Did you say RAT?
Posted on 03/31/2004 11:19:33 AM PST by balrog666
The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
A real saint compared to Rattus Rattus .
Some highlights:
Darwin believed that "natural selection will always act very slowly, often only at long intervals of time"1. The consequences of evolution over timescales of approximately 1,000 millions of years (Myr) and 75 Myr were investigated in publications comparing the human with invertebrate and mouse genomes, respectively2, 3. Here we describe changes in mammalian genomes that occurred in a shorter time interval, approximately 12–24 Myr (refs 4, 5) since the common ancestor of rat and mouse.
The comparison of these genomes has produced a number of insights:
The rat genome (2.75 gigabases, Gb) is smaller than the human (2.9 Gb) but appears larger than the mouse (initially 2.5 Gb (ref. 3) but given as 2.6 Gb in NCBI build 32, see http://www.ncbi.nlm.nih.gov/genome/seq/NCBIContigInfo.html).The rat, mouse and human genomes encode similar numbers of genes. The majority have persisted without deletion or duplication since the last common ancestor. Intronic structures are well conserved.
Some genes found in rat, but not mouse, arose through expansion of gene families. These include genes producing pheromones, or involved in immunity, chemosensation, detoxification or proteolysis.
Almost all human genes known to be associated with disease have orthologues in the rat genome but their rates of synonymous substitution are significantly different from the remaining genes.
About 3% of the rat genome is in large segmental duplications, a fraction intermediate between mouse (1–2%) and human (5–6%). These occur predominantly in pericentromeric regions. Recent expansions of major gene families are due to these genomic duplications.
The eutherian core of the rat genome—that is, bases that align orthologously to mouse and human—comprises a billion nucleotides (40% of the euchromatic rat genome) and contains the vast majority of exons and known regulatory elements (1–2% of the genome). A portion of this core constituting 5–6% of the genome appears to be under selective constraint in rodents and primates, while the remainder appears to be evolving neutrally.
Approximately 30% of the rat genome aligns only with mouse, a considerable portion of which is rodent-specific repeats. Of the non-aligning portion, at least half is rat-specific repeats.
More genomic changes occurred in the rodent lineages than the primate: (1) These rodent genomic changes include approximately 250 large rearrangements between a hypothetical murid ancestor and human, approximately 50 from the murid ancestor to rat, and about the same from the murid ancestor to mouse. (2) A threefold-higher rate of base substitution in neutral DNA is found along the rodent lineage when compared with the human lineage, with the rate on the rat branch 5–10% higher than along the mouse branch. (3) Microdeletions occur at an approximately twofold-higher rate than microinsertions in both rat and mouse branches.
A strong correlation exists between local rates of microinsertions and microdeletions, transposable element insertion, and nucleotide substitutions since divergence of rat and mouse, even though these events occurred independently in the two lineages.
Hot off the presses!
Did you say RAT?
Very cleverly done.
;-)
DemonRats are essentially useless to studies of mammalian evolution, since they have not evolved significantly from primordial slime.
However, the cited research does suggest that Norwegian Brown Rats might have a future as talk radio hosts.
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