| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Genetics and Molecular Biology |
ek2
ena Koukalová2
ík2,42Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265 Brno, Czech Republic; 3School of Biological Sciences, Queen Mary University of London, E1 4NS, UK
Received for publication October 24, 2002. Accepted for publication February 14, 2003.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
Key Words: evolution • gene conversion • Nicotiana • ribosomal RNA genes • synthetic allopolyploids • tobacco
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
; Leitch and Bennett, 1997
; Comai, 2000
; Rieseberg, 2001
). Perhaps one of the most defined genetic events associated with allopolyploid speciation involves alterations in the structure, organization, and activity of ribosomal DNA (rDNA). Such change has been reported in natural Gossypium polyploids (Wendel et al., 1995
) and in Nicotiana tabacum (tobacco) (Volkov et al., 1999
) in which interlocus gene conversion has homogenized the 45S rDNA repeat units but not the 5S rDNA repeats (Cronn et al., 1996
; Fulnecek et al., 2002
). In these cases, most of the parental 45S rDNA units have been replaced by novel variants. Rearrangements of the 45S rDNA loci have also been observed in somatic hybrids between Nicotiana and Atropa (Borisjuk et al., 1988
) and between Medicago species (Cluster et al., 1996
). Genetic change can be fast because in descendent progeny of crosses between maize and Tripsacum, a novel restriction site in rDNA arose and became fixed even after elimination of the Tripsacum chromosomes in backcrossing to maize (Lin et al., 1985
). However, changes in rDNA unit structure and organization are not always associated with allopolyploidy. In Brassica (Bennett and Smith, 1991
) and Arabidopsis (Chen et al., 1998
) allopolyploids, the genetic character of the 45S rRNA genes remained stable although epigenetic silencing of expression does occur (Chen and Pikaard, 1997
). However, in one report of a synthetic autotetraploid of Arabidopsis, there is rDNA locus translocation (Weiss and Maluszynska, 2000
). These studies point to differential stability of individual genetic loci in "foreign" environments and to wide variation between plant species.
Tobacco formed up to six million years ago and is a natural allopolyploid between ancestors of the diploid species Nicotiana sylvestris (the maternal S genome donor) and Nicotinana tomentosiformis (the paternal T genome donor [Goodspeed, 1954
; Okamuro and Goldberg, 1985
; Parokonny and Kenton, 1995
; Lim et al., 2000b
]). In this paper we use synthetic tobacco made from these diploid species (Burk, 1973
) to investigate early evolution of rDNA in synthetic allopolyploids. We compare the data with variation found in natural cultivars of tobacco. Making synthetic tobacco plants can be problematic because crosses between Nicotiana species leads to extensive lethality at the seedling stage (Marubashi et al., 1999
). Most attempts to reconstruct the tobacco genome (man-made) have been largely unsuccessful probably due to the high divergence and numerous genetic differences between the parental diploid species; it is estimated that N. tomentosiformis and N. sylvestris had common ancestors 70 million years ago (Uchiyama et al., 1977
). The Th37 line represents one of the successful attempts to reconstruct tobacco. We used 20 randomly selected plants from derivatives of this cross and show patterns of evolution across rDNA loci.
The structure of the 26–18S intergenic spacer (IGS) allows discrimination rDNA units of N. sylvestris and N. tomentosiformis rDNA units in Southern hybridization experiments (Kovarik et al., 1996
; Volkov et al., 1999
). The IGS variability comes from 
1–3 kilobase (kb) (depending on species) subregions termed SR II and SR VI, located upstream and downstream of the transcription starting site (TSS), respectively (Volkov et al., 1999
). In tobacco these subregions are significant target sites of genetic recombination. The SR II subregion is composed of small (15-base pair [bp]) subrepeats (termed C-subrepeats), and the SR VI subregion has longer (140-bp) subrepeats (termed A1/A2 subrepeats) (Volkov et al., 1999
). Advantage of this variability was taken to analyze rDNA evolution in the synthetic tobacco Th37 plants. The data were compared with the variability found in natural cultivars of tobacco and with the distribution of rDNA signals as observed by fluorescent in situ hybridization (FISH).
|
MATERIALS AND METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
N. sylvestris (2n = 24) x 
N. tomentosiformis (2n = 24) and converted to a fertile amphidiploid by in vitro callus culture (S0; Burk, 1973
). From a single regenerated plant, selfed seeds were obtained (S1). In the 1994 regeneration harvest, S4 seeds were obtained and used in this work. These seeds germinated well (>95%), and recovered plants were fertile. Adult plants look phenotypically normal as observed in the S0 generation (Burk, 1973
), were without morphological abnormalities, and had little plant-to-plant variability. The white-pink flowers closely resembled N. tabacum. The following species were used: N. sylvestris Speg. and Comes; N. tomentosiformis Goodsp. cv. TW142 (NPGS, USDA, North Carolina State University, USA) and cv. NIC479/84 (Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany); N. tabacum L. cv. 095–55 (Vielblattriger, SR-1, Samsung, TBY-2 cell cultures were mostly from the Royal Botanic Gardens, Kew, Richmond, London, UK).
DNA isolation, restriction analysis, and Southern blot hybridization
Total genomic DNA was extracted from a young leaf using a slightly modified cetylammonium bromide (CTAB) protocol (Saghai-Maroof et al., 1984
). DNA was digested with an excess of restriction enzymes (2 x 2 h) and subjected to electrophoresis on agarose gels. To each lane 1–3 µg of DNA was loaded to detect high- and medium-copy repeats. Following electrophoresis, the ethidium-bromide-stained gels were photographed, blotted onto membranes (Hybond N+, Amersham Pharmacia, Buckinghamshire, UK), and hybridized to 
32P-labelled DNA probes (>108 dpm (disintegrations per minute)/µg DNA; Dekaprime kit, Fermentas, Vilnius, Lithuania). Southern hybridization was carried out in 0.25 mol/L Na-phosphate buffer, pH 7.0, supplemented with 7% sodium dodecyl sulfate (SDS) at 65°C for 16 h followed by washing with 2x SSC (1x SSC = 150 mmol/L NaCl, 15 mmol/L Na3-citrate, pH 7.0), 0.1% SDS (twice 5 min), 0.2x SSC, and 0.1% SDS (twice 15 min). The membranes were exposed to X-ray film (Medix, Hradec Kralove, Czech Republic) for 4–48 h. A PhosphorImager (Storm, Molecular Dynamics, Sunnyvale, California, USA) and ImageQuant (Molecular Dynamics) software was used to quantify the hybridization signal.
DNA probes
The 18S rDNA probe contained a 1.7-kb EcoRI fragment of the 18S rRNA gene subunit from Solanum lycopersicum (Kiss et al., 1989
; accession number X51576). The 26S rDNA probe was a 220-bp fragment of the 3' end of the tobacco 26S rRNA gene (accession number X76056) and was obtained by PCR amplification of the region between nt 2901 (5'-GAATTCACC CAAGTGTTGGGAT-3') and nt 3121 (5'-AGAGGCGTTCAGTCATAATC-3') with respect to the transcription starting site of the 26S rRNA gene. The IGS probe was a cloned 280-bp ClaI-ClaI fragment of subregion SR VI from N. tomentosiformis IGS (Volkov et al., 1999
; accession number Y08427). Oligonucleotides were synthezed by Generi Biotech (Hradec Kralove, Czech Republic).
Fluorescent in situ hybridization (FISH)
The FISH was carried out as described in Lim et al. (2000b)
. Two cloned probes were used: (1) pTa 71, a cloned 9-kb EcoRI fragment of the 45S rDNA unit from Triticum aestivum (Gerlach and Bedbrook, 1979
) and (2) NTRS, a 212–219 bp monomeric unit organized in tandem array and isolated from N. tomentosiformis (Lim et al., 2000b
). Inserts of five different NTRS clones were randomly ligated and labeled. These probes were used at a concentration of 4 µg/mL. In all, the hybridization mix contained 50% (v/v) formamide, 10% (m/v) dextran sulphate, 0.1% (m/v) sodium dodecyl sulphate in 2x SSC (0.3 mol/L sodium chloride, 0.03 mol/L sodium citrate). For genomic in situ hybridization (GISH), the hybridization mixture contained 8 µg/mL digoxigenin-labeled N. sylvestris DNA, 8 µg/mL biotin-labeled N. tomentosiformis DNA, and 15 µg/mL of blocking DNA. Slides were denatured in 70% formamide in 2x SSC at 70°C for 2 min. After overnight hybridization at 37°C, the slides were washed in 20% (v/v) formamide in 0.1x SSC at 42°C at an estimated hybridization stringency of 80–85%. Sites of probe hybridization were detected using 20 µg/mL fluorescein-conjugated anti-digoxigenin IgG (Roche Biochemicals, Sussex, UK) and 5 µg/mL Cy3-conjugated avidin (Amersham Pharmacia Biotech). Chromosomes were counterstained with 2 µg/mL 4',6-diamidino-2-phenylindole (DAPI) in 4x SSC, mounted in Vectashield (Vector Laboratories, Peterborough, UK) medium, examined using a Leica DM RA2 (Solms, Germany). Images were captured using Openlab (Improvision, Coventry, UK) and processed using Adobe Photoshop (Adobe Systems, Edinburgh, UK) by treating all images for color contrast and brightness uniformly.
|
RESULTS |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
|
mapped this gene family to chromosome 11 (or 10) (chromosome 6 by their nomenclature). The genetic origin of the bands was confirmed by BstNI/StuI double digestion, which takes advantage of three StuI sites in SR II of N. sylvestris that are absent in N. tomentosiformis. In both the hybrids and in N. sylvestris, StuI digested most DNA in the 2.4–3.1 kb BstNI generated fractions into the 1.4–1.6 kb bands.
|
) followed by hybridization with the 26S rDNA probe produced a single 5.4-kb band as expected from the published sequence (Fig. 2). The N. tomentosiformis-donated 5.4-kb BstNI band was only detected in plants 1 and 9 (Fig. 2A). The absence of this band in plants 2, 3, 4, 5, 8, and 12 indicates a loss of this parental N. tomentosiformis gene family. The elimination of the band was always accompanied by the appearance of extra 6.4-kb, 6.6-kb (weak), and 7.3-kb bands (marked by asterisks on Fig. 2A, B). To discover the origin of the novel BstNI-generated bands, double digestion experiments with BstNI and EcoRV were carried out because there is an EcoRV site within the IGS of N. tomentosiformis but not N. sylvestris (Fig. 1 and Volkov et al., 1999
). The BstNI fragments of N. tomentosiformis were shortened by about 0.5 kb after EcoRV digestion (Fig. 2B). In the hybrids, the normal N. tomentosiformis-derived BstNI band, and the novel hybrid-specific BstNI bands, were also digested with EcoRV to give fragments that are about 0.5 kb shorter (Fig. 2B). These data, combined with the BstNI/StuI double digests (Fig. 2A), indicate that the novel hybrid-specific bands were derived from N. tomentosiformis rDNA. It may be significant that the strong novel BstNI bands are most similar, but not identical, to BstNI restriction fragments from N. otophora (Fig. 2C).
rDNA evolution in the SR VI subregions of the IGS
To search for IGS polymorphisms in the SR VI subregion, genomic DNAs were digested with PaeI and hybridized with the IGS probe. PaeI cuts both 5' and 3' to the SR VI subregion and excises the cluster of the A1/A2 subrepeats (Fig. 1). This restriction enzyme can therefore be used to find deletions or amplifications in this region. The IGS probe hybridized to a single PaeI fragment in N. tomentosiformis (2.3 kb) and to two fragments (1.2 kb, major; 2.2 kb, minor) in N. sylvestris (Fig. 3A). The probe was derived from N. tomentosiformis IGS and has less homology to N. sylvestris, resulting in a weaker hybridization signal. In all the hybrids, the probe hybridized to 1.2-kb and 2.2-kb fragments indicating a lack of change in the N. sylvestris-derived units. The probe strongly hybridized to the N. tomentosiformis-derived 2.3-kb band in hybrid plants 1, 9, and 16. However, the majority of hybrid plants lacked the N. tomentosiformis-derived parental band and had instead novel bands of 2.7 and 3.1 kb, and in some cases, 4.2 kb as well. Because the size of the novel bands was significantly larger than any of the parental bands, the novel rDNA variants may have arisen through amplification of the A1/A2 subrepeats. Plant 1 (Fig. 3A) is interesting because it has the three novel bands and the parental N. tomentosiformis-derived band. This mixed pattern of bands can be explained either by incomplete intralocus gene conversion of N. tomentosiformis-derived units or by locus heterozygosity.
|
Localization of rDNA genes on chromosomes
An analysis of all 20 Th37 hybrid plants for restriction polymorphisms in the SR II and SR VI subregions enabled the identification of three distinct groups of plants (Table 1) and the selection of individual plants for FISH analysis. Plants in group I have an rDNA restriction pattern that is additive of that found in the parents. Group II comprises two plants that have the parental units and additional novel units derived from N. tomentosiformis rDNA. In group III, the N. tomentosiformis-derived units are completely replaced by novel variants that have arisen through amplification of the A1/A2 subrepeats. The synthetic plant numbers 9, 1, and 8, representatives of groups I to III, respectively (Table 1), were analyzed by FISH (Fig. 4A–C). Plants 1 and 8 have a chromosome number of 2n = 48; plant 9 is aneuploid (2n = 49) and has an extra chromosome of N. tomentosiformis origin. There were significant differences in the organization of repeat sequences between these plants, the subject of another paper. Here the distribution of rDNA is presented.
|
|
Plant 1 has the four rDNA loci inherited from the parents and an additional rDNA locus on one of the T4 chromosomes. The second homologue does not carry visible rDNA units. The identity of the T4 chromosome was determined by a bright red interstitial band on the long arm when probed by GISH using N. tomentosiformis genomic DNA (Fig. 4D); a similar morphology is observed when normal tobacco is probed (Lim et al., 2000a
). These T4 homologues have a small terminal translocation of N. sylvestris origin (see Fig. 4D, arrow) a feature not found in natural tobacco. Plant 8 has both T4 chromosomes with rDNA sites giving the plant 10 rDNA sites in root-tip metaphases.
IGS variability in natural cultivars of tobacco
Because the structure of the IGS in the 20 analyzed hybrid plants varied considerably, IGS variability was analyzed in natural cultivars of tobacco. Four tobacco cultivars (cvs. Vielblattriger, 095–55, Samsung, SR-1), a callus culture of cv. Vielblattriger and TBY-2 long-term suspension culture were analyzed by restriction digestion with EcoRV and probing with 18S rDNA (Fig. 5). A single EcoRV site is found in sequenced N. sylvestris rDNA. The enzyme generates an 10-kb rDNA band from N. sylvestris genomic DNA. Two EcoRV sites are found in most N. tomentosiformis rDNA units (Fig. 1), and when genomic DNA is digested with this enzyme, a predominant rDNA band at 4.8 kb is generated. However, a small fraction of units lacks the EcoRV second site and rDNA unit monomers of 12 kb are also observed. The 10-kb EcoRV restriction fragment of N. sylvestris-origin is observed at a variable but low abundance in all cultivars and cultured tobacco materials. Likewise, the predominant 4.8-kb band observed in N. tomentosiformis is also observed in all tobaccos except for cv. SR-1. However, the major rDNA fraction was always a 5.6-kb band consistent with the sequence of major tobacco rDNA unit (Volkov et al., 1999
). A further uncharacterized rDNA variant of 6.2 kb is observed in cvs. Samsung and Vielblattriger. Lim et al. (2000a)
showed that about 8% of total rDNA in N. tabacum cv. 095-55 is of N. sylvestris origin. Here again this can be seen, but some cultivars, especially cv. SR1, have a higher proportion of N. sylvestris units. Thus, although the pattern of bands is similar between cultivars and cultures, the relative abundance of unit types is variable.
|
|
DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
), has a complex evolutionary history across rDNA units (Volkov et al., 1999
; Lim et al., 2000a
). Analyses of tobacco rDNA have shown that most units are of a novel type, closely similar to N. tomentosiformis but differing in the structure of the IGS (Kovarik et al., 1996
; Volkov et al., 1999
; Lim et al., 2000a
). The N. sylvestris-type rDNA units in tobacco might be expected to occur at three of the four rDNA loci and form about 75% of the total rDNA units. However, analyses show that they occur at a much lower frequency (Fig. 5). It is assumed that genetic change through intra- and interlocus gene conversion has altered the rDNA unit array in tobacco evolution. Questions arise as to the time frame of these changes, the factors that govern the direction and occurrence of change, and whether allopolyploidy plays a role. To address these questions, the structure and distribution of rDNA was analyzed in synthetic tobacco plants made by Burk (1973)
.
Novel rDNA units in synthetic tobacco hybrid plants
The synthetic tobacco plants showed remarkable polymorphism in rDNA, particularly in rDNA units derived from N. tomentosiformis. Only three plants out of 20 analyzed had the additive pattern of rDNA units found in the parents. In most plants (75%), the parental N. tomentosiformis rDNA cluster comprising about 2000 copies (Lim et al., 2000a
), was largely but not completely replaced by a novel hybrid-specific cluster of comparable abundance. All the novel rDNA variants were of N. tomentosiformis origin, but were 1–3 kb larger and contained enlarged SR II and SR VI domains, indicating amplification of both the C and A subrepeats of the IGS. Two plants with novel units had also inherited parental rDNA units from both N. sylvestris and N. tomentosiformis. The units derived from the N. sylvestris parent have not undergone any detectable structural change, but there are changes in the relative abundance of the three unit families. One family in particular (generating a 2.4-kb band in BstNI digests, Fig. 2A) was underrepresented in all hybrid plants. Fluorescent in situ hybridization (FISH) with three plants revealed that one locus, here called S12, was large compared to N. sylvestris and natural tobacco. It is assumed that rDNA units of N. sylvestris origin have amplified at this locus. Often this rDNA locus remains fully condensed at all stages of the cell cycle.
The data suggest that rDNA has rapidly evolved in the synthetic tobacco plants within a few generations. The change is marked by an altered abundance of gene families, including the loss of families and the evolution of novel units or, alternatively, the amplification of rare units. It is unlikely that the molecular rearrangements were caused by callus culture for the following reasons: (1) There is a plant-to-plant variability in rDNA restriction polymorphisms. Since the Th37 line was derived from doubled hybrid material, heterozygosity must have occurred after this event, after the doubled material was removed from the culture. This mode of synthetic plant generation and the relatively uniform rDNA patterns across different diploid species varieties also exclude the possibility of heterozygosity in the parents being transmitted to the polyploids. (2) The spectrum of rDNA unit variants is fairly stable in Nicotiana callus culture, long-term TBY-2 cell culture (Fig. 5), and in F1 hybrids of N. sylvestris and N. tomentosiformis (K. Skalická, unpublished data). Thus, the changes reported are probably occurring subsequent to tissue culture and after polyploidization.
Structural change in rDNA units occurring through amplification of intergeneric spacer (IGS) subrepeats has also been observed in rice plants that recovered from radiation stress (Fukuoka et al., 1994
), in interspecific somatic hybrids of Medicago species (Cluster et al., 1996
), and in N. tabacum x Atropa belladonna (Borisjuk et al., 1988
). Strikingly, in the latter, the parental tobacco variants (that are structurally related to those of N. tomentosiformis) have been largely eliminated and replaced by novel types. As in our study, the novel rDNA variants contained amplified subrepeats. Perhaps there is a tendency towards amplification of subrepeats within the unit followed by amplification of the unit itself. It is known that the IGS contains gene promoters and regulators controlled in part by epigenetic modifications (e.g., Chen and Pikaard, 1997
). Possibly changes to the IGS structure alters rDNA activity and enhances the stability of the newly constituted genomic organization.
The number and distribution of rDNA sites
Synthetic tobacco plant 9 has the expected number of rDNA sites with loci found on chromosomes T3, S10, S11, and S12. Thus, root tip metaphases have eight rDNA sites as in natural tobacco. However, this is not observed in the other synthetic plants (plants 1 and 8) in which additionally one or both T4 homologues also have a novel rDNA locus. Clearly, segregation of the heterozygous T4 chromosome pair in plant 1 can give rise to plants that have either 8, 9, or 10 rDNA loci, as observed in plants 9, 1, and 8, respectively. It is significant that the additional site is on chromosome T4 because all species in section Tomentosae, except N. tomentosiformis, has two rDNA loci on chromosomes 3 and 4, respectively (Lim et al., 2000b
). Thus, the evolutionary loss of the rDNA locus on N. tomentosiformis chromosome 4 appears to be reversed in some of these synthetic hybrids. Interestingly, tobacco cv. 35466 has been reported to contain two rDNA loci on T-genome chromosomes (Kenton et al., 1993
). Perhaps evolutionary processes similar to the ones observed in the hybrid material has occurred in tobacco cv. 35466.
rDNA unit evolution at a new rDNA locus
There is compelling evidence that the novel rDNA units occur at the novel rDNA locus. Plant 9 (as a representative of group I) has unchanged parental rDNA units (Table 1) and a distribution of rDNA loci that reflects the parents, i.e., no major change to rDNA is observed. In contrast, plant 1 (group II) and plant 8 (group III) have novel rDNA unit structures and novel rDNA sites on one or both T4 chromosomes. The molecular and cytological observations are probably linked and the novel units are localized on the T4 chromosome. This would explain group II plants with parental and novel rDNA units on chromosomes T3 and T4, respectively. However, in the majority of plants (group III), the novel units must have been replaced by all the parental N. tomentosiformis units and must have amplified across the T3 locus. If the novel units did originally arise on chromosome T4, then amplification and replacement of units at the T3 locus must have involved inter- and intralocus gene conversion. Certainly within a few generations, and from a single plant, the units of N. tomentosiformis origin have undergone complex genetic changes involving the generation and spread of novel rDNA variants.
The locus on chromosome T4 has either arisen de novo or by amplification of a few relic units on this chromosome. Perhaps a few units on N. tomentosiformis chromosome 4 have been missed by Southern and fluorescent in situ hybridization and become amplified in most of these hybrids. There is similarity between the rDNA restriction pattern of N. otophora and the novel rDNA bands particularly at the 5' end of IGS (plant 8, Fig. 2C), although there is none at the 3' end, where much polymorphism occurs in the hybrids (Fig. 3B). However, the similarity that does exist, and the location of novel units on chromosome T4, might point towards the amplification of relic, ancestral Tomentosae units on this chromosome in the hybrid plants. If so, residual copies on chromosome T4 could have been rearranged and amplified as a consequence of genomic stress generated by the fusion of distantly related genomes as described in the "library hypothesis" of satellite repeat evolution (Salser et al., 1976
).
Factors influencing rDNA unit evolution in hybrid tobacco and tobacco cultivars
In all tobacco cultivars and cultures examined, the N. sylvestris-derived rDNA units are in a minority. However, their relative abundance does fluctuate between lines, demonstrating that the distribution of family members is not fixed or stable in tobacco. Overall, bands are less complex in natural tobacco than in the hybrids or in the parents taken together. Possibly after an initial burst of rDNA evolution associated with allopolyploid formation, there is a tendency towards reduced complexity over time. This process may be enhanced by inbreeding and selfing to generate the cultivars.
In the hybrid material, there is no evidence of intergenomic (between S and T genome) gene conversion as observed in natural tobacco. Perhaps interlocus gene conversion between the parental genomes contrast with intragenomic gene conversion in being slower and requiring many more generations than have occurred in the synthetic tobacco. This may be supported by studies on synthetic allopolyploids of Gossypium that retain the parental identity of rDNA units while there is evidence for concerted evolution in natural species (Wendel et al., 1995
).
Despite the small change in the balance of family units derived from N. sylvestris in the hybrid plants, most change was observed in the N. tomentosiformis-derived units. There are several explanations for this. (1) Gene conversion of rDNA units might be a genome specific or dependent on parental origin. The nuclear-cytoplasmic interaction hypothesis of Gill (1991)
suggests that the paternal donor may be more vulnerable to genetic change in a newly formed hybrid because it is exposed to the "hostile" environment of maternal cytoplasm. Certainly, several nontranscribed repeats specific for the paternal N. tomentosiformis genome have been lost in many of these hybrid plants (K. Skalická, unpublished data). (2) The A1/A2 subrepeats in the SR VI subregion of the IGS are more homogenous in N. tomentosiformis than in N. sylvestris. Perhaps mutual homology between subrepeats together with the amplification promoting (aps) element (Borisjuk et al., 2000
) could contribute to recombination potential. (3) Intra- and/or interlocus gene conversion might be influenced by gene/locus activity at interphase. Lim et al. (2000a)
proposed that activity at interphase, and within the domain of the nucleolus, can result in rDNA units being vulnerable to genetic change by gene conversion. Activity of rDNA is known to be influenced by cytosine methylation. In N. tomentosiformis much rDNA at interphase is more decondensed, relatively hypomethylated, and more homogenized compared with N. sylvestris rDNAs (Lim et al., 2000a
; Chen et al., 2002
).
|
FOOTNOTES |
|---|
4 Author for reprint requests (kovarik{at}ibp.cz
)
|
LITERATURE CITED |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
Borisjuk N. L. Borisjuk S. Komarnytsky S. Timeva V. Hemleben Y. Gleba I. Raskin 2000 Tobacco ribosomal DNA spacer element stimulates amplification and expression of heterologous genes. Nature Biotechnology 18: 1303-1306[CrossRef][ISI][Medline]
Borisjuk N. V. V. P. Momot Y. Y. Gleba 1988 Novel class of rDNA repeat units in somatic hybrids between Nicotiana and Atropa. Theoretical Applied Genetics 76: 108-112[CrossRef]
Burk L. G. 1973 Partial self-fertility in a theoretical amphiploid progenitor of N. tabacum. Journal of Heredity 64: 348-350
Chen C. C. S. K. Chen M. C. Liu Y. Y. Kao 2002 Mapping of DNA markers to arms and sub-arm regions of Nicotiana sylvestris chromosomes using aberrant alien addition lines. Theoretical and Applied Genetics 105: 8-15[CrossRef][ISI][Medline]
Chen Z. J. L. Comai C. S. Pikaard 1998 Gene dosage and stochastic effects determine the severity and direction of uniparental ribosomal RNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids. Proceedings of National Academy of Sciences, USA 95: 14891-14896
Chen Z. J. C. S. Pikaard 1997 Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance. Genes and Development 11: 2124-2136
Cluster P. D. O. Calderini F. Pupilli F. Crea F. Damiani S. Arcioni 1996 The fate of ribosomal genes in three interspecific somatic hybrids of Medicago sativa: three different outcomes including the rapid amplification of new spacer-length variants. Theoretical and Applied Genetics 93: 801-808[ISI]
Comai L. 2000 Genetic and epigenetic interactions in allopolyploid plants. Plant Molecular Biology 43: 387-399[CrossRef][ISI][Medline]
Cronn R. C. X. Zhao A. H. Paterson J. F. Wendel 1996 Polymorphism and concerted evolution in a tandemly repeated gene family: 5S ribosomal DNA in diploid and allopolyploid cottons. Journal of Molecular Evolution 42: 685-705[CrossRef][ISI][Medline]
Fukuoka H. Y. Kageyama K. Yamamoto G. Takeda 1994 Rapid conversion of rDNA intergenic spacer of diploid mutants of rice derived from gamma-ray irradiated tetraploids. Molecular and General Genetics 243: 166-172
Fulnecek J. K. Y. Lim A. R. Leitch A. Kovarik R. Matyasek 2002 Evolution and structure of 5S rDNA loci in allotetraploid Nicotiana tabacum and its putative parental species. Heredity 88: 19-25[CrossRef][ISI][Medline]
Gerlach W. L. J. R. Bedbrook 1979 Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Research 7: 1869-1885
Gill B. S. 1991 Nucleocytoplasmic interactions (NCI) hypothesis of genome evolution and speciation in polyploid plants. In J. Sasakuma and T. Kinoshita [eds.], Proceedings of the Kihara Memorial International Symposium on cytoplasmis engineering in wheat, 48–53. Kihara Memorial Yokohama Foundation for the Advancement of Science, Yokohama, Japan
Goodspeed T. H. 1954 The genus Nicotiana. Chronica Botanica, Waltham, Massachusetts, USA
Kenton A. A. S. Parokonny Y. Y. Gleba M. D. Bennett 1993 Characterization of the Nicotiana tabacum L. genome by molecular cytogenetics. Molecular and General Genetics 240: 159-169
Kiss T. A. Szkukalek F. Solymosy 1989 Nucleotide sequence of a 17S (18S) rRNA gene from tomato. Nucleic Acids Research 17: 2127.
Kovarik A. J. Fajkus B. Koukalova M. Bezdek 1996 Species-specific evolution of telomeric and rDNA repeats in the tobacco composite genome. Theoretical and Applied Genetics 8: 1108-1111
Leitch I. J. M. D. Bennett 1997 Polyploidy in angiosperms. Trends in Plant Science 2: 470-476[CrossRef][ISI]
Lim K. Y. A. Kovarik R. Matyasek M. Bezdek C. P. Lichtenstein A. R. Leitch 2000a Gene conversion of ribosomal DNA in Nicotiana tabacum is associated with undermethylated, decondensed and probably active gene units. Chromosoma 109: 161-172[CrossRef][ISI][Medline]
Lim K. Y. R. Matyasek C. P. Lichtenstein A. R. Leitch 2000b Molecular cytogenetic analyses and phylogenetic studies in the Nicotiana section Tomentosae. Chromosoma 109: 245-258[CrossRef][ISI][Medline]
Lin L.-S. T. D. Ho J. R. Harlan 1985 Rapid amplification and fixation of new restriction sites in the ribosomal DNA repeats in the derivatives of a cross between maize and Tripsacum dactyloides. Developmental Genetics 6: 101-112
Marubashi W. T. Yamada M. Niwa 1999 Apoptosis detected in hybrids between Nicotiana glutinosa and N. repanda expressing lethality. Planta 210: 168-171[CrossRef][ISI][Medline]
Murad L. K. Y. Lim V. Christopodulou R. Matyasek C. P. Lichtenstein A. Kovarik A. R. Leitch 2002 The origin of tobacco's T genome is traced to a particular lineage within Nicotiana tomentosiformis (Solanaceae). American Journal of Botany 89: 921-928
Okamuro J. K. R. B. Goldberg 1985 Tobacco single-copy DNA is highly homologous to sequences present in the genomes of its diploid progenitors. Molecular and General Genetics 198: 290-298[CrossRef]
Parokonny A. S. A. Y. Kenton 1995 Comparative physical mapping and evolution of the Nicotiana tabacum L. karyotype. In P. E. Brandham and M. D. Bennet [eds.], Kew Chromosome Conference IV, 301–320. Royal Botanic Gardens, Kew, UK
Rieseberg L. H. 2001 Polyploid evolution: keeping the peace at genomic reunions. Current Biology 11: R925-928[CrossRef][ISI][Medline]
Saghai-Maroof M. A. K. M. Soliman R. A. Jorgensen R. W. Allard 1984 Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proceedings of National Academy of Sciences, USA 81: 8014-8018
Salser W. S. Bowen D. Browne F. el-Aldi N. V. Fedoroff K. Fry H. Heindell G. Paddock R. Poon B. Wallace P. Whitcome 1976 Investigation of the organisation of mammalian chromosomes at the DNA sequence level. Federal Proceedings 35: 23-35
Soltis D. E. P. S. Soltis 1995 The dynamic nature of polyploid genomes. Proceedings of National Academy of Sciences, USA 92: 8089-8091
Uchiyama H. K. Chen S. G. Wildman 1977 Polypeptide composition of fraction I protein as an aid in the study of plant evolution. Stadler Symposium 9: 83-99
Volkov R. A. N. V. Borisjuk I. I. Panchuk D. Schweizer V. Hemleben 1999 Elimination and rearrangement of parental rDNA in the allotetraploid Nicotiana tabacum. Molecular Biology and Evolution 16: 311-320[Abstract]
Weiss H. J. Maluszynska 2000 Chromosomal rearrangement in autotetraploid plants of Arabidopsis thaliana. Hereditas 133: 255-261[CrossRef][ISI][Medline]
Wendel J. F. A. Schnabel T. Seelanan 1995 Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton (Gossypium). Proceedings of the National Academy of Sciences, USA 92: 280-284
This article has been cited by other articles:
|
|
 |
|
  A. Guggisberg, C. Baroux, U. Grossniklaus, and E. Conti Genomic Origin and Organization of the Allopolyploid Primula egaliksensis Investigated by in situ Hybridization Ann. Bot., May 1, 2008; 101(7): 919 - 927. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. J. Leitch, L. Hanson, K. Y. Lim, A. Kovarik, M. W. Chase, J. J. Clarkson, and A. R. Leitch The Ups and Downs of Genome Size Evolution in Polyploid Species of Nicotiana (Solanaceae) Ann. Bot., April 1, 2008; 101(6): 805 - 814. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Kovarik, M. Dadejova, Y. K. Lim, M. W. Chase, J. J. Clarkson, S. Knapp, and A. R. Leitch Evolution of rDNA in Nicotiana Allopolyploids: A Potential Link between rDNA Homogenization and Epigenetics Ann. Bot., April 1, 2008; 101(6): 815 - 823. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Y. Lim, R. Matyasek, A. Kovarik, and A. Leitch Parental Origin and Genome Evolution in the Allopolyploid Iris versicolor Ann. Bot., August 1, 2007; 100(2): 219 - 224. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. R.D. Ganley and T. Kobayashi Highly efficient concerted evolution in the ribosomal DNA repeats: Total rDNA repeat variation revealed by whole-genome shotgun sequence data Genome Res., February 1, 2007; 17(2): 184 - 191. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Y. Lim, K. Souckova-Skalicka, V. Sarasan, J. J. Clarkson, M. W. Chase, A. Kovarik, and A. R. Leitch A genetic appraisal of a new synthetic Nicotiana tabacum (Solanaceae) and the Kostoff synthetic tobacco Am. J. Botany, June 1, 2006; 93(6): 875 - 883. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Koukalova, M. Fojtova, K. Y. Lim, J. Fulnecek, A. R. Leitch, and A. Kovarik Dedifferentiation of Tobacco Cells Is Associated with Ribosomal RNA Gene Hypomethylation, Increased Transcription, and Chromatin Alterations Plant Physiology, September 1, 2005; 139(1): 275 - 286. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Kovarik, J. C. Pires, A. R. Leitch, K. Y. Lim, A. M. Sherwood, R. Matyasek, J. Rocca, D. E. Soltis, and P. S. Soltis Rapid Concerted Evolution of Nuclear Ribosomal DNA in Two Tragopogon Allopolyploids of Recent and Recurrent Origin Genetics, February 1, 2005; 169(2): 931 - 944. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Pires, K. Y. Lim, A. Kovarik, R. Matyasek, A. Boyd, A. R. Leitch, I. J. Leitch, M. D. Bennett, P. S. Soltis, and D. E. Soltis Molecular cytogenetic analysis of recently evolved Tragopogon (Asteraceae) allopolyploids reveal a karyotype that is additive of the diploid progenitors Am. J. Botany, July 1, 2004; 91(7): 1022 - 1035. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Y. Lim, K. Skalicka, B. Koukalova, R. A. Volkov, R. Matyasek, V. Hemleben, A. R. Leitch, and A. Kovarik Dynamic Changes in the Distribution of a Satellite Homologous to Intergenic 26-18S rDNA Spacer in the Evolution of Nicotiana Genetics, April 1, 2004; 166(4): 1935 - 1946. [Abstract] [Full Text] [PDF]
|
|
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
