Freethought & Rationalism Archive

Valentine Pontifex · 06-01-2002, 11:15 PM

<a href="http://www.sciencemag.org/cgi/content/full/296/5573/1661" target="_blank">A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome</a> is in the current issue of Science. Until June 27 the entire contents of this journal can be read by anyone online user without payment if they register. After that free access will be restricted to year-old articles.

Quote:

The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.

Of course the chromosome has lots of pseudogenes and the remains of viruses.

lpetrich · 06-02-2002, 01:27 AM

I read that article, and it stated that the sequencer, Celera, has publicly released only mouse chromosome 16's sequence -- all the other mouse-chromosome sequences are available only to its subscribers. Is charging for access the business model that Celera has settled on?

To tell the truth, I don't object that much to that business model, as long as it is confined to nonhuman genomes

But I hope that this will not get in the way of similar comparisons for the other mouse chromosomes.

Also, Celera has preliminary sequences for cow, pig, dog, and chicken, and is working on rat. However, going to <a href="http://www.celera.com" target="_blank">http://www.celera.com</a> revealed nothing about what genomes are in the works there. Here's a family tree:

(((human (mouse rat)) (dog (cow pig))) chicken)

And if he has one, will Craig Venter's pet dog be the main source of the dog-genome data?

Checking back on <a href="http://wit.integratedgenomics.com/GOLD/" target="_blank">GOLD</a>, I've found plans to close a taxonomic gap. There is a project for sequencing a mollusk, the freshwater snail Biomphalaria glabrata, known for carrying the trematode that causes schistosomiasis. Which is also being sequenced. And also, anoher fish, the zebrafish Danio rerio, often used as a model system.

And checking on <a href="http://www.hgsc.bcm.tmc.edu/" target="_blank">Baylor College of Medicine's Human Genome Sequencing Center</a>, I find that it is working on improving the quality of the assembled human-genome sequence, and working on several other genomes -- though it is hard to tell the extent of its progress:

Mouse
Rat (10 million genome reads at Baylor; 30 million total)
Chimp (not much apparent progress)
Cow (not much apparent progress)
Some microbes

Checking on the <a href="http://genome.wustl.edu/gsc/mouse/" target="_blank">Washington University</a> page of the non-Celera mouse-sequencing effort suggests that sequencing coverage has reached 6-7x (each base was sequenced, on average, that many times). Also, the non-Celera efforts include efforts to find human<->mouse genome maps.

lpetrich · 06-02-2002, 01:48 AM

Here's another interesting bit of information on human genetic variability; as discussed in <a href="http://www-genome.wi.mit.edu/media/press/pr_hapmap.html" target="_blank">this article</a>, some regions of the human genome have their ~10 million "Single Nucleotide Polymorphisms" (variations in single ones) correlated with others in big blocks or haplotypes. These typically have 10,000-50,000 SNP's each, and usually come in three to five variants.

The proposed "HapMap" project would extend this work to the entire genome.

Here is <a href="http://gnn.tigr.org/articles/05_02/genetic_variation.shtml" target="_blank">another article on that, from TIGR's GNN</a>; the article includes a chart on the amount of overlap between European, African, and Asian populations:

Total = 5.3
All three = 2.7
Euro-Asian = 0.3
Euro-African = 0.6
Afro-Asian = 0.1
Euro = 0.1
Asian = 0.1
African = 1.3

Most of the variation is shared, and the population with the most variation is the African one -- suggesting that the European and Asian populations of our species are offshoots of some ancestral African one.

Finally, GNN reports on <a href="http://gnn.tigr.org/articles/05_02/sleepless_flies.shtml" target="_blank">sleep-deprivation experiments on fruit flies</a> -- which share with our species some important genetic controls of the sleep mechanism.

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06-02-2002, 01:27 AM	#2
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	I read that article, and it stated that the sequencer, Celera, has publicly released only mouse chromosome 16's sequence -- all the other mouse-chromosome sequences are available only to its subscribers. Is charging for access the business model that Celera has settled on? To tell the truth, I don't object that much to that business model, as long as it is confined to nonhuman genomes But I hope that this will not get in the way of similar comparisons for the other mouse chromosomes. Also, Celera has preliminary sequences for cow, pig, dog, and chicken, and is working on rat. However, going to <a href="http://www.celera.com" target="_blank">http://www.celera.com</a> revealed nothing about what genomes are in the works there. Here's a family tree: (((human (mouse rat)) (dog (cow pig))) chicken) And if he has one, will Craig Venter's pet dog be the main source of the dog-genome data? Checking back on <a href="http://wit.integratedgenomics.com/GOLD/" target="_blank">GOLD</a>, I've found plans to close a taxonomic gap. There is a project for sequencing a mollusk, the freshwater snail Biomphalaria glabrata, known for carrying the trematode that causes schistosomiasis. Which is also being sequenced. And also, anoher fish, the zebrafish Danio rerio, often used as a model system. And checking on <a href="http://www.hgsc.bcm.tmc.edu/" target="_blank">Baylor College of Medicine's Human Genome Sequencing Center</a>, I find that it is working on improving the quality of the assembled human-genome sequence, and working on several other genomes -- though it is hard to tell the extent of its progress: Mouse Rat (10 million genome reads at Baylor; 30 million total) Chimp (not much apparent progress) Cow (not much apparent progress) Some microbes Checking on the <a href="http://genome.wustl.edu/gsc/mouse/" target="_blank">Washington University</a> page of the non-Celera mouse-sequencing effort suggests that sequencing coverage has reached 6-7x (each base was sequenced, on average, that many times). Also, the non-Celera efforts include efforts to find human<->mouse genome maps.

06-02-2002, 01:48 AM	#3
lpetrich Contributor Join Date: Jul 2000 Location: Lebanon, OR, USA Posts: 16,829	Here's another interesting bit of information on human genetic variability; as discussed in <a href="http://www-genome.wi.mit.edu/media/press/pr_hapmap.html" target="_blank">this article</a>, some regions of the human genome have their ~10 million "Single Nucleotide Polymorphisms" (variations in single ones) correlated with others in big blocks or haplotypes. These typically have 10,000-50,000 SNP's each, and usually come in three to five variants. The proposed "HapMap" project would extend this work to the entire genome. Here is <a href="http://gnn.tigr.org/articles/05_02/genetic_variation.shtml" target="_blank">another article on that, from TIGR's GNN</a>; the article includes a chart on the amount of overlap between European, African, and Asian populations: Total = 5.3 All three = 2.7 Euro-Asian = 0.3 Euro-African = 0.6 Afro-Asian = 0.1 Euro = 0.1 Asian = 0.1 African = 1.3 Most of the variation is shared, and the population with the most variation is the African one -- suggesting that the European and Asian populations of our species are offshoots of some ancestral African one. Finally, GNN reports on <a href="http://gnn.tigr.org/articles/05_02/sleepless_flies.shtml" target="_blank">sleep-deprivation experiments on fruit flies</a> -- which share with our species some important genetic controls of the sleep mechanism.

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