More to junk DNA?

[paulsamuel]

I would like to read more about this. Do you have a journal reference? Are you referring to the Fugu genome, per chance?

really, i can't remember, but i will try to find it. maybe we can search simultaneously. good search term is "genome reduction"

As far as I can remember, I'm not referring to the Fugu (what is that BTW?) genome.

 

[ElectricFetus]

All of it exit for a structural reason at least, remove any large non-coding section of a chromosome and it wont cross over right with it paired in meiosis. It more of a matter of importance, as structural DNA small amounts of it can be replaced or deleted without drastically increasing the chances of chromosomal mutations in reproduction. But considering that structural DNA (what makes up at least 80% of our genomes) are constantly repeating small sequences with little variation, structural DNA has become finally tuned for it brick & mortar role. The again if you look at the Y chromosome which has not been pair for crossing over in eons, it shrunk greatly, no need for most of its structural DNA and proof positive that most of our genomes has a purpose be it mundane

Hercules Rockefeller,

Here a nice article on RNA only genes. http://www.phy.ntnu.edu.tw/~cchen/class/scitran/genome.pdf

 

[paulsamuel]

I would like to read more about this.

Here're a couple references with abstracts on whole genome evolution. I'll keep looking, but the reference lists in these papers may contain some good sources.

Proc Natl Acad Sci U S A. 2004 Feb 10;101(6):1638-43. Epub 2004 Feb 02. Related Articles, Links
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Major events in the genome evolution of vertebrates: paranome age and size differ considerably between ray-finned fishes and land vertebrates.
Vandepoele K, De Vos W, Taylor JS, Meyer A, Van de Peer Y.
Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium.
It has been suggested that fish have more genes than humans. Whether most of these additional genes originated through a complete (fish-specific) genome duplication or through many lineage-specific tandem gene or smaller block duplications and family expansions continues to be debated. We analyzed the complete genome of the pufferfish Takifugu rubripes (Fugu) and compared it with the paranome of humans. We show that most paralogous genes of Fugu are the result of three complete genome duplications. Both relative and absolute dating of the complete predicted set of protein-coding genes suggest that initial genome duplications, estimated to have occurred at least 600 million years ago, shaped the genome of all vertebrates. In addition, analysis of >150 block duplications in the Fugu genome clearly supports a fish-specific genome duplication (approximately equal to 320 million years ago) that coincided with the vast radiation of most modern ray-finned fishes. Unlike the human genome, Fugu contains very few recently duplicated genes; hence, many human genes are much younger than fish genes. This lack of recent gene duplication, or, alternatively, the accelerated rate of gene loss, is possibly one reason for the drastic reduction of the genome size of Fugu observed during the past 100 million years or so, subsequent to the additional genome duplication that ray-finned fishes but not land vertebrates experienced.


Appl Bioinformatics. 2003;2(1):13-34. Related Articles, Links

Innovation from reduction: gene loss, domain loss and sequence divergence in genome evolution.
Braun EL.
Department of Zoology, University of Florida, Gainesville, FL, USA.
Analyses of genome sequences have revealed a surprisingly variable distribution of genes, reflecting the generation of novel genes, lateral gene transfer and gene loss. The impact of gene loss on organisms has been difficult to examine, but the loss of protein coding genes, the loss of domains within proteins and the divergence of genes have made surprising contributions to the differences among organisms. This paper reviews surveys of gene loss and divergence in fungal and archaeal genomes that indicate suites of functionally related genes tend to undergo loss and divergence. Instances of fungal gene loss highlighted here suggest that specific cellular systems have changed, such as Ca 2+ biology in Saccharomyces cerevisiae and peroxisome function in Schizosaccharomyces pombe. Analyses of loss and divergence can provide specific predictions regarding protein-protein interactions, and the relationship between networks of protein interactions and loss may form a part of a parametric model of genome evolution.

 

[paulsamuel]

I would like to read more about this.

Here are a couple more

Dev Cell. 2004 May;6(5):614-6. Related Articles, Links

Reduction and Compaction in the Genome of the Apicomplexan Parasite Cryptosporidium parvum.
Keeling PJ.
Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, 3529-6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada.
The complete genome of the apicomplexan parasite Cryptosporidium parvum reveals many new insights into apicomplexan biology and evolution, as well as the general process of genome reduction in parasites. The genome is globally compacted, but gene loss seems to be focused, in particular in relation to organelles. Massive losses of mitochondrial genes have taken place and there is no evidence of any plastid-related genes, providing a useful tool for examining putative plastid proteins in Plasmodium and other apicomplexans.

Mol Microbiol. 2004 Mar;51(6):1535-50. Related Articles, Links

Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome.
Weaver D, Karoonuthaisiri N, Tsai HH, Huang CH, Ho ML, Gai S, Patel KG, Huang J, Cohen SN, Hopwood DA, Chen CW, Kao CM.
Department of Chemical Engineering, MC 5025, Stanford University, Stanford, CA 94305, USA.
The chromosomes of several widely used laboratory derivatives of Streptomyces coelicolor A3(2) were found to have 1.06 Mb inverted repeat sequences at their termini (i.e. long-terminal inverted repeats; L-TIRs), which are 50 times the length of the 22 kb TIRs of the sequenced S. coelicolor strain M145. The L-TIRs include 1005 annotated genes and increase the overall chromosome size to 9.7 Mb. The 1.06 Mb L-TIRs are the longest reported thus far for an actinomycete, and are proposed to represent the chromosomal state of the original soil isolate of S. coelicolor A3(2). S. coelicolor A3(2), M600 and J1501 possess L-TIRs, whereas approximately half the examined early mutants of A3(2) generated by ultraviolet (UV) or X-ray mutagenesis have truncated their TIRs to the 22 kb length. UV radiation was found to stimulate L-TIR truncation. Two copies of a transposase gene (SCO0020) flank 1.04 Mb of DNA in the right L-TIR, and recombination between them appears to generate strains containing short TIRs. This TIR reduction mechanism may represent a general strategy by which transposable elements can modulate the structure of chromosome ends. The presence of L-TIRs in certain S. coelicolor strains represents a major chromosomal alteration in strains previously thought to be genetically similar.

 

[paulsamuel]

really, i can't remember, but i will try to find it. maybe we can search simultaneously. good search term is "genome reduction"

As far as I can remember, I'm not referring to the Fugu (what is that BTW?) genome.

It appears that I was talking about the Fugu genome.

 

[Buckaroo Banzai]

Hi. Just annoyingly trying to let my analogy clear again. What I tryed to say was basically the same thing that Douglas Theobald meant with evolutionary opportunism and molecular suboptimal function in Talk.Origins archive.