| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Genetics and Molecular Biology |
2Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; 3National Institute for Working Life, SE-907 13 Umeå, Sweden
Received for publication May 2, 2002. Accepted for publication August 8, 2002.
 |
ABSTRACT |
|---|
 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
Key Words: concerted evolution • Pinaceae • Pinus • 5S rDNA • sequence heterogeneity
|
INTRODUCTION |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
; Sastri et al., 1992
). The 5S rDNA repeat usually consists of a 120-base pair (bp) genic region and a nontranscribed spacer of variable length. The 120-bp genic region is conservative and can be aligned well at broad taxonomic levels (Szymanski et al., 1998
). The intergenic spacer region is much more variable among plant taxa and ranges in size from 100 to 700 bp (Cox, Bennett, and Dyer, 1992
; Sastri et al., 1992
). The number of repeats per genome can vary from less than 1000 to over 100 000 (Schneeberger, Creissen, and Cullis, 1989
; Sastri et al., 1992
; Cronn et al., 1996
). As in other tandemly repeated multigene families, multiple copies of rDNA families can undergo concerted evolution due to homogenizing forces. This can result in sequences of all gene copies of such a family being virtually identical within a species, despite the presence of normal levels of divergence between orthologous genes in different species (Brown, Wensink, and Jordan, 1972
; Arnheim et al., 1980
; Dover, 1982
; Nagylaki, 1990
; Ohta, 1990
; Wendel, Schnabel, and Seelanan, 1995
). Mechanisms most commonly invoked to explain homogenization are gene conversion, unequal crossing over, and gene amplification/deletion (Smith, 1976
; Nagylaki and Petes, 1982
; Hillis et al., 1991
; Li, 1997
; Liao, 2000
). Nevertheless, in several plant groups, sequence heterogeneity among 5S rDNA repeats within individual arrays and genomes has been reported, indicating that the homogenizing forces have not been strong enough to overcome processes that generate variation (Gottlob-McHugh et al., 1990
; Gorman, Teasdale, and Cullis, 1992
; Kellogg and Appels, 1995
; Cronn et al., 1996
; Campbell et al., 1997
).
The structure and organization of 5S rDNA in gymnosperms is little known, although studies on 5S rDNA repeat composition have been reported for a limited number of Pinaceae species. In Picea glauca (Brown and Carlson, 1997
), Pseudotsuga menziesii (Amarasinghe and Carlson, 1998
), Larix decidua, and L. kaempferi (Trontin, Grandemange, and Favre, 1999
), 5S rDNA repeats vary in size from 220 to 880 bp and are mainly located at one or a few chromosomal site(s). In Pinus radiata, 5S rDNAs exist in two repeat size classes (850 bp and 525 bp), but they are dispersed among all the chromosomes, with approximately 3000 copies per diploid genome organized in tandem arrays (Gorman, Teasdale, and Cullis, 1992
; Moran et al., 1992
). In a recent study, we analyzed the chromosomal locations of 5S rDNA in five Asian pines using fluorescence in situ hybridization (Liu et al., 2002
) and detected one major and one minor 5S rDNA site in each species. These studies provided basic information on 5S rDNA distribution and repeat composition in different Pinaceae species. However, the lack of intragenomic sampling of repeat sequences prevented detailed evaluation of the degree of sequence divergence, either within individual genomes or between closely related species, and therefore, analysis of 5S rDNA evolution in Pinaceae.
In the present study we analyzed patterns of 5S rDNA sequence variation in five Asian Pinus species through cloning and sequencing multiple 5S rDNA repeats from individual trees of P. tabuliformis, P. yunnanensis, P. massoniana, P. densata, and P. bungeana. Pinus bungeana is from the subgenus Strobus (haploxylon) while the other four species are from the subgenus Pinus (diploxylon), sect. Pinus, subsect. Sylvestres (Little and Critchfield, 1969
). During the Cretaceous the genus was already differentiated into the two subgenera (Millar, 1998
; Wang, Tank, and Sang, 2000
), and at many gene loci there is distinct divergence between them (Liston et al., 1999
; Wang et al., 1999
; Wang, Tank, and Sang, 2000
). This led us to ask whether 5S rDNA sequences would reveal the same pattern. Pinus densata is of hybrid origin with P. tabuliformis and P. yunnanensis as its parents according to allozyme, chloroplast, and mitochondrial DNA data (Wang and Szmidt, 1994
; Wang, Szmidt, and Savolainen, 2001
; Song et al., 2002
). We hypothesized that at nrDNA loci polymorphic parental types might be maintained in the hybrid genome. Therefore, our aims in this study were to characterize the structural features of 5S rDNA in pines, to quantify intragenomic and interspecific 5S rDNA divergence and, thus, understand the patterns of 5S rDNA evolution, and to characterize the 5S rDNA repeat types in the hybrid genome.
|
MATERIALS AND METHODS |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
). Pd-s has P. yunnanensis as maternal parent and P. tabuliformis as paternal parent while the parentage of Pd-t is reversed, with P. tabuliformis as maternal parent and P. yunnanensis as paternal parent.
|
). Primers (5'-TCCCATCAGAACTCCGCAG-3' and 5'-ATCCGGTGCATTAACGCTGG-3') for polymerase chain reaction (PCR) amplification of 5S rDNA were designed based on the 5S rRNA gene of Picea glauca (Brown and Carlson, 1997
). High fidelity Taq DNA polymerase, TaKaRa Ex Taq (TaKaRa Biotech, Shiga, Japan), was used in the PCR amplifications. The PCR conditions for 5S rDNA amplification were as follows: 95°C for 2 min, followed by 35 cycles of 94°C for 30 s, 55°C for 20 s, and 72°C for 25 s; the final step at 72°C was extended to 10 min. The PCR products were separated by agarose gel electrophoresis. The four diploxylon pines gave a main band about 700 bp in length and in P. bungeana the main band was about 500 bp. The predominant PCR products were purified with a GFX PCR DNA and Gel Band Purification Kit (Amersham Biosciences, Uppsala, Sweden), cloned into the TA vector, and transformed into JM109 cells using the pGEM-T Easy Vector System II (Promega, Madison, Wisconsin, USA).
We isolated 10–31 clones for each individual tree. Plasmid DNAs were extracted by the mini alkaline lysis method (Ausubel et al., 1995
). Sequencing reactions were carried out with T7 and SP6 vector primers using a BigDye Terminator Cycle Sequencing Ready Reaction Kit v2.0 (Applied Biosystems, Foster City, California, USA) and sequencing was performed using an ABI 377 sequencer (Applied Biosystems). All clones were sequenced from both directions. Unique clone sequences have been submitted to GenBank (Table 1).
Sequence analysis
Sequences were aligned using ClustalX software (Thompson et al., 1997
) and further modified manually. Separate alignments were made for clones from each individual, for the four diploxylon pines and for all five pines. Sequence divergence, within individuals and between species, was computed as the mean number of nucleotide differences per site between pairs of sequences according to Kimura's two-parameter model (Kimura, 1980
) using the program MEGA v.2.1 (Kumar et al., 2001
). Standard errors of the sequence divergence estimates were obtained applying 1000 bootstrap replicates. Indels were excluded from pairwise sequence comparisons. The distance matrices for all pairwise sequence combinations were analyzed with the neighbor-joining (NJ) method (Saitou and Nei, 1987
) of phylogenetic tree construction with 1000 bootstrap replicates using MEGA v.2.1 software.
Maximum parsimony analysis was performed on the entire 5S rDNA repeat sequences using PAUP v.4.0b4a program (Swofford, 2000
). Heuristic searches were performed with random sequence additions, 100 replicates and tree-bisection-reconnection (TBR) branch swapping. All character states, including indels, were specified as unordered and equally weighted. A strict consensus tree was constructed of the most parsimonious trees retrieved. The support for individual clades was evaluated by running 1000 bootstrap replicates.
|
RESULTS |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
; Moran et al., 1992
; Brown and Carlson, 1997
). This region was 120 bp long in most of the 122 clones we sequenced, except for a 1-bp deletion in two clones of P. tabuliformis and a 2-bp deletion in one clone of P. bungeana. Sequence similarity in the genic region was high, ranging from 93 to 100%, among all these clones. A conserved sequence element known as the Intragenic Control Region (including Box A and Box C) in Arabidopsis (Cloix et al., 2000
) can also be identified in the pines (Fig. 1).
|
). Another conserved region is the approximately 40-bp sequence upstream of the 5S gene (Fig. 2), including a CT-rich box followed by a duplication of the AGGGGG motif (GA-rich) (Fig. 2), which is also thought to be a regulatory factor in transcription (Brown and Carlson, 1997
; Trontin, Grandemange, and Favre, 1999
). In the alignment matrix of the four diploxylon pines a TC-rich island is present between nucleotide positions 449 and 480. A similar TC island is also present between positions 229 and 248 in the P. bungeana spacer alignment matrix. A region approximately 20 bp long before this TC island is also conserved between the two subgenera. The function of this conserved region is unclear. Apart from these regions, alignment between the two subgenera was difficult.
|
|
|
Interspecific sequence divergence
Among the four diploxylon pines, the degree of interspecific sequence divergence in the genic region ranged from 0.011 to 0.019 (Table 4), similar to the observed levels of intragenomic divergence (Tables 3 and 4). Between P. bungeana and the diploxylon pines, however, sequence divergence was about twofold greater, ranging from 0.019 to 0.027 (Table 4). Among the 122 clones, 50 unique 5S gene sequences were found. There were 47 polymorphic sites in this region among the clones, but no substitutions were fixed for a species, and seven polymorphisms were shared among species. Of all these 47 polymorphic sites, 74% were located in the stem regions of the 5S rRNA secondary structure and may represent a potential source of alteration of the secondary structure (Barciszewska, Erdmann, and Barciszewski, 1994
; Trontin, Grandemange, and Favre, 1999
). Considerable variation was found between nucleotide positions 73 and 78, which harbored 13% of the substitutions. This region is identified as Loop E of the 5S rRNA secondary structure and is highly conserved among eukaryotes (Curtiss and Vournakis, 1984
). Thus, the variation found in this study could either be due to the presence of pseudogenes among our clones or it may reflect a pattern unique to pines. A distance-based phylogenetic scheme (NJ tree) was constructed for the 50 unique 5S gene sequences. In this tree the 5S gene copies were clustered neither by species groups nor by subgenera (tree not shown). Identical sequences were shared by different species from both subgenera.
|
Looking at the whole 5S rDNA repeats, the sequence divergence ranged from 0.046 to 0.058 between the four diploxylon pines. The largest distances (0.055 to 0.058) were between P. massoniana and the other pines. One of the P. densata individuals, Pd-s, was closer to P. yunnanensis (0.046) than to P. tabuliformis (0.054) while the other, Pd-t, is of equal distance to the two parents (0.052). The distance between the two P. densata individuals was 0.051. These relationships are also reflected in the distribution of diagnostic indels in the spacer (Table 5). The indel (329–331) characteristic of P. massoniana was not found in the other three pines. The three indels characteristic of P. tabuliformis (271–274) and P. yunnanensis (389–398, 516–527) were all found in P. densata. However, one indel (299–301) shared by P. tabuliformis and P. yunnanensis (although not fixed) was not detected in P. densata, and Pd-s had a unique indel that was not found in any of the other genomes (Table 5).
|
|
|
DISCUSSION |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
; Cloix et al., 2000
). In Pinaceae this intragenic transcription control region is similar to that in Arabidopsis (Cloix et al., 2000
). However, mutations are observed in this region as well as in the region defined as Loop E, which is generally highly conserved in eukaryotes (Curtiss and Vournakis, 1984
). This variation is very likely due to the presence of pseudogene copies among the clones. Pseudogenes of rDNA internal transcribed spacers (ITS) have been reported for pines (Gernandt, Liston, and Piñero, 2001
) and various other plants (Buckler and Holtsford, 1996
; Kita and Ito, 2000
) and in each case was associated with increased substitution rates. An alternative explanation for these mutations is that the selection pressure on any single gene copy may be weak in such cases, thus allowing a certain degree of variation in the genic region (Kellogg and Appels, 1995
; Allaby and Brown, 2001
). In our samples the possibility for pseudogene copies could be examined by comparing the secondary structure, Gibbs-free energy values for folding, GC contents, and by comparing branch lengths of normal sequences and putative pseudogenes. A preliminary evaluation of the 122 clones indicated that some of clones are putative pseudogenes. In a separate report we present the detailed secondary structure of the 122 5S rDNA clones and the examination of pseudogenes.
The spacers, especially the regions flanking the 5S gene, are thought to play some role in transcription initiation and termination (Scoles et al., 1988
). The poly-T sequence downstream of the genic region is considered a transcription-ending signal. This structure is present in pines, although it is preceded by a poly-C sequence. Thymine and adenine- (TA-) and GC-rich elements upstream of the gene region are found in most angiosperms and are thought to have regulatory functions (Venkateswarlu, Lee, and Nazar, 1991
; Sastri et al., 1992
), but this structure is not found in pines and other conifers (this study; Brown and Carlson, 1997
; Trontin, Grandemange, and Favre, 1999
). Instead, a conserved CT-rich followed by a GA-rich element is found in pines. This structure is thought to functionally resemble the TA-rich and GC-rich elements in angiosperms and to play a regulatory role (Trontin, Grandemange, and Favre, 1999
). The difference in regions regulating 5S rDNA transcription between conifers and angiosperms together with the conserved region in the middle of the spacer suggest their regulatory mechanisms may differ.
5S rDNA evolution in pines
There appears to have been a distinct difference in the rate of evolution between the 5S genic region and spacer in the pines we studied. The genic region is conserved, and many clones of the different species shared the same sequences and polymorphic sites. Furthermore, different sequences cannot be grouped by either species or subgenus and 5S repeats within individual genomes are polyphyletic. These indicate that diversification in the 5S gene occurred before the divergence of the two subgenera. In contrast, the spacer can hardly be aligned between the two subgenera, except for a few conserved regions. Thus, most of the diversification in the spacer occurred after the divergence of the two subgenera. Among the four diploxylon pines, the spacer diverged 3–6 times faster than the genic region. This difference in the rate of evolution could be due to functional constraints on the genic region, resulting in slower evolution here than in the spacers. Another possible explanation is that gene conversion responsible for homogenization normally occurs within the genic sequence (Liao, 2000
). The conservation of the flanking regions in the spacer may be partly due to gene conversion initiated in the genic sequences, as well as to putative regulatory constraints (Liao, 2000
).
It is generally accepted that although intraspecific variation occurs among the rDNA genes, it is greatly reduced compared to interspecific variation, due to concerted evolution (Hillis and Dixon, 1991
). Our data do not fully support this hypothesis. On average, we found interspecific divergence in the gene and spacer to be similar to that found within genomes. However, we found considerably more divergence when comparing P. bungeana with the diploxylon pines. Gene conversion can slow down the sequence divergence within species but does not slow down the sequence divergence between species. This is reflected in the twofold higher genic divergence between the two subgenera than within the diploxylon pines. This indicates that processes of concerted evolution have been acting after the diversification of the two subgenera, but they have been very weak and insufficient to remove all the mutations created by other forces after the speciation of the four diploxylon pines, as indicated by their similar levels of intragenomic and interspecific sequence divergence. The phylogenetic position of P. bungeana is close to the basal of subgenus Strobus, and its diversification much precedes the four relatively new diploxylon pines included in this study (Liston et al., 1999
; Wang et al., 1999
). Thus, the time passed since the speciation of the four diploxylon pines may not have been enough to achieve a proper homogenization among rDNA repeats. The little homogenization in the diploxylon pines is also reflected in the spacer region, in which both substitutions and indels were more common as compared to P. bungeana in which all the length variation was in the poly-C, poly-T region immediately downstream of the 5S gene. The divergence in the spacer between the two subgenera far exceeded the rate of divergence among the diploxylon pines making the spacer alignment between the two subgenera difficult. Thus, the observed patterns in these pines resulted from both sequence divergence and homogenization, and the gene and spacer are evolving together, with the latter region being faster. As pointed out by Allaby and Brown (2001)
, this is a paradoxical situation, as the high intragenomic variation suggests that little selection is acting on individual genes, but the conservation of genes between species implies that variation is periodically removed (homogenized) at a rate approximately equal to that of speciation (Cronn et al., 1996
). In our samples, however, the removal rate appears to have been much slower than the diploxylon speciation rate.
Variability within multigene families depends on many factors, including the number of gene copies, rates of mutation, speciation, and concerted evolution; number and chromosomal location of loci; generation time; and the relative proportions of sexual and asexual reproduction (Arnold, Bennnet, and Zimmer, 1990
; Bobola, Smith, and Klein, 1992
; Cronn et al., 1996
; Campbell et al., 1997
; Ganley and Scott, 1998
). Hybridization certainly has contributed to the higher variation in the P. densata genome manifested in its high rate of intragenomic sequence divergence (Table 3). However, this factor cannot be applied to other species such as P. bungeana, which is endemic, isolated, and highly divergent from the other pines (Liston et al., 1999
; Wang et al., 1999
). Slow concerted evolution is found at ITS loci in pines (Gernandt, Liston, and Piñero, 2001
). The intragenomic ITS polymorphism in pines is attributed to the large number of rDNA loci and rDNA copy numbers, high outcrossing rate, and long generation time (Moran et al., 1992
; Karvonen and Savolainen, 1993
; Gernandt, Liston, and Piñero, 2001
). 5S rDNA loci are located separately from the major 18S-5.8S-26S rDNA loci. Two 5S rDNA sites located on two chromosomes are found in pines, as compared to 5–10 18S-5.8S-26S rDNA sites per haploid genome (Karvonen and Savolainen, 1993
; Doudrick et al., 1995
; Liu et al., 2002
). The relatively low number of 5S loci should promote their homogenization. However, in an in situ hybridization study using one 5S rDNA clone (Pb2B05) as a probe, equal intensities of hybridization signals were detected from the two chromosomal sites, indicating that the 5S rDNA unit is not restricted to one site but dispersed between the two sites (Z.-L. Liu, unpublished data). Interlocus homogenization, especially between nonhomologous chromosomes, generally proceeds more slowly than intralocus homogenization (Dover, 1982
; Schlötterer and Tautz, 1994
; Cronn et al., 1996
), which would tend to reduce the effectiveness of 5S rDNA homogenization in pines.
Inheritance and evolution of 5S rDNA in P. densata
Pinus densata is a diploid hybrid between P. tabuliformis and P. yunnanensis (Wang and Szmidt, 1994
; Wang, Szmidt, and Savolainen, 2001
). Homoploid speciation is not as common as polyploid speciation, and genomic reorganizations, such as losses and/or duplications of genome segments and recombination, often occur in the process of hybrid speciation (Rieseberg, Baird, and Gardner, 2000
). The relatedness of P. densata to P. tabuliformis and P. yunnanensis at 5S rDNA loci is clear, with Pd-s biased more toward P. yunnanensis. This difference could reflect differences in the evolutionary history of individual P. densata populations, since Pd-s and Pd-t are from two distant populations. Previous studies have revealed that P. densata populations differ in their direction of initial hybridization and the degree of backcrossing (Wang and Szmidt, 1994
; Wang, Szmidt, and Savolainen, 2001
; Song et al., 2002
). Such difference would have a strong impact on the genome composition of different populations and produced founder effect on the rDNA repeats composition in individuals.
It has been suggested that the origin of P. densata is related to the uplift of the Tibetan Plateau, which would date back more than 20 million years ago (Wang and Szmidt, 1994
). In an old hybrid, one should not expect a complete additivity of parental genomes, as genome reorganization and recombination would have created new characters in it. For examples, the absence of an indel characteristic of the parents may be due to segregation within the hybrid genomes, to its occurrence at very low frequency, or to its loss in the hybrid. Backcrossing can also lead to the loss of some minority parental types of repeat (Campbell et al., 1997
). Genome rearrangements in hybrids are revealed by 5S rDNA fluorescence in situ hybridization. For example, two 5S rDNA sites located on two chromosome pairs are found in P. tabuliformis and P. yunnanensis, but only one is detected in Pd-t (Liu et al., 2002
). The loss of a site in the hybrid genome could have resulted from events such as unequal crossing-over, gene conversion, or transpositional events (Leitch and Heslop-Harrison, 1993
; Taketa, Harrison, and Heslop-Harrison, 1999
; Zhang and Sang, 1999
; Hasterok et al., 2001
).
Phylogenetic analysis of the 5S rDNA repeats in P. tabuliformis, P. yunnanensis, and P. densata suggests that P. densata repeats are either nearly identical to the parental types or of its unique types. Group II consisted mainly of P. densata and P. tabuliformis clones, suggesting these copies in the hybrid are likely developed from a few P. tabuliformis clones. Group III of these repeats, which is mainly composed of P. densata clones, could be recombinants or new types unique to the hybrid. Close examination of these repeats revealed a few clones (e.g., Pd-t608) with segments from both parents. However, most of the others are not of simple two-parental segments combinations, rather they seem to represent multiple recombination events as one would have expected from an old hybrid going through frequent recombinations. The distribution of P. densata clones among all the main paraphyletic groupings suggest that substantial time has passed since the hybrid speciation and that concerted evolution has not been effective in homogenizing the 5S rDNA repeats in the hybrid genome. From a phylogenetic perspective, our present results show the potential pitfalls in using data from multigene families to construct phylogenies and infer species relationships. Unless the orthologous and paralogous relationships can be established among the rDNA repeats, the use of a limited number of repeats in phylogeny could lead to erroneous conclusions.
|
FOOTNOTES |
|---|
4 Author for reprint requests (Fax: +46-90176123; Xiao-Ru.Wang{at}niwl.se
)
|
LITERATURE CITED |
|---|
|
TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
|---|
Amarasinghe V. J. E. Carlson 1998 Physical mapping and characterization of 5S rRNA genes in Douglas-fir. Journal of Heredity 89: 495-500
Arnheim N. M. Krystal R. Schmickel G. Wilson O. Ryder E. Zimmer 1980 Molecular evidence for genetic exchanges among ribosomal genes on nonhomologous chromosomes in man and apes. Proceedings of the National Academy of Sciences, USA 77: 7323-7327
Arnold M. L. B. D. Bennnet E. A. Zimmer 1990 Natural hybridization between Iris fulva and Iris hexagona: pattern of ribosomal DNA variation. Evolution 44: 1512-1521[CrossRef][ISI]
Ausubel F. M. R. Brent R. E. Kingston D. D. Moore J. G. Seidman J. A. Smith K. Struhl 1995 Short protocols in molecular biology, 3rd ed. John Wiley & Sons, New York, New York, USA
Barciszewska M. Z. V. A. Erdmann J. Barciszewski 1994 A new type of RNA editing. 5S ribosomal DNA transcripts are edited to mature 5S rRNA. Biochemistry and Molecular Biology International 34: 437-448[ISI][Medline]
Bobola M. S. D. E. Smith A. S. Klein 1992 Five major nuclear ribosomal repeats represent a large and variable fraction of the genomic DNA of Picea rubens and P. mariana. Molecular Biology and Evolution 9: 125-137[Abstract]
Brown D. D. P. C. Wensink E. Jordan 1972 A comparison of the ribosomal DNAs of Xenopus laevis and Xenopus mulleri: the evolution of tandem genes. Journal of Molecular Biology 63: 57-73[CrossRef][ISI][Medline]
Brown G. R. J. E. Carlson 1997 Molecular cytogenetics of the genes encoding 18s–5.8s–26s rRNA and 5s rRNA in two species of spruce (Picea). Theoretical and Applied Genetics 95: 1-9[CrossRef][ISI]
Buckler E. S. I. T. P. Holtsford 1996 Zea ribosomal repeat evolution and substitution patterns. Molecular Biology and Evolution 13: 623-632[Abstract]
Campbell C. S. M. F. Wojciechowski B. G. Baldwin L. A. Alice M. J. Donoghue 1997 Persistent nuclear ribosomal DNA sequence polymorphism in the Amelanchier agamic complex (Rosaceae). Molecular Biology and Evolution 14: 81-90[Abstract]
Ciliberto G. G. Rangei F. Constanzo L. Dente R. Cortese 1983 Common and interchangeable elements in the promoters of genes transcribed by RNA polymerase III. Cell 32: 725-733[CrossRef][ISI][Medline]
Cloix C. S. Tutois Y. Yukawa O. Mathieu C. Cuvillier M. C. Espagnol G. Picard S. Tourmente 2000 Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNA. Genome Research 12: 132-144
Cox A. V. M. D. Bennett T. A. Dyer 1992 Use of the polymerase chain reaction to detect spacer size heterogeneity in plant 5S-rRNA gene clusters and to locate such clusters in wheat (Triticum aestivum L). Theoretical and Applied Genetics 83: 684-690[ISI]
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]
Curtiss W. C. J. N. Vournakis 1984 Quantitation of base substitutions in eukaryotic 5S rRNA: selection for the maintenance of RNA secondary structure. Journal of Molecular Evolution 20: 351-361[CrossRef][ISI][Medline]
Doudrick R. L. J. S. Heslop-Harrison C. D. Nelson T. Schmidt W. L. Nance T. Schwarzacher 1995 Karyotype of slash pine (Pinus elliottii var elliottii) using patterns of fluorescence in situ hybridization and fluorochrome banding. Journal of Heredity 86: 289-296
Dover G. A. 1982 Molecular drive: a cohesive model of species evolution. Nature 299: 111-117[CrossRef][Medline]
Doyle J. J. J. L. Doyle 1987 A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19: 11-15
Ganley A. R. B. Scott 1998 Extraordinary ribosomal spacer length heterogeneity in a Neotyphodium endophyte hybrid: implications for concerted evolution. Genetics 150: 1625-1637
Gernandt D. S. A. Liston D. Piñero 2001 Variation in the nrDNA ITS of Pinus subsection Cembroides: implications for molecular systematic studies of pine species complexes. Molecular Phylogenetics and Evolution 21: 449-467[CrossRef][ISI][Medline]
Goldsbrough P. B. T. H. Ellis C. A. Cullis 1981 Organisation of the 5S RNA genes in flax. Nucleic Acids Research 9: 5895-5904
Gorman S. W. R. D. Teasdale C. A. Cullis 1992 Structure and organization of the 5S rRNA genes (5S DNA) in Pinus radiata (Pinaceae). Plant Systematics and Evolution 183: 223-234[CrossRef][ISI]
Gottlob-McHugh S. G. M. Levesque K. MacKenzie M. Olson O. Yarosh D. A. Johnson 1990 Organization of the 5S rRNA genes in the soybean Glycine max (L.) Merrill and conservation of the 5S rDNA repeat structure in higher plants. Genome 33: 486-494[Medline]
Hasterok R. G. Jenkins T. Langdon R. N. Jones J. Maluszynska 2001 Ribosomal DNA is an effective marker of Brassica chromosomes. Theoretical and Applied Genetics 103: 486-490[CrossRef][ISI]
Hillis D. M. M. T. Dixon 1991 Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology 66: 411-453[CrossRef][Medline]
Hillis D. M. C. Moritz C. A. Porter R. J. Baker 1991 Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science 251: 308-310
Karvonen P. O. Savolainen 1993 Variation and inheritance of ribosomal DNA in Pinus sylvestris L. (Scots pine). Heredity 71: 614-622[ISI]
Kellogg E. A. R. Appels 1995 Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives. Genetics 140: 325-343[Abstract]
Kimura M. 1980 A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120[CrossRef][ISI][Medline]
Kita Y. M. Ito 2000 Nuclear ribosomal ITS sequences and phylogeny in East Asian Aconitum subgenus Aconitum (Ranunculaceae), with special reference to extensive polymorphism in individual plants. Plant Systematics and Evolution 225: 1-13
Kumar S. K. Tamura I. B. Jakobsen M. Nei 2001 MEGA 2: molecular evolution genetics analysis software. Arizona State University, Tempe, Arizona, USA
Leitch I. J. J. S. Heslop-Harrison 1993 Physical mapping of 4 sites of 5S rDNA sequences and one site of the alpha-amylase-2 gene in barley (Hordeum vulgare). Genome 36: 517-523[ISI]
Li W.-H. 1997 Molecular evolution. Sinauer, Sunderland, Massachusetts, USA
Liao D. 2000 Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea. Journal of Molecular Evolution 51: 305-317[ISI][Medline]
Liston A. W. A. Robinson D. Piñero E. R. Alvarez-Buylla 1999 Phylogenetics of Pinus (Pinaceae) based on nuclear ribosomal DNA internal transcribed spacer region sequences. Molecular Phylogenetics and Evolution 11: 95-109[CrossRef][ISI][Medline]
Little E. L., Jr. W. B. Critchfield 1969 Subdivisions of the genus Pinus (pines). USDA Forest Service, Miscellaneous Publication Number 1144
Liu Z.-L. D. Zhang D.-Y. Hong X.-R. Wang 2002 Chromosomal localization of 5S and 18S–5.8S–25S ribosomal DNA sites in five Asian pines using fluorescence in situ hybridization. Theoretical and Applied Genetics (in press)
Millar C. I. 1998 Early evolution of pines. In D. M. Richardson [ed.], Ecology and biogeography of Pinus, 69–91. Cambridge University Press, Cambridge, UK
Moran G. F. D. Smith J. C. Bell R. Appels 1992 The 5S RNA genes in Pinus radiata and the spacer region as a probe for relationship between Pinus species. Plant Systematics and Evolution 183: 209-221[CrossRef][ISI]
Nagylaki T. 1990 Gene conversion, linkage, and the evolution of repeated genes dispersed among multiple chromosomes. Genetics 126: 261-276[Abstract]
Nagylaki T. T. D. Petes 1982 Intrachromosomal gene conversion and the maintenance of sequence homogeneity among repeated genes. Genetics 100: 315-337
Ohta T. 1990 How gene families evolve. Theoretical Population Biology 37: 213-219[CrossRef][ISI][Medline]
Rieseberg L. H. S. J. E. Baird K. A. Gardner 2000 Hybridization, introgression, and linkage evolution. Plant Molecular Biology 42: 205-224[CrossRef][ISI][Medline]
Saitou N. M. Nei 1987 The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425[Abstract]
Sastri D. C. K. Hilt R. Appels E. S. Lagudah J. Playford B. R. Baum 1992 An overview of evolution in plant 5S DNA. Plant Systematics and Evolution 183: 169-181[CrossRef][ISI]
Schlötterer C. D. Tautz 1994 Chromosomal homogeneity of Drosophila ribosomal DNA arrays suggests intrachromosomal exchanges drive concerted evolution. Current Biology 4: 777-783[CrossRef][Medline]
Schneeberger R. G. G. P. Creissen C. A. Cullis 1989 Chromosomal and molecular analysis of 5S RNA gene organization in the flax, Linum usitatissimum. Gene 83: 75-84[CrossRef][ISI][Medline]
Scoles G. J. B. S. Gill Z.-Y. Xin B. C. Clarke C. L. McIntyre C. Chapman R. Appels 1988 Frequent duplication and deletion events in the 5S-RNA genes and the associated spacer regions of the Triticeae. Plant Systematics and Evolution 160: 105-122[CrossRef][ISI]
Smith G. P. 1976 Evolution of repeated DNA sequences by unequal crossover. Science 191: 528-535
Song B.-H. X.-Q. Wang X.-R. Wang L.-J. Sun D.-Y. Hong P.-H. Peng 2002 Maternal lineages of Pinus densata, a diploid hybrid. Molecular Ecology 11: 1057-1063[CrossRef][Medline]
Swofford D. L. 2000 PAUP: phylogenetic analysis using parsimony. Version 4. Sinauer, Sunderland, Massachusetts, USA
Szymanski M. T. Specht M. Barciszewska J. Barciszewski V. A. Erdmann 1998 5S rRNA data bank. Nucleic Acids Research 26: 156-159
Taketa S. G. E. Harrison J. S. Heslop-Harrison 1999 Comparative physical mapping of the 5S and 18S–25S rDNA in nine wild Hordeum species and cytotypes. Theoretical and Applied Genetics 98: 1-9[CrossRef][ISI]
Thompson J. D. T. J. Gibson F. Plewniak F. Jeanmougin D. G. Higgins 1997 The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research 24: 4876-4882
Trontin J. F. C. Grandemange J. M. Favre 1999 Two highly divergent 5S rDNA unit size classes occur in composite tandem array in European larch (Larix decidua Mill.) and Japanese larch (Larix kaempferi (Lamb.) Carr). Genome 42: 837-848[Medline]
Van de Peer Y. R. De Baere J. Cauwenberg R. De Watcher 1990 Evolution of green plants and their relationship with other photosynthetic eucaryotes as deduced from 5S ribosomal RNA sequences. Evolution 170: 85-96
Venkateswarlu K. S.-W. Lee R. N. Nazar 1991 Conserved upstream sequence elements in plant 5S ribosomal RNA-encoding genes. Gene 105: 249-253[CrossRef][ISI][Medline]
Wang X.-Q. D. C. Tank T. Sang 2000 Phylogeny and divergence times in Pinaceae: evidence from three genomes. Molecular Biology and Evolution 17: 773-781
Wang X.-R. A. E. Szmidt 1994 Hybridization and chloroplast DNA variation in a Pinus species complex from Asia. Evolution 48: 1020-1031[CrossRef][ISI]
Wang X.-R. A. E. Szmidt O. Savolainen 2001 Genetic composition and diploid hybrid speciation of a high mountain pine, Pinus densata, native to the Tibetan Plateau. Genetics 159: 337-346
Wang X.-R. Y. Tsumura H. Yoshimaru K. Nagasaka A. E. Szmidt 1999 Phylogenetic relationships of Eurasian pines (Pinus, Pinaceae) based on chloroplast rbcl, matK, rpl20-rps18 spacer, and trnV intron sequences. American Journal of Botany 86: 1742-1753
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
Zhang D. T. Sang 1999 Physical mapping of ribosomal RNA genes in peonies (Paeonia, Paeoniaceae) by fluorescent in situ hybridization: implications for phylogeny and concerted evolution. American Journal of Botany 86: 735-740
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
