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Topic: Genome reduction

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	Genome reduction - Wikipedia, the free encyclopedia
		Genome reduction (Genome degradation) is the process by which a genome shrinks relative to its ancestor.
		Genomes fluctuate in size regularly, especially in Bacteria, but in some situations a genome has drastically lost content in some period.
		The most evolutionary significant cases of genome reduction may be the eukaryotic organelles that are derived from bacteria.
	en.wikipedia.org /wiki/Genome_reduction (226 words)

	Genome reduction Definition / Genome reduction Research (Site not responding. Last check: 2007-10-21)
		Genome reduction (Genome degradation) is the process by which a genomeIn biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA).
		Genome reduction is a common phenomenon in obligatory intracellular parasites.
		Genome reduction is a consequence of obligate intracellular lifestyle rendering numerous genes expendable.
	www.elresearch.com /Genome_reduction (487 words)

	Potential Bioweapon: Q Fever Genome Is Sequenced (Site not responding. Last check: 2007-10-21)
		Scientists have sequenced the genome of the bacterium that causes Q fever, an illness that leaves a person incapacitated for several weeks with a debilitating headache and fever.
		This genome reduction is typical of parasitic bacteria that exist symbiotically with their hosts: As they become increasingly dependent on their hosts to fulfill their biological needs, parasitic bacteria eliminate genes they no longer need.
		Genome News Network is an editorially independent online publication of the J. Craig Venter Institute.
	www.genomenewsnetwork.org /articles/05_03/q_fever.shtml (623 words)

	Genome Biology \| Full text \| Accelerated evolution associated with genome reduction in a free-living prokaryote
		Furthermore, this genome reduction is clearly accompanied by a drift in G+C content, a phenomenon that commonly occurs during the evolution of host-dependent genomes [23].
		The mere reduction in genome size per se is a potential source of substantial economies for the cell, as it reduces the amount of nitrogen and phosphorus, two particularly limiting elements in the upper part of the ocean, which are necessary, for instance, in DNA synthesis.
		We hypothesize that a reduction in genome size (which allows a concomitant reduction in cell size and substantial economies in energy and nutrients) can constitute a selective advantage for life in the open ocean, both at depths where photon energy is low and in surface waters where nutrients are scarce.
	genomebiology.com /2005/6/2/R14 (5797 words)

	Insights into genome evolution: The sequence of Rickettsia conorii (Site not responding. Last check: 2007-10-21)
		Both bacteria are parasites with a relatively small genome, in part because they tend to inactivate their own genes when they can make use of genes from their host.
		Both Rickettsia genomes are much smaller than they were at the point of their divergence from a common ancestor millions of years ago, according to a comparative analysis by the researchers.
		This supports the theory that small genome size is useful for preserving the organisms' energy and improving its efficiency.
	www.genomenewsnetwork.org /articles/10_01/Rickettsia.shtml (346 words)

	PPD - Proteome Profile Database
		Comparative genomics is a powerful approach for identifying genetic variation that could explain differences in the anatomy, physiology and biochemistry of the organisms compared, and the factors responsible for their life-styles in general.
		Comparative genomics utilizes the large number of sequences in databases not only for elucidating commonality in all of life, but also for understanding the evolutionary diversity within various groups, as well as for comprehending the evolutionary processes or mechanisms producing such diversity.
		The flux, streamlining and elimination of genes in bacterial genomes of obligate intracellular parasitic species represent an ongoing process and could be a function of bacterial life-style and coding capacity of the genomes in terms of compactness.
	www.bioinfo.de /isb/2004040019/main.html (1881 words)

	MICROBIOLOGY: ON MOLLICUTES
		Eight mycoplasma genomes have been fully sequenced, ranging in size from the ~580 kilobase genome of Mycoplasma genitalium to the ~1.4 megabase genome of M. penetrans.
		Mycoplasmas apparently evolved from other bacteria by reduction of genome size: the smallest genome of the mycoplasmas is little more than twice the genome size of certain large viruses.
		The genome of Mycoplasma genitalium (an organism that causes one form of the urinary tract infection urethritis), which has been completely sequenced, consists of 580 kilobases comprising 517 genes (480 protein-coding genes; 37 genes for RNAs), and this is the smallest gene complement for any independently replicating cell so far identified.
	scienceweek.com /2005/sw050812-4.htm (844 words)

	More Information about Mycoplasma (Site not responding. Last check: 2007-10-21)
		The smallest mycoplasmal genomes, of about 600 kb, may be the minimal genetic complexity for a living organism, since this is the minimal size obtained on at least three independent lines of mycoplasmas (Maniloff, 1992).
		It is capable of reduction reactions under both anaerobic or aerobic conditions, and both hydrogen peroxide and the superoxide anion are by-products of glucose metabolism.
		One major factor in reducing genome size of this parasitic microbe is the substantial loss of genes encoding enzymes needed for many anabolic pathways, in particular biosynthesis of amino acids, purines and pyrimidines, and fatty acids.
	globin.cse.psu.edu /globin/html/pip/more_myco.html (1903 words)

	Dongsheng Zhou 2004 5138
		Twenty-two genomic regions that were absent in at least one of strains studied were identified by extensive microarray analysis (Table 4).
		With the integration of the bacteriophage genome into the bacterial chromosome, the virulence factors encoded by the prophage can convert their bacterial host from a nonpathogenic strain to a virulent one or to a strain with increased virulence (3).
		pestis genomes leads to the discrete segregation between the progenitor and offspring strains, and this genome reduction gradually causes the offspring strains to inhabit a more specific host niche, not overlapping with its progenitor.
	www.bionewsonline.com /r/4/dongsheng_zhou_2004_5138.htm (3999 words)

	Space Studies Board
		Recombination enables organisms to maintain maximum genome sizes that are larger than those capable without gene exchange (escape of Muller's ratchet), but does not mediate potential reduction of genome size.
		As the aggregation of the genes into a cluster does not necessarily affect the fitness of the cell, the cluster may be considered to be a selfish property of the constituent genes.
		Horizontal transfer serves to disseminate selfish operons among bacterial genomes, where they may confer a beneficial function to their host cells and be maintained by natural selection.
	www7.nationalacademies.org /ssb/nanopanel1lawrence.html (2968 words)

	ABSTRACTS
		A genomic library of total DNA extracted from the fungal spores was demonstrated to be representative of the bacterial genome, and was used to investigate the prokaryotic genome.
		In order to reconstruct the steps in genome reduction in one such lineage, the tiny genome of the endosymbiont Buchnera aphidicola was compared to the larger ancestral genome reconstructed on the basis of closely related bacteria including E. coli.
		One explanation is that large deletions, possibly associated with rearrangements, occurred early in the process of genome reduction, soon after the acquisition of an obligate endosymbiotic lifestyle.
	www.mbl.edu /CASSLS/oggiabstracts.htm (5737 words)

	Siefert-HGT
		The single DNA-circle configuration of the plastid genome in apicomplexans, which contrasts with the unique minicircle plastid genes in peridinin dinoflagellates and the nuclear location of tufA in A. tamarense, suggests that extensive plastid gene transfer in dinoflagellates probably occurred independently after their split from apicomplexans.
		The extreme genome reduction evident in apicoplasts surely results from the evolution of an intracellular lifestyle with the loss of genes no longer needed for photosynthesis (e.g., as in the nonphotosynthetic parasitic plant Epifagus[29]).
		This type of reduction appears, however, to be quite different from that in dinoflagellates, many of which are photosynthetic and have for unknown reasons transformed the plastid genome required for this function into minicircles and undergone wholesale photosynthetic gene transfer to the nucleus.
	www.stat.rice.edu /~siefert/LGT/Euk.html (480 words)

	[No title] (Site not responding. Last check: 2007-10-21)
		Another consequence of intracellular lifestyle is reduction of effective population size and limited possibility of gene acquirement via lateral transfer.
		While causes of genome reduction are rather indisputable, those resulting in genome expansion seem to be less obvious.
		Presumably, the genome enlargement is an indirect consequence of adaptation to changing environmental conditions and requires the acquisition and integration of numerous genes.
	www.actabp.pl /html/2_2001/367-381.htm (266 words)

	Genome Biology \| Abstract \| Accelerated evolution associated with genome reduction in a free-living prokaryote
		As all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in Prochlorococcus is the first documented example of such a process in a free-living organism.
		We assume that the major driving force behind genome reduction within the Prochlorococcus radiation has been a selective process favoring the adaptation of this organism to its environment.
		A scenario is proposed for genome evolution in this genus.
	genomebiology.com /2005/6/2/R14/abstract (304 words)

	Simplicity and Complexity of Microsporidian Genomes -- Keeling and Slamovits 3 (6): 1363 -- Eukaryotic Cell
		Numbers are genome size estimates in millions of base pairs (see reference 38 for a review).
		Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi.
		Keeling, P. Reduction and compaction in the genome of the apicomplexan parasite, Cryptosporidium parvum.
	ec.asm.org /cgi/content/full/3/6/1363 (4537 words)

	Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis -- Sakharkar et ...
		Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis -- Sakharkar et al.
		Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis
		genome reduction by gene loss over time in the context of their
	ijs.sgmjournals.org /cgi/content/abstract/54/6/1937 (282 words)

	Genome complexity reduction for SNP genotyping analysis -- Jordan et al. 99 (5): 2942 -- Proceedings of the National ...
		Thirty-two unrelated human genomic DNA samples from the CEPH reference panel (http://www.cephb.fr/) were amplified with a DOP-PCR primer.
		amplified, relative to the fraction of the mammalian genomes amplified.
		Specific primers designed to amplify predicted products from three electronic DOP-PCRs (e1-e3) were tested for their ability to amplify genuine products from genomic DNA (row A-positive control), a 1:10,000 dilution of an uncycled, mock DOP-PCR (row B-negative control for amplifying any remaining genomic DNA), and a 1:10,000 dilution of cycled DOP-PCR (row C).
	pnas.org /cgi/content/full/99/5/2942?maxtoshow=&HITS=10&hits=10&... (4458 words)

	FIELDS, MARY B., JENNIFER M. MCGEE, JENNIFER LATTANZE, LAURA A. BROUSE, AND ROBERT M. DAWLEY. (Site not responding. Last check: 2007-10-21)*
		The doubling of genome size that accompanied each tetraploid event in the latter species' history must have been followed by an equally dramatic decrease in genome size during the subsequent diploidization of these species' genomes.
		This suggests that the ecologies of these Mimulus species require that they have fairly small genomes whatever their ploidy may be, although we must examine a larger sample of species within the genus before drawing conclusions.
		The reduction in genome size implied by our data could have hace been accomplished solely by the loss of non-genic DNA, or some duplicated functional loci could also have been lost during diploidization.
	www.ou.edu /cas/botany-micro/bsa-abst/section5/abstracts/16.shtml (266 words)

	Loss of DNA Recombinational Repair Enzymes in the Initial Stages of Genome Degeneration -- Dale et al. 20 (8): 1188 -- ...
		Genome size determination and coding capacity of Sodalis glossinidius, an enteric symbiont of tsetse flies, as revealed by hybridization to Escherichia coli gene arrays.
		Genome size characterisation of the principal endocellular symbiotic bacteria of the weevil Sitophilus oryzae, using pulsed field gel electrophoresis.
		Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp.
	mbe.oxfordjournals.org /cgi/content/full/20/8/1188 (4020 words)

	Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life -- Gil et al. 99 (7): ...
		Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life -- Gil et al.
		Agarose plugs containing Buchnera genomic DNA were obtained as described (22, 23).
		To determine the genome size of the Buchnera genus, we analyzed the chromosomes of Buchnera obtained from five of the main
	www.pnas.org /cgi/content/full/99/7/4454 (2913 words)

	Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization ...
		Small genome of Candidatus Blochmannia, the bacterial endosymbiont of Camponotus, implies irreversible specialization to an intracellular lifestyle -- Wernegreen et al.
		Charles, H. and Ishikawa, H. Physical and genetic map of the genome of Buchnera, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.
		Wernegreen, J. J., Ochman, H., Jones, I. and Moran, N. The decoupling of genome size and sequence divergence in a symbiotic bacterium.
	mic.sgmjournals.org /cgi/content/full/148/8/2551 (2427 words)

	UBC Department of Botany - People (Site not responding. Last check: 2007-10-21)
		As genomes are reduced in size, there are likely to be changes in the amounts of non-coding material.
		In metazoans, where genomes tend to be quite large, introns can be quite long (sometimes several kb), and the spliceosome is extremely large with over a hundred proteins.
		Using microsporidia as a model system, we are examining the effects of genome reduction on the evolution of introns and the spliceosomal machinery.
	www.botany.ubc.ca /People/fast.htm (570 words)

	Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in Arabidopsis -- Devos et al. 12 ...
		in the 44% of the genome that is genic (25,000 genes with an average
		Genome Res., August 1, 2004; 14(8): 1474 - 1482.
		Genome Res., August 1, 2003; 13(8): 1897 - 1903.
	www.genome.org /cgi/content/full/12/7/1075 (4083 words)

	An Appraisal of the Potential for Illegitimate Recombination in Bacterial Genomes and Its Consequences: From ... (Site not responding. Last check: 2007-10-21)
		An Appraisal of the Potential for Illegitimate Recombination in Bacterial Genomes and Its Consequences: From Duplications to Genome Reduction
		genome reduction that is characterized by a loss of a significant
		Mira, A., Ochman, H., and Moran, N.A. Deletional bias and the evolution of bacterial genomes.
	www.genome.org /cgi/content/full/13/6a/1123 (5355 words)

	Annika Nilsson: Doktorsavhandling från Karolinska Institutet
		Evolution towards reduced bacterial genome size is associated with an intracellular lifestyle that is characterized by small bacterial population sizes and relaxed selection pressures.
		The data agrees well with the observation that genome reduction in bacteria with small genomes initially was a rapid process mediated via large deletions.
		RecA functions have been suggested to be important for the decrease in genome size of small genomes.
	diss.kib.ki.se /2005/91-7140-192-X (637 words)

	Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia ...
		This method corroborated the previous Wigglesworthia genome annotation, identifying only five genes named differently in the two genomes; these mismatched genes were not among the putative high or low-expression genes used in our analyses.
		Birdsell, J. Integrating genomics, bioinformatics, and classical genetics to study the effects of recombination on genome evolution.
		Clark, M. A., Baumann, L. and Baumann, P. Sequence analysis of a 34·7-kb DNA segment from the genome of Buchnera aphidicola (endosymbiont of aphids) containing groEL, dnaA, the atp operon, gidA, and rho.
	mic.sgmjournals.org /cgi/content/full/149/9/2585 (5831 words)

	First-Generation Linkage Map of the Gray, Short-Tailed Opossum, Monodelphis domestica, Reveals Genome-Wide Reduction in ...
		and rearrangement relative to eutherian genomes agrees with
		Marsupial genomes are about the same size as those of eutherian
		and fathers to the expressed genomes of their offspring.
	www.genetics.org /cgi/content/full/166/1/307 (7030 words)

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