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Evolution of interspersed repetitive elements inGossypium (Malvaceae)¹

^a Department of Soil and Crop Sciences, TexasA&M University, College Station, Texas 77843-2474; ^b Department of Biology, Texas A&M University,College Station, Texas 77843-3258

	ABSTRACT

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Very little is known regarding how repetitive elements evolve inpolyploid organisms. Here we address this subject by fluorescent insitu hybridization (FISH) of 20 interspersed repetitive elements tometaphase chromosomes of the cotton AD-genome tetraploid Gossypiumhirsutum and its putative A- and D-genome diploid ancestors. Theseelements collectively represent an estimated 18% of the G.hirsutum genome, and constitute the majority of high-copyinterspersed repetitive elements in G. hirsutum. Seventeen ofthe elements yielded FISH signals on chromosomes of both G.hirsutum subgenomes, while three were A-subgenome specific. Hybridization of eight selected elements, two of which were A-subgenomespecific, to the A₂ genome of G. arboreum yielded asignal distribution that was similar to that of the G. hirsutumA-subgenome. However, when hybridized to the D₅ genome ofG. raimondii, the putative diploid ancestor of the G.hirsutum D-subgenome, none of the probes, including elements thatstrongly hybridized to both G. hirsutum subgenomes, yieldeddetectable signal. The results suggest that the majority, although notall, G. hirsutum interspersed repetitive elements haveundergone intergenomic concerted evolution following polyploidizationand that this has involved colonization of the D-subgenome byA-subgenome elements and/or replacement of D-subgenome elements byelements of the A-subgenometype.

Key Words: concertedevolution • fluorescent in situ hybridization(FISH) • Gossypium • interspersedrepetitiveelement • Malvaceae • polyploidy

	INTRODUCTION

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Repetitive DNA comprises a significant proportion of most plantgenomes, and accounts for much of the variation in DNA content observedamong plant species (Bennett and Smith,1976; Murray, Cuellar, and Thompson,1978, Murray et al., 1979;Flavell, 1980, 1982a, b). Two main classes of repetitive DNA can be distinguished: interspersedrepeats, which include many families of mobile elements and processedpseudogenes, and tandem repeats, including centromeric, telomeric, andsatellite repeats (Singer, 1982;Lapitan, 1991; Charlesworth, Sniegowski, and Stephan,1994). A shared characteristic of all classes of repetitiveelements is that they tend to exhibit "concerted evolution,"the nonindependent evolution of sequences at multiple loci leading to agreater similarity of repetitive DNA within, rather than between,species (Dover and Coen, 1981; Dover, 1982). The mechanisms responsible forconcerted evolution are not well understood, but are generallyattributed to a number of causes including unequal crossing over, geneamplification, gene conversion, and replicative transposition (Dover, 1982; Elder andTurner, 1995).

Concerted evolution of dispersed repeats has most commonly beenattributed to replicative transposition mechanisms, which are consistentwith the highly interspersed distribution of this class of elements(review by Smith, Young, and Schmeckpeper,1987). Gene conversion can also be an important mechanism inthe concerted evolution of interspersed repeats, however. Studies usingfungal systems have demonstrated that gene conversion occurs not onlybetween alleles, but also between homologous sequences on nonhomologouschromosomes (Lichten, Borts, and Haber,1987; Petes and Hill, 1988). Gene conversion between nonhomologous loci, termed ectopic geneconversion, has more recently been described for the germline of mice(Murti, Bumbulis, and Schimenti, 1994). The frequency of ectopic gene conversion in yeast is comparable to thatof allelic sequences indicating the mechanism has the potential to playa significant role in concerted evolution (Lichten, Borts, and Haber, 1987; Petes and Hill, 1988; Haberet al., 1991).

A topic of particular interest is how repetitive elements evolve inpolyploid genomes. This is especially true for plants, of which30–70% of species have been estimated to be polyploid,although the actual percentage may be higher (Stebbins, 1971; Soltisand Soltis, 1993; Masterson,1994). This phenomenon was previously investigated byWendel, Schnabel, and Seelanan (1995)in five species of tetraploid cotton, demonstrating that rDNA repeatshave homogenized bidirectionally in particular tetraploids towards onediploid type of repeat or the other, and that this process has gone tocompletion in some of the tetraploid species. Hillis et al., (1991) demonstrated that inparthenogenic lizards ribosomal sequences of different lineages evolveat multiple loci in a directionally biased fashion and that thedirectionality of the mechanism is influenced by the parental genotype. Little is still known, however, about how interspersed repeats evolveand interact within a polyploid genome. In an effort to investigatethis question we used fluorescent in situ hybridization (FISH) todetermine the chromosomal and genomic representations of 20 interspersedrepetitive elements in the cotton AD tetraploid Gossypiumhirsutum. Eight selected elements were then used for FISH tometaphase chromosomes from A-genome and D-genome Gossypiumdiploids putatively representing the ancestors of the tetraploid. FISHallowed for direct comparisons to be made between individualchromosomes, genomes, and subgenomes, providing inferences about theevolutionary histories of the elements.

	MATERIALS AND METHODS

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Plant material, pre-treatment, and metaphasepreparation
Gossypium hirsutum (2n = 4x= 52 = 2[AD]₁) (Deltapine 50, Deltaand Pineland Company, Scott, MS), and G. arboreum (2n= 2x = 26 = 2A₂) (accessionnumber A2-92) root tips were clipped in 1-2 cm lengths and pretreatedfor 4 h with 2.5 mmol/L 8-hydroxyquinoline (aqueous) at roomtemperature. Gossypium raimondii (2n =2x = 26 = D₅) (accession number D5-1A22) and an A₂D₅ synthetic diploid (1n= 2x = 26 = A₂D₅)root tips were clipped in 2-3 cm lengths and pretreated with 2.5 mmol/L8-hydroxyquinoline (aq) at room temperature for 5 h. Followingpretreatment, root tips were fixed in 4:1 ethanol:acetic acid overnightat room temperature. All accessions, with the exception of theA₂D₅ synthetic diploid, which was kindly providedby James McD. Stewart, were obtained from the National Collection ofGossypium Germplasm, College Station, TX. Metaphase spreadswere prepared as described by Jewell andIslam-Faridi (1994).

Probe DNA isolation and probe labeling
Repetitive element clones were isolated by alkaline-lysis plasmidmaxipreps as described by Silhavy, Berman, andEnquist (1984). The repetitive element clones were previouslydescribed by Zhao, Wing, and Paterson(1995). Whole plasmid DNA was labeled with biotin14-dATP (BRL) using the Gibco BRL BioNick Labeling System. Theresulting probes ranged between 200 and 500 base pairs in length, onaverage.

In situhybridization
Slides were immersed in 30 µg/mL RNase in 2x SSC (salinesodium citrate) for 45 min at 37°C, denatured at 70°C in70% formamide/2x SSC for 2.5 min, dehydrated in 70, 85, 95,and 100% ethanol for 2 min each at -20°C andair-dried. Approximately 25 µL of probe mix per slide was denaturedat 80°C for 7 min, chilled on ice 1 min, applied to the dry slide,covered with a 20 x 40 mm coverslip, and sealed with rubbercement.

Following overnight incubation at 37°C, coverslips were floatedoff in 2x SSC and slides were rinsed at 40°C in: 2x SSC 5 min,2x SSC 5 min, 2x SSC/50% formamide 10 min, 2xSSC 5 min, 2x SSC 5 min, and 4x SSC 5 min. Forlow-stringency series, the formamide wash was replaced with a 2xSSC wash for 5 min at 40°C. Slides were blocked 10 min at roomtemperature with 5% (w/v) bovine serum albumin (BSA) in 4xSSC 0.2% Tween 20. Excess block was then blotted from the sideof the slide and signal was detected with 60 µL of 3 µg/mL mouseanti-biotin antibodies (Jackson ImmunoResearch Laboratories, Inc., WestGrove, PA)/4x SSC 0.2% Tween 20/5% BSA for 15 min at37°C. Slides were washed three times in 4x SSC 0.2%Tween 20 for 6 min at 37°C, blocked 10 min at room temperature with5% normal goat serum (NGS) in 4x SSC 0.2% Tween 20,blotted to remove excess blocking solution, and amplified with 60 µLof 1 µg/mL Cy3-conjugated anti-mouse antibodies (JacksonImmunoResearch Laboratories, Inc., West Grove, PA)/4x SSC0.2% Tween 20/5% NGS for 20 min at 37°C. Followingthree washes in 4x SSC 0.2% Tween 20 (5 min each at 37°C)slides were stained in 2 µg/mL DAPI in McIlvaines buffer (9 mmol/Lcitric acid, 80 mmol/LNa₂HPO₄·H₂0, 2.5 mmol/LMgCl_2, pH 7.0) for 20 min at room temperature, destained 20in 2x SSC, and finally antifade was applied under a 22 x 40mm coverslip.

Metaphaseobservation and photography
Images were photographed directly on Fuji HG ASA 400 professionalfilm with a 35 mm camera.

	RESULTS

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Twenty repetitive elements were used as probes for FISH to metaphasechromosomes of G. hirsutum. Elements used for FISH vary incopy number from 6 000 to 100 000, individuallyrepresenting between 0.1 and 2% of the haploid genome of G.hirsutum and collectively accounting for >17% of thegenome (Table 1) (Zhao, Wing, and Paterson, 1995). The elements areestimated to represent the majority of the high-copy elements in theG. hirsutum genome. Seventeen of the 20 elements hybridized toboth subgenomes of G. hirsutum while three, pXP095, pXP128(Fig. 5), and pXP137 (Fig. 7), were specific to theA-subgenome. All elements had highly interspersed distributions on allG. hirsutum chromosomes, with the exception of the threesubgenome-specific probes, which were dispersed only on all A-subgenomechromosomes. The probes all yielded more intense signal on A-subgenomechromosomes relative to the D-subgenome.

View larger version (33K): [in this window] [in a new window]   Figs. 1–9. FISH photomicrographs of Gossypium hirsutum repetitive elements hybridized to metaphase chromosomes of G. hirsutum , G. arboreum, G. raimondii , and an A2D5 synthetic diploid. FISH signal from non-genome-specific elements pXP004 and pXP018 can be seen on all chromosomes of G. hirsutum (Figs. 1, 3 ) and the A2 genome of an A2D5 synthetic diploid but on none of the chromosomes of the D5 genome (Figs. 2, 4 ). FISH signals from the genome-specific elements pXP128 and pXP137 were observable on all chromosomes of the G. hirsutum A-subgenome (in G. hirsutum , the largest 13 pairs of chromosomes make up the A-subgenome) (Figs. 5, 7 ), the A2 genome of the A2D5 synthetic diploid (Fig. 6 ), and G. arboreum (Fig. 8 ) but not on the chromosomes of the G. hirsutum D-subgenome (Figs. 5, 7 ), the D5 genome of the A2D5 synthetic diploid (Fig. 6 ) or G. raimondii (Fig. 8 ). 1. pXP004, G. hirsutum . 2. pXP004, A2D5. 3. pXP018, G. hirsutum . 4. pXP018, A2D5. 5. pXP128, G. hirsutum . 6. pXP128, A2D5 7. pXP137, G. hirsutum . 8. pXP137, G. arboreum. 9. pXP137, G. raimondii .

	DISCUSSION

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The putative A- and D-genome diploid ancestors of G.hirsutum are hypothesized to have diverged from a common ancestor4-10 million years prior to polyploidization (Wendel, 1989; Wendel andAlbert, 1992). In view of this, and the substantial weight ofevidence indicating that most repetitive elements evolve quite rapidly,it was expected that there would be significant qualitative differencesin repetitive DNA content between the A- and D-subgenomes. The findingthat only three of 20 interspersed repetitive elements were subgenomespecific in G. hirsutum was, therefore, unexpected. This wasparticularly so given the strength of signal detected in both subgenomesof G. hirsutum, and the use of high-stringency washes (seeMaterials and Methods), which indicate a high degree of homologybetween repetitive element copies in the A and D-subgenomes of G.hirsutum.

The relative paucity of subgenome-specific elements is most readilyaccounted for by assuming the occurrence of inter-subgenomic concertedevolution of elements that were not genome specific immediatelyfollowing polyploidization. FISH of six elements selected for highrepresentation in both subgenomes of G. hirsutum(A_h, D_h) yielded strong to moderate signal in theA₂ genome of G. arboreum, but none in theD₅ genome of G. raimondii. Their distribution inthe A_h and D_h subgenomes and the A₂genome but not the D₅ genome, the putative ancestorof the D_h genome, suggests that (1) most or all of the 17subgenome-nonspecific elements are of A-genomic origin and (2)subsequent to polyploidization A-genome elements have"infected" the D-subgenome or "converted"homeologous but divergent elements to sequences homologous to those inthe A-subgenome.

An alternative explanation is that G. raimondii is not themodern antecedent of the G. hirsutum D-subgenome donor. Assuming such an explanation alone to account for our findings, all ofthe elements that were not genome specific must have been highlyconserved between the A-subgenome donor and the actual D-subgenomeancestor during the estimated 4–10 million years of diploiddivergence prior to polyploidization (Wendel,1989; Wendel and Albert,1992). If the D₅ genome of G. raimondii isnot the modern antecedent of the D-subgenome donor, it is likely closelyrelated to the ancestral D-genome diploid. It thus would be expected toshare a similar complement of repetitive DNAs, and the complete absenceof the elements observed in G. raimondii would be highlyincongruous with this hypothesis. A similar possibility is that G.raimondii is the modern antecedent of the D_h genome, butthat elements previously common to both A- and D-genome diploidprogenitors have been lost in G. raimondii subsequent topolyploidization. This hypothesis is unlikely because it implicitlyrequires differential conservation and elimination of specificrepetitive elements prior to versus subsequent to the time ofpolyploidization. Under the hypothesis, all of the 17 elements that wefound not to be AD-subgenome-specific would necessarily have beenconserved prior to polyploidization, but some or most of these sameelements (at least the six tested) would necessarily have beendifferentially eliminated from the G. raimondii lineage afterthe time polyploidization gave rise to the AD lineage.

The two mechanisms most commonly suggested to cause concertedevolution of interspersed repetitive elements are gene conversion andreplicative transposition (Dover, 1982;Elder and Turner, 1995). The highlyinterspersed distribution of the repetitive elements used in this studysuggests that many of these elements may at one time have been mobile. Copy-number estimates of the elements used from Zhao, Wing, and Paterson (1995), and roughestimates based on FISH signal, suggest that many of the elements thatare not genome specific are present in tens of thousands of copies inthe G. hirsutum D-subgenome. Insertion of such high numbers ofelements could potentially lead to decreased fitness. Effects due toinsertional mutagenesis, however, would be moderated by two factors: (1)the pericentromeric regions where genome-nonspecific elements tend toaccumulate have a much lower proportion of single- and low-copysequences than do distal regions (Zwick et al.,1997), and (2) the polyploid nature of G. hirsutumwould minimize phenotypic effects through redundancy of codingsequences. Further, because of the significant period of time sincepolyploidization, a high rate of transposition would not be necessary toaccount for our findings. Alternatively, gene conversion as a cause forour findings cannot be ruled out.

The fact that some interspersed repetitive elements exhibit strongsubgenome specificity whereas others do not indicates that there is morethan a single mechanism responsible for concerted evolution ofinterspersed repeats in Gossypium. The differences amongelements that underlie such differences in behavior are not clear,though some may be proposed. Subgenome-specific elements may representtransposable elements that have lost their ability to "jump"within the G. hirsutum genome, either due to strict regulationof elemental activity by the host genome or because of defects withinthe elements. Constraints on elemental activity may have arisen priorto polyploidy or concomitantly with it. If gene conversion wereresponsible for the concerted evolution of subgenome-nonspecificelements, then failure to convert repeats in the D-subgenome could bedue to position within the genome or specific regulation ofrecombination between these elements (Keil andMcWilliams, 1993; Murti, Bumbulis, andSchimenti, 1994).

The results presented previously on rDNA (Hanson et al., 1996), and herein indicate thatGossypium repetitive elements behave in a dynamic and variedmanner, suggesting repetitive DNA may play a significant role in theevolution of polyploid genomes. It is likely genomic elasticity isgenerated by the variable nature of repetitive DNA, creating a dynamicand powerful force in the evolution of polyploid organisms. The resultspresented here indicate the need for more investigations of both theeffects of polyploidy on repetitive element behavior and, conversely, onthe effects of repetitive element behavior on the evolution of polyploidorganisms. More generally the results indicate the utility ofGossypium as a model organism for studies of polyploidevolution and warrant the increased study of repetitive DNA in polyploidorganisms.

	FOOTNOTES

 
¹

³ Current address: University of Michigan Medical Center, MRSB-II, C568, Ann Arbor, Michigan 48109.

⁵ Author for correspondence (Ph: 409 845-2745; FAX: 409 862-4733; e-mail:monosom{at}tamu.edu ).

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This Article Abstract Full Text (PDF) Submit a response Alert me when this article is cited Alert me when eLetters are posted Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via ISI Web of Science (28) Citing Articles via Google Scholar Google Scholar Articles by Hanson, RobertE. Articles by Price, H.J. Search for Related Content PubMed Articles by Hanson, RobertE. Articles by Price, H.J. Agricola Articles by Hanson, RobertE. Articles by Price, H.J.