lpetrich

The <a href="http://gnn.tigr.org/main.shtml" target="_blank">Genome News Network</a> has lots of interesting genetic and genome-related news.

One recent article is about depriving some (Drosophila) fruit flies of sleep in order to study why sleeplessness is so troublesome -- flies also have to sleep, and two of their sleep-control genes are known to have human counterparts. Which suggests that the late-Precambrian common ancestor had also had to sleep! Imagine a tiny worm snoozing in the mud of some Vendian sea.

The experimenters are also doing similar experiments on rats, which are much closer to our species, but which are much bulkier than flies.

Also, a public Mouse Genome Sequencing Consortium has caught up with Celera and announced a rough draft of the mouse genome -- a year after Celera has done so. However, one has to pay a subscription fee to get access to Celera's data. This must be Celera's business model -- charge for superfast sequencing. However, the proper practice of science involves making as much data public as possible. But if Celera achieves some reasonable approximation of that within its business model, I don't object very much, except with their human-genome data.

Another report described the recent comparison of mouse chromosome 16 to the human genome. Only 16 genes out of more than 700 in that chromosome had no clear matches to human genes, and the matching ones were generally arranged in the same order on their chromosomes. Also, some sequences were very strongly conserved, suggesting that they are very structurally constrained to a shared function.

The article mentioned that Celera has rough drafts of the dog, bovine, pig, and chicken genomes, though I found no mention of any of these in Celera's site. The article mentioned an effort to sequence the rat genome, though there was no hint as to whether Celera was working on that one also, though I do know of a public effort to sequence that genome.

There is lots of other interesting stuff there, but I have to go now...

lpetrich

Not quite TIGR's Genome News Network, but here's some nice news on the genome-sequencing front:

As the public, as opposed to Celera , human, mouse, and rat genome efforts approach completion, the next question is which species are next. The National Human Genome Research Institute has now selected which ones will be next:

Chimp
Chicken
Sea Urchin (Strongylocentrotus purpuratus)
Honeybee
Various Fungi
Ciliate Protozoan (Tetrahymena thermophila)

Behind them are:

Rhesus monkey
Frog (Xenopus)

The institute has a received a proposal to do the cow genome, though not the pig, dog, or cat genomes. But since their genomes are human-genome-sized, deciding which to sequence will be a delicate job. However, the agricultural importance of cows and pigs, and also chickens and bees, has been enough to interest the US Department of Agriculture.

Looking elsewhere, the US Department of Energy's <a href="http://www.jgi.doe.gov" target="_blank">Joint Genome Institute</a> is working on:

Fugu Pufferfish (Fugu rubripes)
Sea squirt (ascidian) (Ciona intestinalis)
White Rot Fungus (Phanerochaete chrysosporium)(eats the wood material lignin)
Several microbes

And at MIT's <a href="http://www-genome.wi.mit.edu/" target="_blank">Whitehead Institute</a>, I find

Pufferfish (Tetraodon nigroviridis)
Sea squirt (ascidian) (Ciona savignyi)
Bread-mold fungus (Neurospora crassa)
A methanogen with a big genome (Methanosarcina acetivorans)

The animal-kingdom genomes sequenced so far:
Human
Fruit Fly (Drosophila melanogaster)
Nematode (Caenorhabditis elegans)

The plant-kingdom ones:
Rice
Small Mustard-like Plant (Arabidopsis thaliana)

Which will be acquiring a lot of competition over the next 5 years or so.

It will be interesting to construct a family tree of all these genomes as they get sequenced; so far, most of the better-established parts of the tree have been confirmed as genes have been sequenced, and one can reasonably expect continued confirmation from whole-genome comparisons.

By comparison, creationists do not have any real theory; they do not propose any alternative pattern for genes to follow. Instead, they gripe about discordant molecular family trees and they make unsubstantiated claims about the closeness of certain proteins to corresponding human ones. Examples:

<a href="http://members.aol.com/dwise1/cre_ev/bullfrog.html" target="_blank">Gary Parker:</a>
Fetal Hemoglobin -- Horse
Tear Enzymes -- Chicken
Albumin -- Bullfrog
Blood Antigen A -- Butterbean
Cholesterol Level -- Gartersnake
Milk Chemistry -- Donkey
(that link explains why these comparisons are bogus)

Likewise, <a href="http://www.talkorigins.org/faqs/kouznetsov.html" target="_blank">Dmitri Kouznetsov</a> has claimed that the creatine kinases of the African elephant and the common housefly (Musca domestica) are closely related. However, those proteins have never been sequenced!

scigirl

Hey Lpetrich,

Thanks for all these good links. At some point, I hope to use them. . .

And why isn't Xenopus sequenced yet!!

scigirl

Edited to add, Just because amphibians have 3 or four times the DNA a human does, doesn't mean they shouldn't be a priority. We frogs get no respect, I tell ya!

[ June 06, 2002: Message edited by: scigirl ]</p>

lpetrich

It's the <a href="http://www.nhgri.nih.gov/" target="_blank">National Human Genome Research Institute</a>, complete with link. There are a few news stories there, but not as much as (say) the GNN.

As to why Xenopus hasn't been sequenced, it's a matter of priorities, of how much will be gained per unit of sequencing effort. As a result, most of the sequenced species have relatively small genomes, and some of the bigger-genome ones were selected for their relatively small genomes, like the pufferfish and the rice plant. The <a href="http://wit.integratedgenomics.com/GOLD/" target="_blank">Genomes OnLine Database</a> lists 81 complete prokaryote genomes and 283 in progress, genomes which typically have a few million base pairs. Thus, the human genome is 3 times the size of all the complete and in-progress prokaryote genomes, and 12 times the size of the all the complete ones!

[ June 06, 2002: Message edited by: lpetrich ]</p>