tag:blogger.com,1999:blog-36768584.post3016019904191063798..comments2024-03-03T18:49:34.382-05:00Comments on Omics! Omics!: Plenty of Genomes are Still Fair Game for SequencingKeith Robisonhttp://www.blogger.com/profile/04765318239070312590noreply@blogger.comBlogger6125tag:blogger.com,1999:blog-36768584.post-41129335901507199672010-11-20T18:45:28.314-05:002010-11-20T18:45:28.314-05:00My brother used to enter pumpkins in the Topsfield...My brother used to enter pumpkins in the Topsfield Fair back when 800 pounds was a big one. When they started soaking seeds in colchicine to increase ploidy he called it quits. <br /><br />I agree completely and more. The pumpkin, the lobster, the weird bug in a South American jungle. Where are we getting the new discovery that will impact on human health? From one of those outlier genomes no doubt. <br /><br />We might have to hunker down for the analysis and storage of genome data get out of kindergarten where we seem to be stuck for the time being. But we'll fix it.Paul Morrisonhttp://mbcf.dfci.harvard.edunoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-6070209889037154572010-11-02T16:52:06.386-04:002010-11-02T16:52:06.386-04:00Most of the species of organisms on this planet ha...Most of the species of organisms on this planet have not even been identified, and it is possible that the genomic sequences of organisms could become the chief criteria for their classification. This should drive the sales of DNA sequencing machines and employ armies of gene sequencing technicians for another few decades at least. A few might argued that with mass extinction of many species on our planet due to human activity that we have a moral obligation to do this more quickly. The sequencing of genomes of life forms from other worlds, if they have genomes, will most certainly also keep the gene sequencing stakeholders happy when we run out of organisms on this planet. Intriguingly, even the concept of an interplanetary "Noah's" ark for the preservation of life from Earth to distant worlds when we ruin this one may not even require a broad selection of living animals, planets and microbes, but just their genomic sequences and the capacity to produce synthetic life.<br /><br />With the drop in the cost of gene sequencing, all kinds of fanciful ideas will abound. Just because we can undertake certain activities, does means that we should do so now. The main issue I have with the currently proposed gene sequencing efforts is not so much the direct costs but rather the lost opportunity to make sense and use of the genetic and proteomics information that we already possess. With increasingly reduced funding for biomedical researchers trained and engaged in enzymology, metabolism and basic biochemistry, our capacity from actually benefiting from the genomics legacy we already have will diminish rather than improve.S. Pelech - Kinexushttp://www.kinexus.canoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-58394898457951031572010-11-01T22:44:42.393-04:002010-11-01T22:44:42.393-04:00Nice to see some good feedback.
Titus: Definitely...Nice to see some good feedback.<br /><br />Titus: Definitely you have some good suggestions. I had a jawless fish tagged as done; I guess it still has a way to go. The 10K genome project should cover a lot of important unsequenced vertebrates -- lots of good targets there.<br /><br />I'll fully admit I don't know my invertebrates well. Arthropods are obvious to me since there are so many forms & it is easy to see some interesting developmental questions there (starting with all those appendages but also different styles of metamorphosis and the acquisition of flight).<br /><br />And yes, I agree there is still a lot of interesting fungi, bacteria and whatnot worth sequencing -- particularly to discover novel biochemistry. Just imagine all the complex metabolite biosynthesis operons that must still lie in the Streptomyces alone!Keith Robisonhttps://www.blogger.com/profile/04765318239070312590noreply@blogger.comtag:blogger.com,1999:blog-36768584.post-70044413272882441382010-11-01T14:37:02.990-04:002010-11-01T14:37:02.990-04:00Genome sequencing is getting much cheaper. At UCS...Genome sequencing is getting much cheaper. At UCSC, there is an attempt to sequence the campus mascot (the banana slug) with essentially no funding.<br /><br />https://banana-slug.soe.ucsc.edu/Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-60526722284609640762010-11-01T12:37:39.490-04:002010-11-01T12:37:39.490-04:00Of course there are a lot of interesting genomes w...Of course there are a lot of interesting genomes which are still waiting for sequencing. In my experience, I can say that many plants of agricultural relevance (such as wheat) are still far from being sequenced, their genomes are huge and highly repetitive. However, their genomes could be extremely useful since these plants feed the world.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-36768584.post-35760089661197654232010-11-01T09:24:04.804-04:002010-11-01T09:24:04.804-04:00Dude!
I'm kind of shocked that you look at th...Dude!<br /><br />I'm kind of shocked that you look at the tree of metazoa and conclude that - hey! we need more Arthropod genomes!<br /><br />Ecdysozoa and chordates as a whole are severely overrepresented, in fact. We have only a few lophotrochozoa, even if you include the unpublished ones. We need more!<br /><br />Only a few nonchordate deuterostomes have been sequenced, too: sea urchins and some related echinoderms, as well as one or two hemichordates (Saccoglossus kowaleskii). If we want to know more about origin of chordates and vertebrates, there's where we should look.<br /><br />Note that neither the lamprey nor hagfish genomes are available yet (although we're working on lamprey quite feverishly). What, you think all vertebrates have jaws?<br /><br />Very few plants have been sequenced, and they're going to be a real bitch because of the repeat content.<br /><br />Hey, and microbes! The Tree of Life is not well covered at the microbial level, even with all the bacteria and archaea that have been sequenced in recent years. See the GEBA project for an example of the impact that some judiciously chosen genomes can have on protein discovery.<br /><br />We've got another decade of genome sequencing ahead of us before we can say that we're even close to well sampled. People who claim otherwise just don't know their biology.<br /><br />--titusTitus Brownhttps://www.blogger.com/profile/01789918783866021532noreply@blogger.com