Rapid evolution of parental rDNA in a synthetic tobacco allotetraploid line

Skalická, Kamila; Lim, K. Yoong; Matyášek, Roman; Koukalová, B.; Leitch, Andrew R.; Kovařı́k, Aleš

doi:10.3732/ajb.90.7.988

Cited by 79 publications

(110 citation statements)

References 29 publications

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“…A rapid homogenization model of concerted evolution is consistent with the results from numerous previous studies (Liao et al 1997;Scott 1998, 2002;Skalicka et al 2003;Averbeck and Eickbush 2005;Kovarik et al 2005). Furthermore, rDNA polymorphisms between individuals in a population (e.g., Carbone and Kohn 2001;James et al 2001;Ganley et al 2005) are also evidence for rapid homogenization.…”

Section: Discussionsupporting

confidence: 79%

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.

328

268

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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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Section: Discussionsupporting

confidence: 79%

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.

328

268

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“…From the previous information, the size of 45S rDNA site might vary among the cucumber cultivars. The similar phenomenon has been observed in several plant species (Schubert and Wobus 1985, Hall and Parker 1995, Galasso et al 1998, Baeza et al 2007, and such a difference often occurs in a process of the speciation in plants ( Thomas et al 1996, Skalicka et al 2003. Variation of numbers of the rDNA site in cucumber, which was observed as a difference of small rDNA site, might be due to variation of copy number of rDNA sequence and/or difference of FISH procedure.…”

Section: Discussionmentioning

confidence: 68%

Cytogenetic comparison among three cultivars of cucumber (Cucumis sativus L.) by using post-heated DAPI band, 45S and 5S rDNA sites

et al. 2009

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ABSTRACT. The positions of heterochromatic bands, 45S and 5S rDNA regions were detected on the chromosomes in three cultivars of cucumber (Cucumis sativus L.). The post-heated DAPI bands, which revealed heterochromatic region, were observed on the both terminal and pericentromeric regions of most of the chromosomes in three cultivars. However, these band patterns were different between European and Eastern Asian cultivars. The major 45S rDNA sites were found around the centoromeric region of the chromosomes 1, 2 and 5, and the minor 45S rDNA sites were found around centoromeric region of the chromosomes 3 and 7. The positional variation of this region was not found among three cultivars, but size difference was observed in the chromosome 5. The 5S rDNA site was observed on the interstitial region of the chromosome 6 in all of the cultivars studied. These results indicated that the variation of chromosome structure among cucumber cultivars occurred in the heterochromoatic region and suggested that the genetic variation in cucumber cultivars would be revealed by strict analysis and comparison for the position and size of heterochromatic region.

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“…The other possibility is the case where parental IGS variants are not represented in the interspecific hybrid or autopoliploid, as in the genera Nicotiana (Kovarik et al 1996), Oryza (Cordesse et al 1990) and Medicago (Cluster et al 1996). The studies by Skalická et al (2003) in a synthetic tobacco allotetraploid line are interesting as well; he observed that unidirectional gene conversion of rDNA untis may occur and also that newly amplified rDNA units may be identified.…”

Section: Discussionmentioning

confidence: 91%

“…Polyploidization of O. tuberosa may resemble the case where parental IGS variants are not represented in the interspecific hybrid or autopoliploid (Kovarik et al 1996;Cordesse et al 1990;Cluster et al 1996;Skalická et al 2003). Other possibility could be that the diploid species included in this study were not involved in the octoploid origin, in this case, the IGS pattern revealed for O. tuberosa was unique enough to be a useful tool for prospection in other species that belong to the O. tuberosa chromosome alliance.…”

Section: Discussionmentioning

confidence: 94%

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Characterization of the nuclear ribosomal DNA unit in Oxalis tuberosa Oxalidacea and related species

Tosto¹,

Hopp²

2008

Electron. J. Biotechnol.

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Rapid evolution of parental rDNA in a synthetic tobacco allotetraploid line

Cited by 79 publications

References 29 publications

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

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

Cytogenetic comparison among three cultivars of cucumber (Cucumis sativus L.) by using post-heated DAPI band, 45S and 5S rDNA sites

Characterization of the nuclear ribosomal DNA unit in Oxalis tuberosa Oxalidacea and related species

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