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2 School of Biological Sciences, Queen Mary and Westfield College, University of London, E1 4NS, UK; and 3 Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
Received for publication September 17, 1999. Accepted for publication January 21, 2000.
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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400 species) share a conserved bimodal karyotype with a basic genome of four large and three small submetacentric/acrocentric chromosomes. We investigated the physical organization of 18S–5.8S–26S and 5S ribosomal DNA (rDNA) using fluorescent in situ hybridization (FISH) to 13 Aloe species. The organization was compared with a phylogenetic tree of 28 species (including the 13 used for FISH) constructed by sequence analysis of the internal transcribed spacer (ITS) of 18S–5.8S–26S rDNA. The phylogeny showed little divergence within Aloe, although distinct, well-supported clades were found. FISH analysis of 5S rDNA distribution showed a similar interstitial location on a large chromosome in all species examined. In contrast, the distribution of 18S–5.8S–26S rDNA was variable, with differences in number, location, and size of loci found between species. Nevertheless, within well-supported clades, all species had the same organizational patterns. Thus, despite the striking stability of karyotype structure and location of 5S rDNA, the distribution of 18S–5.8S–26S rDNA is not so constrained and has clearly changed during Aloe speciation.
Key Words: 5S and 18S-5.8S-26S rDNA • Aloe • Asphodelaceae • bimodal karyotype • chromosomes • ITS phylogeny
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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400 species native to Africa, Madagascar, and Arabia (Viljoen, van Wyk, and van Heerden, 1998
). Although most are spiny succulents, aloes vary in size and morphology from dwarf rosettes 30 mm across to trees growing over 15 m high. Most species of Aloe are diploid (2n = 14), although a few are tetraploid, and one hexaploid is known (Brandham, 1971
). All aloes have a bimodal karyotype with a basic genome structure of one long submetacentric (L1), three long acrocentric (L2, L3, L4), and three short acrocentric (S1, S2, S3) chromosomes.
Despite the uniform bimodal karyotype of all species, the 1C DNA amount varies, e.g., in diploids from 10.5 pg in A. tenuior to 23.9 pg in A. peckii (Brandham and Doherty, 1998
). In addition, heterozygous chromosomal rearrangements often occur in wild plant populations; 12% of individuals of A. rabaiensis in a population have a single rearrangement (Brandham, 1976
; Brandham and Johnson, 1977
). Previously, no wild plants homozygous for any rearrangements have been reported, although this condition has been bred in glasshouse-grown material (Brandham, 1983
). Certainly no rearrangements disrupting bimodality have become fixed during Aloe speciation, which indicates a strong selection pressure must be acting against such karyotypic changes.
Using fluorescent in situ hybridization (FISH), we investigated the distribution of 5S and 18S–5.8S–26S rDNA sequences in 13 Aloe species selected to include species from across the geographic range (Arabian peninsula, East and South Africa, and Madagascar), a range in ploidy levels (diploid, tetraploid, and hexaploid), and a range in morphological types (mesophytes, rosettes, shrubs, and trees). We also constructed a phylogenetic tree of 28 Aloe species including the 13 species used for FISH to determine whether patterns of rDNA were reflected in relationships evaluated with nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) sequences.
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MATERIALS AND METHODS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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. All samples were then purified on caesium chloride–ethidium bromide gradients (1.55 g/mL). Amplification of the ITS1, 5.8S, and ITS2 regions was carried out using the primers "ITS 4" (TCC TCC GCT TAT TGA TAT GC) and "ITS 5" (GGA AGT AAA AGT CGT AAC AAG G) of White et al. (1990)
. We used the following PCR (polymerase chain reaction) profile: 26 cycles of 97°C for 1 min, 50°C for 1 min, and 72°C for 3 min, followed by a final extension at 72°C for 7 min. Products were cleaned on QIAquick purification columns (QIAGEN Inc., Sussex, UK) following the manufacturer's protocols. Cycle sequencing directly on the amplified product was conducted with the ABI Prism Dye Terminator Cycle Sequencing Ready Reaction kit (PE Applied Biosystems, Warrington, Cheshire, UK), using 2.5 ng of primer in a 5-µL reaction volume. Sequencing conditions were the following: 26 cycles of 10 sec denaturation (96°C), 5 sec annealing (50°C), and 4 min elongation (60°C) in a Perkin Elmer 9600 thermocycler. Sequencing reaction products were purified by ethanol precipitation and run on an ABI Prism 377 automated sequencer (PE Applied Biosystems).
Analysis of DNA sequence data
Electropherograms were edited with Sequence Navigator version 1.0 software (PE Applied Biosystems), and complementary strands were compared using the software AutoAssembler version 1.4.0 (PE Applied Biosystems). The sequences for all the species studied were manually aligned, and phylogenetic reconstructions were obtained using the maximum parsimony method. Bulbine wiesei was used as an outgroup for the analysis based on the results of Chase et al. (2000).
All molecular characters were assessed as independent, unordered and equally weighted (Fitch parsimony; Fitch, 1971
). The maximum parsimony analyses were conducted with heuristic searches with PAUP 3.1.1 (Swofford, 1993
) using 100 replicates of random-taxon additions, subtree-pruning-regrafting (SPR) with MULPARS option on (i.e., saving all shortest trees). No more than five trees were saved in each replicate so that the time spent swapping on trees of longer lengths was limited. After completion of the 100 replicates, the shortest trees found were used as starting trees in a search without a tree limit to collect all trees at the shortest tree length. These trees (Fitch trees) were then used for successive weighting (Farris, 1969
) with a base weight of 1000 based on the rescaled consistency index (RC) on the best trees. Rounds of reweighting were continued until the same tree length was obtained in two successive replicates. Fitch bootstrap percentages (Felsenstein, 1985
) were calculated for each node (bootstrap option in PAUP 3.1.1., with 1000 replicates of heuristic search with SPR, swapping one random sequence addition per replicate but keeping up to 15 trees per replicate).
DNA probes
Two rDNA probes were used in the FISH experiments. (1) The probe pTa71 is a clone containing a 9 kb EcoRI fragment of 18S–5.8S–26S rDNA from wheat (Gerlach and Bedbrook, 1979
). (2) The probe for 5S rDNA was amplified by PCR from total genomic DNA of each Aloe species. Genomic DNA was extracted from leaves using methods described above, and 5S rDNA sequence amplified using the primers in Cox, Bennett, and Dyer (1992)
: 5S F (AGT TAA GCT TTG GGC GAG AGT A) and 5S R (AGT TCT GAT GGA ATT CGG TGY TKT A). Probes were labeled by nick translation using either biotin-11-dUTP (Sigma-Aldrich Company Ltd, Poole, Dorset, UK) or digoxigenin-11-dUTP (Roche Molecular Biochemicals, Sussex, UK).
Fluorescent in situ hybridization (FISH)
Chromosomes were prepared using enzyme-softened root tips, and FISH was carried out as described by Leitch et al. (1994)
with the following modifications. Chromosomes were denatured in 70% formamide in 2x SSC (saline sodium citrate) at 68°C for 2 min, dehydrated in an ethanol series and air-dried. The probe mixture was denatured at 75°C for 15 min, added to the denatured chromosomes and hybridized at 37°C overnight. Following hybridization the slides were given a stringent wash in 20% formamide in 0.1x SSC at 42°C for 10 min and washed in 2x SSC. Detection of hybridization was carried out using anti-digoxigenin FITC (Roche Molecular Biochemicals) and avidin Cy3 (Vector Laboratories, Peterborough, UK). In double-labeling experiments the detection reagents were applied simultaneously. Chromosomes were counterstained with 4',6-diamidino-2-phenylindole (DAPI, 2 µg/mL). Fluorescence was viewed with a Leitz Aristoplan microscope, and photographs were taken with Fujicolor 400 film. For each species analyzed, 20 or more metaphases were scored. Images were processed using Adobe Photoshop®. Whole images were treated uniformly by changing contrast, brightness, and color balance only.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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). All three were examined cytologically. They clustered in a clade with <50% bootstrap support.
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85% of the distance from the centromere (Fig. 2A, C, E, G, I, K, M, O, Q, S, U, W, Y). Polyploid plants had the expected multiple number of loci. Thus the tetraploids A. nyeriensis and A. ngobitensis had two loci (four hybridization sites; Fig. 2W and Y), and the hexaploid A. ciliaris had three loci (six hybridization sites, Fig. 2C). Of the long chromosomes in the Aloe genome, L1 is the longest and L4 is the shortest. Although L2 is usually longer than L3, it cannot regularly be distinguished with confidence by morphology. In metaphases in which differences in length could be determined, the signal was always on L2. This assumes that L2 from each species are homoeologues.
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Species in well-supported clades were found to have the same organization of 18S-5.8S-26S rDNA sites, although the organization differed between clades. Thus the diploid A. tenuior and the hexaploid A. ciliaris (Fig. 2B and D), which form a sister clade to the other species (Fig. 1), had terminal sites at ends of the long arm of L3 chromosomes and the short arm of one of the short chromosomes. In a separate clade, A. vera and A. scobinifolia also had 18S–5.8S–26S rDNA sites on a short chromosome, but unlike A. tenuior and A. ciliaris, there were sites on the long arms of chromosomes L1 and L4 (Fig. 2F and H). In another well-supported clade, the two Madagascan species A. bakeri and A. acutissima had terminal loci on the long arms of chromosomes L3 and L4 (Fig. 2J and L). Aloe peckii and A. morijensis also had this arrangement, although they are in a separate clade with lower bootstrap support (Fig. 2R and T).
The phylogenetic relationship between the remaining species analyzed was less clear, but the following patterns of 18S–5.8S–26S rDNA organization were found. Aloe ammophila had sites on L2, linked to a 5S rDNA site, and L4 (Fig. 2M and N). This was the only species with both classes of rDNA on the same chromosome. Aloe glauca (Fig. 2P), A. arborescens (Fig. 2V), A. nyeriensis (Fig. 2X), and A. ngobitensis (Fig. 2Z) had 18S–5.8S–26S rDNA sites on L1, L3, and L4, but the distribution of sites was not the same. They all had a terminal site on L4. However, A. glauca had an interstitial site on L1, whereas in A. arborescens, A. nyeriensis, and A. ngobitensis the sites were terminal and unbalanced since they lacked a signal on one of their L1 homologues. Aloe glauca and A. arborescens had terminal sites on L3, but the tetraploids A. nyeriensis and A. ngobitensis only had two L3 homologues with terminal sites. The other L3 homologues had interstitial sites. As stated above, A. nyeriensis and A. ngobitensis are similar morphologically and biochemically and have an identical rDNA site distribution, but they differ in arrangement from the proposed diploid progenitor A. morijensis.
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DISCUSSION |
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TOPABSTRACTINTRODUCTIONMATERIALS AND METHODSRESULTSDISCUSSIONLITERATURE CITED |
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With the exceptions of A. ngobitensis and A. nyeriensis (see below), the locations of 18S–5.8S–26S rDNA appear to be consistent with the ITS tree; species within the same clade of the ITS phylogeny had the same number and distribution of loci. This number of shared rDNA locations and clade memberships is unlikely to be due to chance. The patterns seem too congruent to be an artifact. There are two possible explanations for this. (1) The ITS sequence data reflect the history of rDNA chromosome distributions in Aloe arising by amplifications and reductions of different rDNA units at individual loci rather than a phylogeny of species relationships. (2) The ITS sequence data do reflect a phylogeny of evolutionary relationships, and related species have similar distributions and sequence composition of 18S–5.8S–26S rDNA.
Reynolds (1950, 1966)
classified Aloe using morphological and floral features. Descriptions of plant morphology are given for each species in Fig. 1. In some cases species considered closely related by Reynolds' classifications appear to be closely related on the phylogenetic tree (e.g., the mesophytic scramblers A. tenuior and A. ciliaris). Other species occur in the same geographical region and are closely related on the phylogenetic tree (e.g., A. bakeri and A. acutissima from Madagascar). However, there are discrepencies between classical taxonomy and the phylogeny. For example, A. ngobitensis and A. nyeriensis are considered to be closely related or even synonymous by Reynolds, and yet they are well separated on the ITS tree. These two species do occur in unresolved clades, and it is possible that by increasing the number of species sampled and sequencing other regions this discrepency would be resolved. It may also be significant that some grossly dissimilar species from the same geographical region occur close together on the tree (i.e., A. inermis and A. pendens from Saudi Arabia, A. penduliflora and A. nyeriensis from Kenya, A. distans and A. glauca from S. Africa, A. aff. jacksonii and A. scobinifolia from Ethiopia and Somalia).
The phylogenetic analysis (Fig. 1) showed that A. tenuior and A. ciliaris formed a well-supported divergent sister group to all the other aloes analyzed. This agrees with Brandham and Doherty (1998)
, who considered these to be "primitive aloes," and Viljoen, van Wyk, and van Heerden (1998)
who suggested from biochemical analyses that they are basal to the rest. These species both had 18S–5.8S–26S rDNA at a terminal location on all copies of L3 and on a small chromosome. The sister group relationship of the clade suggests that the ITS tree could indeed be a record of ancestry.
Two of the Madagascan species, A. acutissima and A. bakeri, were shown to be closely related to one another and have an identical 18S–5.8S–26S rDNA distribution. The third Madagascan species analyzed, A. bulbillifera, was in a different and well-supported clade, indicating a second founder event into Madagascar.
The clade containing A. nyeriensis, A. morijensis, A. peckii, and A. ngobitensis is not well resolved, and different patterns of 18S–5.8S–26S rDNA organization were observed. In particular, it is noteworthy that A. morijensis is believed to be the diploid progenitor of the morphologically similar tetraploids A. nyeriensis and A. ngobitensis (Cutler et al., 1980
). If they are tetraploid derivatives, then polyploidy must be associated with a redistribution and increase in number of rDNA sites. If ITS sequence phylogeny is not a record of ancestry, but is instead a record of 18S–5.8S–26S rDNA locus distribution, then further arguments are required to explain the identical distributions of rDNA in A. ngobitensis and A. nyeriensis and their separate locations on the phylogenetic tree.
In addition to polyploidy as a possible source of 18S–5.8S–26S rDNA variability, the following points could be involved (each may not be mutually exclusive):
1) The data taken together show 18S–5.8S–26S rDNA sites on L1, L2, L3, L4, and a small chromosome. Possibly all species have all sites, but if copy number falls below the threshold for in situ hybridization (>10 kb [Jiang and Gill, 1994
], i.e., approximate length of one copy of the rDNA gene unit), we may not be able to reliably detect the site. Childs, Maxson, and Kedes (1981)
suggested that it is possible for single rDNA sequences at different chromosomal sites to amplify quickly and form functional nucleolar organizing regions (NORs) under certain conditions.
2) Biochemical analysis has provided some evidence of interspecific hybridization in Aloe (Viljoen, van Wyk, and van Heerden 1998
). Interspecific hybridization may result in gene conversion and change in rDNA locus location and number.
3) Ribosomal DNA sequences are mobile predominantly at the ends of the chromosomes. Mobile 18S–5.8S–26S rDNA, particularly at the chromosome ends, has been observed in the genus Allium (Alliaceae; Bougourd and Parker, 1976
; Schubert and Wobus, 1985
). Allium belongs to the monocot order Asparagales as does Aloe (Chase et al., 1995, 1999
) and both lack the Arabidopsis-type telomere repeat (TTTAGGG)n (Pich, Fuchs, and Schubert 1996
; Adams et al., in press). Allium shows variation in the location and number of rDNA sites and NORs within and between species as well as within individual plants (Schubert and Wobus, 1985
). Aloes show clade-specific differences in the location of 18S–5.8S–26S rDNA including unbalanced numbers of sites, but there is not as much variability as in Allium. How these unbalanced sites in Aloe segregate at meiosis is unknown, although heterozygous karyotypes in populations of other species are known to occur (e.g., 12% of individuals of A. rabaiensis in a single population are heterozygous for a single rearrangement; Brandham, 1976
). However, there is no indication that these changes ever become fixed, suggesting some strong selection pressure against heterozygosity. As far as we know the only other member of Asparagales (over 80 genera; Chase et al., 1995
) that has been examined is Clivia (1990–1999 BIDS search, rDNA + genus). Four Clivia species were examined, and three patterns of rDNA observed (Ran et al., 1999
). Thus rDNA mobility may be an evolutionary feature of the Asparagales.
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FOOTNOTES |
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2 Author for correspondence (Tel: 0207-975-5294; e-mail: a.r.leitch{at}qmw.ac.uk
FAX: 0208-983-0973).
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50% below the line). Arrows indicate groups not present in all 740 Fitch trees. The 18S–5.8S–26S rDNA chromosome distribution is also shown. T indicates a telomeric site, and I indicates an interstitial site of 18S–5.8S–26S rDNA on chromosomes L1, L2, L3, L4, or a short chromosome (S). All sites on long chromosomes are found on the long arm and on short chromosomes, the short arm. Asterisks indicate a missing site of 18S–5.8S–26S rDNA on one of the homologues. The other columns show the geographic locality and the habit of each species (according to Reynolds 1950, 1966