tag:blogger.com,1999:blog-32079676.post7676096850988168606..comments2024-02-13T21:22:02.522-08:00Comments on RRResearch: Bacterial pseudogenes and within-species diversityRosie Redfieldhttp://www.blogger.com/profile/06807912674127645263noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-32079676.post-46493290066125986512010-08-21T08:07:23.307-07:002010-08-21T08:07:23.307-07:00Hi Rosie,
I just re-read the paper and I'd li...Hi Rosie,<br /><br />I just re-read the paper and I'd like to get your take on a contrarian viewpoint to Cho and Ochman.<br /><br />They seem to assume that rates of pseudogene formation (or fixation) are consistent across the Salmonella genomes. However, fig. 1 shows that some of these strains are likely undergoing slightly different selection pressures (leading to slightly higher Ka/Ks ratios). Could it be that there is just differential fixation of slightly deleterious pseudogenes within these lineages instead of faster clearing, leading to the inflated values of new pseudogenes? Am I missing something?Unknownhttps://www.blogger.com/profile/11890027871561694348noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-46849451914482373552010-08-12T09:48:04.545-07:002010-08-12T09:48:04.545-07:00Hi Mark,
I'm still floundering around trying ...Hi Mark,<br /><br />I'm still floundering around trying to get a grip on pseudogene evolution. I'm particularly interested because many H. influenzae strains have defects in competence, that we think are due to recent mutations in DNA uptake genes.Rosie Redfieldhttps://www.blogger.com/profile/06807912674127645263noreply@blogger.comtag:blogger.com,1999:blog-32079676.post-45601973129825940022010-08-10T15:52:51.961-07:002010-08-10T15:52:51.961-07:00Great synopsis. I tend to agree that most pseudog...Great synopsis. I tend to agree that most pseudogenes are of recent origin, but then I think there is the occasional odd player. <br /><br />I was part of a group that recently sequenced and annotated a gram + bacterial pathogen of salmon, <i>Renibacterium salmoninarum</i> (J. Bact. 2008 vol. 190 (21) pp. 6970-82). This genome is littered with pseudogenes, and out of 3507 ORFs, 730 were putative pseudogenes (21%). 360 of these were frameshifts, 208 were disrupted by point mutations, and 162 were disrupted by insertion sequences an deletions. (By the way these are all real and not sequencing errors--I looked at the contig alignments of every single one of them!) Whether these are unique to the strain sequenced (and possibly new) or old and maintained awaits sequencing of other strains (one group I know of is taking this on). However limited PCR and sequencing showed several of them to be maintained among different strains, and other evidence shows strains of this species are highly homogeneous at least with respect to broad geographical niches.<br /><br />I'd be interested in any thoughts you might have!<br /><br />-Markmarkhttps://www.blogger.com/profile/01505037990942027438noreply@blogger.com