lpetrich

This question came up when I wondered about a recent comparison of the human, fruit-fly, and nematode genomes. So I decided to research it some more.

I've found <a href="http://ergo.integratedgenomics.com/GOLD/" target="_blank">GOLD</a>, the Genomes Online Database, and some similar sites like <a href="http://www.ncbi.nlm.nih.gov/Entrez/Genome/org.html" target="_blank">the NIH Completed Genomes list</a>, <a href="http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/bact.html" target="_blank">the NIH Microbial Genomes list</a> (some incomplete), <a href="http://www.infobiogen.fr/doc/data/complete_genome.html" target="_blank">the Infobiogen list of completed microbial genomes</a> (has some nice links), and <a href="http://www.tigr.org/tdb/mdb/mdbcomplete.html" target="_blank">TIGR's list</a>.

It's interesting to look at some statistics. The large majority of sequenced genomes are of microbes, mostly prokaryotes. GOLD lists 77 completed prokaryote sequences and 281 prokaryote sequencing efforts in progress. It must help that they have relatively small genomes. Many of them are various pathogenic ones, such as Yersinia pestis, which causes Bubonic Plague. Here are the eukaryotic genomes sequenced so far:


A few chomosomes of the parasites Plasmodium falciparum (causes malaria) and Leishmania major.

The cryptomonad alga Guillardia theta, more specifically, its "nucleomorph", a vestigial cell nucleus left over from that cell having been "eaten" in an endosymbiosis event, making it much like mitochondria and chloroplasts.

The small flowering plant Arabidopsis thaliana, a close relative of several familiar crop plants like cabbage and radish; it is a favorite model system because it's small and matures fast.

Rice, Oryza sativa. Of grasslike plants, it has a relatively small genome, at least if one calls 450 million bases small (some others, like wheat, have much bigger genomes).

The familiar yeast Saccharomyces cerevisiae and a less well-known ones, Schizosaccharomyces pombe.

The nematode Caenorhabditis elegans, a favorite model system.

The fruit fly Drosophila melanogaster, a long-time favorite model system.

Homo sapiens; about which it appears that 2/3 of the genetic material sequenced came from the head of one of the sequencing efforts, Dr. Craig Venter.


And here are those in the works; in some cases, the genome is only being mapped, with distinctive sequences being located in it.

Several protozoa, many of them parasites like Toxoplasma and Trypanosoma.

Some green algae, like Chlamydomonas

Several plants, mostly cultivated ones, including:

Brassica oleracea, which has such varieties as cauliflower, cabbage, kale, asparagus, broccoli, and Brussels sprouts. And some close relatives of it.

And coffee, cotton, wheat, (American) corn, barley, sorghum, sugar cane, soybean, another bean (Phaseolus vulgaris), alfalfa, tomato, potato, pine trees, eucalyptus trees and poplar trees.

Lots of fungi, including various yeasts and multicellular fungi like the mold Neurospora.

Some parasitic worms and nematodes.

Several insects, mostly mosquitoes, but also including the honeybee, the corn rootworm Diabrotica, and a tick, Amblyomma americanum. Why mostly mosquitoes and no spiders or crustaceans or cockroaches or centipedes or ... ?

The sea urchin Strongylocentrotus purpuratus, another model system.

Some sea squirts (Ciona).

One wonders why no snails or squid or clams or leeches or earthworms or other such free-living invertebrates.

The fish are all teleost fish; no lampreys or sharks or sturgeon.

The most interesting one is the Fugu pufferfish, Takifugu rubripes. This fish makes tetrodotoxin, a very dangerous poison, in its guts; eating fugu is a game of Russian Roulette that some Japanese gourmands are more than willing to play. But the main interest in this fish is because it has a relatively small genome, with a size of 400 million bases (the human size is 3 billion bases).

A close relative is also being sequenced, as is the Tilapia fish.

Getting closer, we find sequences of axolotl salamanders, Xenopus frogs, chicken, and turkey.

And among mammals, we find such well-known species as domestic bovines, sheep, pigs, dogs, laboratory mice and rats, and chimpanzees. Mice and rats are commonly used as mammalian model systems, because of their being small and fast-breeding; the chimp genome should be especially interesting because of the chimp's closeness to our species.

Peez

Cool post, I will just pick a couple of nits (if I may). There are a number of free-living invertebrate animals being studied, as you yourself list [The nematode Caenorhabditis elegans... The fruit fly Drosophila melanogaster... Several insects, mostly mosquitoes, but also including the honeybee... The sea urchin Strongylocentrotus purpuratus... Some sea squirts (Ciona)], and sturgeons are considered <a href="http://students.washington.edu/matthewr/zoo451/introduction.html" target="_blank">teleost fishes</a>, I believe. Of course, there are so many groups of organisms out there that it shouldn't be surprising that some groups have not been looked at yet (10 phyla of plants, 5 phyla of fungi, 13 phyla of animals [6 classes in Phylum Chordata], etc., depending on the authority). The other issue is that certain labs, with an interest in a particular group, tend to put out a lot of this type of data. Also, once we know something about one species it becomes interesting to compare that to closely-related species. These are the minorest of nits, and I do think that it is a great post.

Peez

lpetrich

Sorry for having misstated myself on what invertebrates were being sequenced; the real question is why such limited taxonomic variety. Why several mosquito species and not some more distant insect-pest species like cockroaches or fleas or termites or grasshoppers or certain moths or beetles or ...

But you do have an interesting point about comparing related species; one of the fish species being sequenced is a close relative of the fugu pufferfish -- and is being sequenced for that reason. And that is the reason for sequencing the chimpanzee genome.

But sturgeons are not classified as teleost fish; they have some differences, such as their tails -- the spinal cord extending into the tail's upper lobe, as with sharks, instead of stopping before the tail, as with teleosts (the large majority of present-day bony fish).

[ May 16, 2002: Message edited by: lpetrich ]</p>

Peez

I stand corrected. Somewhere in my brain I seem to have transposed "Osteichthyes" and Teleostei". Sorry for the brain fart.

Peez