tag:blogger.com,1999:blog-32079676.post1441951349010066807..comments2024-02-13T21:22:02.522-08:00Comments on RRResearch: Planning my CIfAR talkRosie Redfieldhttp://www.blogger.com/profile/06807912674127645263noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-32079676.post-6699464818844076532010-08-18T18:55:17.943-07:002010-08-18T18:55:17.943-07:00Sharing a percentage of genes in order to qualify ...Sharing a percentage of genes in order to qualify as a species (or be split into another species) gets complicated in plants for at least a couple reasons I can see. <br /><br />First, as genome size gets quite large, a much larger number of genes would be required to reach the 1% threshold. Thus two Arabidopsis-like samples would need far fewer genes to be divided into different species than say two Allium or two Triticum-like samples. <br /><br />And secondly, simply defining what a gene is becomes a bit arbitrary for genomes where there is so much redundancy. Do we count all putative ORFs (regardless of whether they are ever transcribed)? Do we count all transcripts (regardless of whether they're ever translated)? How do we deal with different mRNA splicing events? <br /><br />I originally took exception to the description of eukaryotic genetic diversity as "Not a lot". But the more I think about it the more I'm more inclined to think its phenotypic diversity that matters more, and there seems to be a sufficient amount of that. <br /><br />And as for levels of intraspecific genetic diversity (at least within angiosperms) it might be best to look at genomes where quite a bit of sequence has been determined. Some of our crop species may help in this regard.Clem Weidenbennernoreply@blogger.comtag:blogger.com,1999:blog-32079676.post-13644088518089974542010-08-18T07:03:23.592-07:002010-08-18T07:03:23.592-07:00It's certainly true that these ideas need a lo...It's certainly true that these ideas need a lot more thinking. A quick google search suggests there's not much data out there about intraspecies genome diversity in eukaryotes.<br /><br />If we were to define eukaryote species as groupings of individuals who shared >99% of their genes (excluding obvious new genetic parasites) with no more than, say, 1% sequence divergence, which kinds of organisms would be included and which excluded?Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-14892543165017639292010-08-18T05:04:13.839-07:002010-08-18T05:04:13.839-07:00You start by noting that within a eukaryotic speci...You start by noting that within a eukaryotic species there isn't much genetic diversity, but then upon trying to define what a bacterial species might be you start narrowing the range of genetic diversity. Then you note the greater level of bacterial diversity (relative to eukaryotic) because of the other 10% or 25% or 50%. So you lost me. <br /><br />It seems to me there is a fairly wide gap in intra-species diversity between plants and animals. This might be due to the largely different levels of tolerance to polyploidy (animals tolerating ploidy differences far less than plants - esp. angiosperms). If you have several genomes to draw upon you can tolerate an inversion or a major chromosomal translocation because of the redundancy. <br /><br />But there may be another reason that genetic diversity - at least in terms of the straight DNA sequence diversity - is so different between prokaryotic and eukaryotic systems. The eukaryotic systems, at least the more sophisticated large critter systems, have to regulate gene expression in many different cell types and have many more regulatory mechanisms that will eventually translate (pun intended) a more limited sequence space into a wider phenotypic space. And at the end of the day - its really all about the phenotype.Clem Weidenbennernoreply@blogger.com