Purifying selection and birth-and-death evolution in the ubiquitin gene family

Nei, Masatoshi; Rogozin, Igor B.; Piontkivska, Helen

doi:10.1073/pnas.97.20.10866

Cited by 133 publications

(111 citation statements)

References 31 publications

(33 reference statements)

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“…In this model, the members of multigene families evolve independently through the frequent duplication and loss of genes. This model fits the process observed in the evolution of large multigene families, such as the major histocompatibility complex (MHC) and immunoglobin (Ig) families [13], as well as of smaller multigene families, such as the ubiquitins [14].…”

Section: Introductionsupporting

confidence: 65%

“…The family of Hox genes, which number 4 (platyhelminth) to 48 (teleost fish) per genome, is one of the most investigated genes with regard to gene duplication. Mammals (mouse, human), Cephalochordates, Sea urchin, Nematoda, and Fruit flies have 39,14,11,6, and 10 Hox genes, respectively [16]. Recent sequence data from various genome projects has documented the number of olfactory receptor (OR) genes in many vertebrate species [17].…”

Section: Introductionmentioning

confidence: 99%

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Comparative genomic analysis of the mouse and rat amylase multigene family

Sugino¹

2007

FEBS Letters

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The rat and mouse amylase gene families were characterized using sequence data from the UCSC genome assembly. We found that the rat genome contains one amylase-1 and two amylase-2 genes, lying close to one another on the same chromosome. Detailed analysis revealed at least six additional amylase pseudogenes in the rat genome in the region adjacent to the amylase-2 genes. In contrast, the mouse has one amylase-1 gene and five amylase-2 genes; the latter are tandemly and systematically arranged on the same chromosome and were generated by segmental duplication. Detailed analysis revealed that the mouse has two amylase pseudogenes, located 5 0 to the five amylase-2 segments. Thus, the amylase genes of mouse and rat tend to be amplified; the sequences of some of them are fixed while others have become pseudogenes during evolution. This is the second report of amylase genomic organization in mammals and the first in the rodents.

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Section: Introductionsupporting

confidence: 65%

Section: Introductionmentioning

confidence: 99%

Comparative genomic analysis of the mouse and rat amylase multigene family

Sugino¹

2007

FEBS Letters

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“…We used the nucleotide diversity ( ) statistic (Nei and Li 1979) to represent the level of repeat array variation, as it can be used to compare repeat families with different copy numbers. The polyubiquitin gene repeats (poly-u repeats) were chosen for comparison, as they were previously shown to be undergoing birth-and-death evolution rather than concerted evolution (Nei et al 2000). Within a repeat array the amino acid sequences of the poly-u repeats are usually invariant, but synonomous sites in the nucleotide sequence are variable.…”

Section: Resultsmentioning

confidence: 99%

“…The molecular process responsible for concerted evolution is known as homogenization (Dover 1982), and although not fully elucidated, is thought to involve continual turnover of repeat copies by unequal recombination (e.g., Smith 1973;Szostak and Wu 1980;Kobayashi et al 1998). However, recent studies have shown that several repeat families previously thought to evolve by concerted evolution actually evolve via a different evolutionary process known as birth-and-death evolution (e.g., Nei et al 1997Nei et al , 2000Rooney and Ward 2005). In birth-anddeath evolution it is selection, not homogenization, that maintains the repeats as a coherent family, and occasional duplication/deletion is also thought to play a role.…”

mentioning

confidence: 99%

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data

Ganley¹,

Kobayashi²

2007

Genome Res.

320

260

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Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by concerted evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of evolution, birth-and-death evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support concerted evolution over birth-and-death evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via concerted evolution. Comparisons with a repeat array undergoing birth-and-death evolution provide a clear contrast in the level of repeat array variation between these two forms of evolution, confirming that the rDNA indeed does evolve via concerted evolution. These low levels of intra-genomic variation are consistent with a model of concerted evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.[Supplemental material is available online at www.genome.org.]Repetitive elements are an abundant feature of genomes (Britten and Kohne 1968) and play critical roles in cell biology, genome structure, and adaptive evolution (Andersson et al. 1998;Shapiro and von Sternberg 2005). In many cases, repeats from a repeat family are highly similar to one another within a genome, a pattern that persists through evolutionary time even though sequence differences are apparent between species (Brown et al. 1972). Thus, the repeats seem to be maintained as a coherent family. This pattern is contrary to the expectations of conventional evolution, where repeats are expected to evolve independently ( Fig. 1) and diverge with time. This unusual mode of evolution, where repeats within a genome are more similar to each other than they are to "orthologous" repeats in a related species, is defined as concerted evolution (Zimmer et al. 1980). The molecular process responsible for concerted evolution is known as homogenization (Dover 1982), and although not fully elucidated, is thought to involve continual turnover of repeat copies by unequal recombination (e.g., Smith 1973;Szostak and Wu 1980;Kobayashi et al. 1998). However, recent studies have shown that several repeat families previously thought to evolve by concerted evolution actually evolve via a different evolutionary process known as birth-...

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“…These expansions include both intact OR genes as well as pseudogenes and are probably the product of a neutral process of duplication and deletion (Nei et al 2000). Alternatively, these expansions could be the result of species-specific sensory needs, as the number of functional genes within any given OR subfamily may be proportional to the breadth of binding sites within a subfamily (Malnic et al 1999).…”

Section: Discussionmentioning

confidence: 99%

A comparison of the human and chimpanzee olfactory receptor gene repertoires

Gilad¹,

Man²,

Glusman³

2005

Genome Res.

125

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Olfactory receptor (OR) genes constitute the basis of the sense of smell and are encoded by the largest mammalian gene superfamily, with >1000 members. In humans, but not in mice or dogs, the majority of OR genes have become pseudogenes, suggesting that OR genes in humans evolve under different selection pressures than in other mammals. To explore this further, we compare the OR gene repertoire of human with its closest living evolutionary relative, by taking advantage of the recently sequenced genome of the chimpanzee. In agreement with previous reports based on a small number of ORs, we find that humans have a significantly higher proportion of OR pseudogenes than chimpanzees. Moreover, we can reject the possibility that humans have been accumulating OR pseudogenes at a constant neutral rate since the divergence of human and chimpanzee. The comparison of the two repertoires reveals two chimpanzee-specific OR subfamily expansions and three expansions specific to humans. It also suggests that a subset of OR genes are under positive selection in either the human or the chimpanzee lineage. Thus, although overall there is relaxed constraint on human olfaction relative to chimpanzee, species-specific sensory requirements appear to have shaped the evolution of the functional OR gene repertoires in both species.

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Purifying selection and birth-and-death evolution in the ubiquitin gene family

Cited by 133 publications

References 31 publications

Comparative genomic analysis of the mouse and rat amylase multigene family

Comparative genomic analysis of the mouse and rat amylase multigene family

Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data

A comparison of the human and chimpanzee olfactory receptor gene repertoires

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