up as either a worker or a queen; what genes get switched on and off? Other sequenced insects are the malaria mosquito Anopheles gambiae and the fruit fly Drosophila melanogaster. A closely-related one, Drosophila pseudoobscura is now being sequenced, and there are proposals for sequencing some additional species, D. yakuba and D. simulans. This should provide some clues as to speciation -- what makes closely-related species distinct? Is it some sperm/egg recognition mechanisms? Mating behavior? Pheromones and their production and detection? The remaining animal genome sequenced is that of the nematode / roundworm Caenorhabditis elegans; the sequence of a closely-related one, C. briggsae is coming along, and there's a proposal to sequence a third one. These are tiny worms about a millimeter long, and they are studied in hopes of providing clues on development mechanisms. Looking further, the closest relatives to the animal kingdom to be sequenced are the fungi. And of these, the yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe have now been joined by the bread mold Neurospora crassa and the rice blast Magnaporthe grisea, and they will soon be joined by several other fungi. Only a few plant genomes have been sequenced -- the small mustard weed Arabidopsis thaliana and rice. But they may soon be joined by the genome of the poplar tree. Also at the Joint Genome Institude is work on the one-celled green alga Chlamydomonas reinhardtii and the diatom Thalassiosira pseudonana. Not many other eukaryotic organisms are being sequenced, though the malaria parasite Plasmodium falciparum and some other Plasmodium species have been sequenced, and work is underway on the slime mold Dictyostelium discoideum. But there are over a hundred genome sequences of prokaryotic organisms now available, and these have enough coverage of their diversity to make possible the reconstruction of some features of the common ancestor of all existing life on Earth.

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05-29-2003, 01:20 AM	#2
Wounded King Veteran Member Join Date: Mar 2003 Location: Edinburgh Posts: 1,211	Dont forget the frogs!

05-29-2003, 07:45 AM	#3
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	Yes, a frog is on its way, with a 6X-8X draft sequence to be done in 2005.

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