Species-specific Repeats Research Articles

Worldwide sequence conservation of transmission-blocking vaccine candidate Pvs230 in Plasmodium vivax

Pfs230, surface protein of gametocyte/gamete of the human malaria parasite, Plasmodium falciparum, is a prime candidate of malaria transmission-blocking vaccine. Plasmodium vivax has an ortholog of Pfs230 (Pvs230), however, there has been no study in any aspects on Pvs230 to date. To investigate whether Pvs230 can be a vivax malaria transmission-blocking vaccine, we performed evolutionary and population genetic analysis of the Pvs230 gene (pvs230: PVX_003905). Our analysis of Pvs230 and its orthologs in eight Plasmodium species revealed two distinctive parts: an interspecies variable part (IVP) containing species-specific oligopeptide repeats at the N-terminus and a 7.5kb interspecies conserved part (ICP) containing 14 cysteine-rich domains. Pvs230 was closely related to its orthologs, Pks230 and Pcys230, in monkey malaria parasites. Analysis of 113 pvs230 sequences obtained from worldwide, showed that nucleotide diversity is remarkably low in the non-repeat 8-kb region of pvs230 (θπ=0.00118) with 77 polymorphic nucleotide sites, 40 of which results in amino acid replacements. A signature of purifying selection but not of balancing selection was seen on pvs230. Functional and/or structural constraints may limit the level of polymorphism in pvs230. The observed limited polymorphism in pvs230 should ground for utilization of Pvs230 as an effective transmission-blocking vaccine.

Characteristics analysis of complete ribosomal DNA sequence in Chinese mitten crab (<I>Eriocheir sinensis</I>)

Ribosomal DNA is usually selected as molecular marker for phylogenetic study and the sequence variances especially in IGS region can affect the growth rate of organisms to certain extent. A complete rDNA of Chinese mitten crab (Eriocheir sinensis) was isolated in this study. The rDNA is 11 660 bp in size and consists of 18S(1 873 bp),ITS-1(317 bp),5. 8S(163 bp),ITS-2(614 bp),28S(4 461 bp) and IGS(4 240bp). The (AT) contents of different regions range from 40. 1% to 48. 6% ,which are lower than those in Drosophila melanogaster (55. 8% - 80. 0% ) and higher than Cyprinus carpio (22. 0% - 43. 7% ). The SSR loci per 100 nucleotides in the sequence of descending are ITS-2(0. 98% ),IGS(0. 49% ),28S(0. 38% ), ITS-1(0. 32% ),18S(0. 21% ),5. 8S(0% ). The results of ITS2 intra-variances analysis showed that two types of ITS-2 existed in Chinese mitten crab,with a 12 bp(CGCAGGACCACC) insertion at 405 nt. The IGS region is 4 240 bp in size and there are 136 - 139 bp species-specific repeats that contain an Xho I restriction site. And a stem-loop structure (182 pairs stem and 21 nucleotides loop) is located following the specific repeats. The sequence of rDNA in the Chinese mitten crab will provide the foundation of studying the variances among different geographical populations and exploring the molecular marker associated with the fast growth rate of the Chinese mitten crab.

Detection of species‐specific long VNTRs in mitochondrial control region and their application to identifying sympatric Hong Kong grouper (Epinephelus akaara) and yellow grouper (Epinephelus awoara)

Length variation and heteroplasmy were observed in PCR products of the first half of mtDNA control region of both Hong Kong grouper (Epinephelus akaara) and yellow grouper (Epinephelus awoara). DNA sequencing unveiled the phenomena were caused by the presence of species-specific long variable number tandem repeats (VNTRs). This is the first report on the mtDNA VNTRs and their heteroplasmy in groupers. Moreover, these VNTRs are also the longest such structure found in teleost fish. Thereafter, we designed two species-specific PCR reverse primers according to the 3' end sequences of the VNTRs and successfully established assays for the identification of these two sympatric grouper species.

Conservation of Silk Genes in Trichoptera and Lepidoptera

Larvae of the sister orders Trichoptera and Lepidoptera are characterized by silk secretion from a pair of labial glands. In both orders the silk filament consists of heavy (H)- and light (L)-chain fibroins and in Lepidoptera it also includes a P25 glycoprotein. The L-fibroin and H-fibroin genes of Rhyacophila obliterata and Hydropsyche angustipennis caddisflies have exon/intron structuring (seven exons in L-fibroin and two in H-fibroin) similar to that in their counterparts in Lepidoptera. Fibroin cDNAs are also known in Limnephilus decipiens, representing the third caddisfly suborder. Amino acid sequences of deduced L-fibroin proteins and of the terminal H-fibroin regions are about 50% identical among the three caddisfly species but their similarity to lepidopteran fibroins is <25%. Positions of some residues are conserved, including cysteines that were shown to link the L-fibroin and H-fibroin by a disulfide bridge in Lepidoptera. The long internal part of H-fibroins is composed of short motifs arranged in species-specific repeats. They are extremely uniform in R. obliterata. Motifs (SX)n, GGX, and GPGXX occur in both Trichoptera and Lepidoptera. The trichopteran H-fibroins further contain charged amphiphilic motifs but lack the strings of alanines or alanine-glycine dipeptides that are typical lepidopteran motifs. On the other hand, sequences composed of a motif similar to ERIVAPTVITR surrounded by the (SX)4-6 strings and modifications of the GRRGWGRRG motif occur in Trichoptera and not in Lepidoptera.

Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms.

Motivation: The concentration of pathogen DNA in biological samples is often very low. Therefore, the sensitivity of diagnostic tests is always a critical factor.Results: We have developed a novel computational method that identifies species-specific repeats from microbial organisms and automatically designs species-specific PCR primers for these repeats. We tested the methodology on 30 randomly chosen microbial species and we demonstrate that species-specific repeats longer than 300 bp exist in all these genomes. We also used our methodology to design species-specific PCR primers for 86 repeats from five medically relevant microbial species. These PCR primers were tested experimentally. We demonstrate that using species-specific repeats as a PCR template region can increase the sensitivity of PCR in diagnostic tests.Availability and Implementation: A web version of the method called MultiMPrimer3 was implemented and is freely available at http://bioinfo.ut.ee/multimprimer3/.Contact: maido.remm@ut.eeSupplementary information: Supplementary data are available at Bioinformatics online.

Modeling and structure function analysis of the putative anchor site of yeast telomerase

Telomerase is a ribonucleoprotein reverse transcriptase responsible for extending one strand of the telomere terminal repeats. Unique among reverse transcriptases, telomerase is thought to possess a DNA-binding domain (known as anchor site) that allows the enzyme to add telomere repeats processively. Previous crosslinking and mutagenesis studies have mapped the anchor site to an N-terminal region of TERT, and the structure of this region of Tetrahymena TERT was recently determined at atomic resolutions. Here we use a combination of homology modeling, electrostatic calculation and site-specific mutagenesis analysis to identify a positively charged, functionally important surface patch on yeast TERT. This patch is lined by both conserved and non-conserved residues, which when mutated, caused loss of telomerase processivity in vitro and telomere shortening in vivo. In addition, we demonstrate that a point mutation in this domain of yeast TERT simultaneously enhanced the repeat addition processivity of telomerase and caused telomere elongation. Our data argue that telomerase anchor site has evolved species-specific residues to interact with species-specific telomere repeats. The data also reinforce the importance of telomerase processivity in regulating telomere length.

Telomere-associated endonuclease-deficient Penelope -like retroelements in diverse eukaryotes

The evolutionary origin of telomerases, enzymes that maintain the ends of linear chromosomes in most eukaryotes, is a subject of debate. Penelope-like elements (PLEs) are a recently described class of eukaryotic retroelements characterized by a GIY-YIG endonuclease domain and by a reverse transcriptase domain with similarity to telomerases and group II introns. Here we report that a subset of PLEs found in bdelloid rotifers, basidiomycete fungi, stramenopiles, and plants, representing four different eukaryotic kingdoms, lack the endonuclease domain and are located at telomeres. The 5' truncated ends of these elements are telomere-oriented and typically capped by species-specific telomeric repeats. Most of them also carry several shorter stretches of telomeric repeats at or near their 3' ends, which could facilitate utilization of the telomeric G-rich 3' overhangs to prime reverse transcription. Many of these telomere-associated PLEs occupy a basal phylogenetic position close to the point of divergence from the telomerase-PLE common ancestor and may descend from the missing link between early eukaryotic retroelements and present-day telomerases.

Centromere separation and association in the nuclei of an interspecific hybrid between Torenia fournieri and T. baillonii (Scrophulariaceae) during mitosis and meiosis

In the nuclei of some interspecific hybrid and allopolyploid plant species, each genome occupies a separate spatial domain. To analyze this phenomenon, we studied localization of the centromeres in the nuclei of a hybrid between Torenia fournieri and T. baillonii during mitosis and meiosis using three-dimensional fluorescence in situ hybridization (3D-FISH) probed with species-specific centromere repeats. Centromeres of each genome were located separately in undifferentiated cells but not differentiated cells, suggesting that cell division might be the possible force causing centromere separation. However, no remarkable difference of dividing distance was detected between chromatids with different centromeres in anaphase and telophase, indicating that tension of the spindle fiber attached to each chromatid is not the cause of centromere separation in Torenia. In differentiated cells, centromeres in both genomes were not often observed for the expected chromosome number, indicating centromere association. In addition, association of centromeres from the same genome was observed at a higher frequency than between different genomes. This finding suggests that centromeres within one genome are spatially separated from those within the other. This close position may increase possibility of association between centromeres of the same genome. In meiotic prophase, all centromeres irrespective of the genome were associated in a certain portion of the nucleus. Since centromere association in the interspecific hybrid and amphiploid was tighter than that in the diploid parents, it is possible that this phenomenon may be involved in sorting and pairing of homologous chromosomes.

Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons

Orthologous gene structures in eight vertebrate species were compared on a genomic scale to detect the birth and maturation of new internal exons during the course of evolution. We found that 40% of new human exons are alternatively spliced, and most of these are cassette exons (exons that are either included or skipped in their entirety) with low inclusion rates. This proportion decreases steadily as older and older exons are examined, even as splicing efficiency increases. Remarkably, the great majority of new cassette exons are composed of highly repeated sequences, especially Alu. Many new cassette exons are 5' untranslated exons; the proportion that code for protein increases steadily with age. New protein-coding exons evolve at a high rate, as evidenced by the initially high substitution rates (K(s) and K(a)), as well as the SNP density compared with older exons. This dynamic picture suggests that de novo recruitment rather than shuffling is the major route by which exons are added to genes, and that species-specific repeats could play a significant role in recent evolution.

High-resolution comparative mapping among man, cattle and mouse suggests a role for repeat sequences in mammalian genome evolution

BackgroundComparative mapping provides new insights into the evolutionary history of genomes. In particular, recent studies in mammals have suggested a role for segmental duplication in genome evolution. In some species such as Drosophila or maize, transposable elements (TEs) have been shown to be involved in chromosomal rearrangements. In this work, we have explored the presence of interspersed repeats in regions of chromosomal rearrangements, using an updated high-resolution integrated comparative map among cattle, man and mouse.ResultsThe bovine, human and mouse comparative autosomal map has been constructed using data from bovine genetic and physical maps and from FISH-mapping studies. We confirm most previous results but also reveal some discrepancies. A total of 211 conserved segments have been identified between cattle and man, of which 33 are new segments and 72 correspond to extended, previously known segments. The resulting map covers 91% and 90% of the human and bovine genomes, respectively. Analysis of breakpoint regions revealed a high density of species-specific interspersed repeats in the human and mouse genomes.ConclusionAnalysis of the breakpoint regions has revealed specific repeat density patterns, suggesting that TEs may have played a significant role in chromosome evolution and genome plasticity. However, we cannot rule out that repeats and breakpoints accumulate independently in the few same regions where modifications are better tolerated. Likewise, we cannot ascertain whether increased TE density is the cause or the consequence of chromosome rearrangements. Nevertheless, the identification of high density repeat clusters combined with a well-documented repeat phylogeny should highlight probable breakpoints, and permit their precise dating. Combining new statistical models taking the present information into account should help reconstruct ancestral karyotypes.

DNA forensics and the poaching of wildlife in Italy: A case study

DNA molecular techniques were used in a forensic investigation involving the poaching of wildlife in a national park of Italy. A poacher, after having snared a wild boar ( Sus scrofa) sow, knifed it to death. The animal was retrieved by conservation officers at the scene before the poacher could remove the carcass. Subsequently, the suspect denied the charges. During a search of his home, a bloodstained knife was confiscated. A method to identify the species from the DNA extracted from the stains revealed the blood to be that of the non-domestic form of Sus scrofa. Further DNA typing for individual identity using species-specific single tandem repeats or microsatellites (STRs) showed that the DNA on the knife matched that of the poached boar. Based upon the forensic evidence obtained, the suspect was convicted of poaching and of cruelty to animals.

Meiotic behaviour of individual chromosomes in allotriploid Alstroemeria hybrids.

Chromosome association and chiasma formation were studied in pollen mother cells at metaphase I of four allotriplod BC1 plants (2n=3x=24) obtained from the backcross of the hybrid Alstroemeria aurea x A. inodora with its parent A. inodora. We distinguished the chromosomes of both parental species by genomic in situ hybridization (GISH), whereas the individual chromosomes were identified on the basis of their multicolour FISH banding patterns obtained after a second hybridization with two species-specific satellite repeats as probes. All the four BC1 plants possessed two genomes of A. inodora and one of A. aurea. Variable numbers of recombinant chromosomes, resulting from meiotic recombination in the interspecific hybrid, were present in these plants. The homologous A. inodora chromosomes generally formed bivalents, leaving the homoeologous A. aurea chromosomes unassociated. High frequencies of trivalents were observed for the chromosome sets that contained recombinant chromosomes, even when the recombinant segments were small. Chromosome associations in the trivalents were restricted to homologous segments. The implications of the absence of homoeologous chromosome pairing on gamete constitution and prospects for introgression in Alstroemeria are discussed.

Molecular markers predictive of the capacity of expanded human articular chondrocytes to form stable cartilage in vivo.

To establish a model and associated molecular markers for monitoring the capacity of in vitro-expanded chondrocytes to generate stable cartilage in vivo. Adult human articular chondrocytes (AHAC) were prepared by collagenase digestion of samples obtained postmortem and were expanded in monolayer. Upon passaging, aliquots of chondrocyte suspensions were either injected intramuscularly into nude mice, cultured in agarose, or used for gene expression analysis. Cartilage formation in vivo was documented by histology, histochemistry, immunofluorescence for type II collagen, and proteoglycan analysis by 35S-sulfate incorporation and molecular sieve chromatography of the radiolabeled macromolecules. In situ hybridization for species-specific genomic repeats was used to discriminate human-derived from mouse-derived cells. Gene expression dynamics were analyzed by semiquantitative reverse transcription-polymerase chain reaction. Intramuscular injection of freshly isolated AHAC into nude mice resulted in stable cartilage implants that were resistant to mineralization, vascular invasion, and replacement by bone. In vitro expansion of AHAC resulted in the loss of in vivo cartilage formation. This capacity was positively associated with the expression of fibroblast growth factor receptor 3, bone morphogenetic protein 2, and alpha1(II) collagen (COL2A1), and its loss was marked by the up-regulation of activin receptor-like kinase 1 messenger RNA. Anchorage-independent growth and the reexpression of COL2A1 in agarose culture were insufficient to predict cartilage formation in vivo. AHAC have a finite capacity to form stable cartilage in vivo; this capacity is lost throughout passaging and can be monitored using a nude mouse model and associated molecular markers. This cartilage-forming ability in vivo may be pivotal for successful cell-based joint surface defect repair protocols.

Self-amplification of satellite DNA in vitro

We describe a PCR-like reaction in which genomic DNA acts as a template as well as a primer. Interaction between genomic tandem repeat units leads to self-amplification of satellite DNA. This genomic self-priming PCR (GSP-PCR) allowed the rapid amplification of species-specific tandem repeats of horse, cattle, dolphin, and chicken. A novel specific satellite of ostrich with a repeat unit of 60 bp was isolated using this method.

Mutational analysis of the Tetrahymena telomerase RNA: identification of residues affecting telomerase activity in vitro.

Telomere-specific repeat sequences are essential for chromosome end stability. Telomerase maintains telomere length by adding sequences de novo onto chromosome ends. The template domain of the telomerase RNA component dictates synthesis of species-specific telomeric repeats and other regions of the RNA have been suggested to be important for enzyme structure and/or catalysis. Using enzyme reconstituted in vitro with RNAs containing deletions or substitutions we identified nucleotides in the RNA component that are important for telomerase activity. Although many changes to conserved features in the RNA secondary structure did not abolish enzyme activity, levels of activity were often greatly reduced, suggesting that regions other than the template play a role in telomerase function. The template boundary was only altered by changes in stem II that affected the conserved region upstream of the template, not by changes in other regions, such as stems I, III and IV, consistent with a role of the conserved region in defining the 5' boundary of the template. Surprisingly, telomerase RNAs with substitutions or deletion of residues potentially abolishing the conserved pseudoknot structure had wild-type levels of telomerase activity. This suggests that this base pairing interaction may not be required for telomerase activity per se but may be conserved as a regulatory site for the enzyme in vivo.

A new family of dispersed repeats from Brassica nigra: characterization and localization

The 459-bp HindIII (pBN-4) and the 1732-bp Eco RI (pBNE8) fragments from the Brassica nigra genome were cloned and shown to be members of a dispersed repeat family. Of the three major diploid Brassica species, the repeat pBN-4 was found to be highly specific for the B. nigra genome. The family also hybridized to Sinapis arvensis showing that B. nigra had a closer relationship with the S. arvensis genome than with B. oleracea or B. campestris. The clone pBNE8 showed homology to a number of tRNA species indicating that this family of repeats may have originated from a tRNA sequence. The species-specific 459-bp repeat pBN-4 was localized on the B. nigra chromosomes using monosomic addition lines. In addition to the localization of pBN-4, the chromosomal distribution of two other species-specific repeats, pBN34 and pBNBH35 (reported earlier), was studied. The dispersed repeats pBN-4 and pBNBH35 were found to be present on all of the chromosomes, whereas the tandem repeat pBN34 was localized on two chromosomes.

Comparison of the 5′-flanking sequences of the human and bovine von Willebrand factor-encoding genes reveals alternation of highly homologous domains with species-specific Alu-type repeats

von Willebrand factor (vWF), a multimeric glycoprotein important for hemostasis, is specifically synthesized in endothelial cells and in platelet precursors (megakaryocytes). Recent studies from two laboratories, including ours, were published regarding the cell-specific transcription of reporter genes controlled by the human (hu) vWF promoter in transfected bovine (bo) endothelial cells and cells of non-endothelial origins. In order to verify that the regulatory domains previously characterized in the 5′ region of hu vWF are also present in bo vWF, we have sequenced 1.9 kb unstream from the cap site, plus five exons. The comparison of human and bovine exons two to five shows homology of 83% at the nucleotide (nt) level and 78% at the deduced amino-acid sequence level. The bovine and human exons one, which are non-coding and span 233 and 250 bp, respectively, are only 64% homologous. In the first exon, potentially involved in endothelial-cell-specific transcription, the binding site for factor Sp1 is present in bo vWF, whereas the GATA sequence is replaced by a GACA sequence. The sequence corresponding to the human basal promoter, located between nt −89 and +19, is well conserved with 82% homology. However, the human TAATTA sequence (at nt −32) considered to be a TATA box, is replaced by TCATTA, and the CCAAT element at nt −18 is replaced by CCTGT. Among domains involved in transcription, the negative regulatory domain located 5′ from the core promoter is highly conserved. The bovine sequence upstream from the first intron can be aligned with the human sequence up to nt −656 which is located in a polymorphic poly(GT) 18–26 sequence. At this site, the bovine DNA contains an insertion of 523 bp which corresponds to a bovine Alu-type art2 repeat of 331 bp flanked by bovine microsatellites. The art2 sequence is an Alu-type repeat in artiodactyls with at least 100 000 copies in the bovine genome. Upstream from this insertion, 368 bp of the bovine sequence can be aligned with the human counterpart up to a 9-bp element which flanks an human Alu repeat which is absent from the bovine DNA. Upstream of the human Alu insertion and a duplicate of the 9-bp element, the two sequences are again homologous.

Telomeres: No end in sight

Why do eukaryotic chromosomes end the way they do? One basic function of teiomeres, the ends of chromosomes, is to preserve themselves; they allow replenishment of the chromosomai DNA termini by an independent mechanism of DNA synthesis, to make up for the incomplete replication of the 5’ end of each chromosomal DNA strand by the primary cellular DNA replication machinery. But why is a special DNA sequence needed at teiomeres? Obsetvations of teiomere behavior indicate that teiomeres play multiple roles, some new and surprising. This minireview highlights recent work that throws into sharp relief the question of why a specific DNA sequence is required to stabilize chromosomes. The Correct Telomeric DNA Sequence Is Necessary to Stabilize Chromosomes In a great phyiogenetic variety of eukaryotes, teiomeric DNA consists of a terminal stretch of tandem, speciesspecific repeats of very short (typically 5-8 bp) simple sequences, characterized by clusters of G residues on the strand that forms the 3’ end of each chromosomai DNA strand. This strand is synthesized by the ribonucieoprotein enzyme telomerase (reviewed by Blackburn, 1992) an essential cellular reverse transcriptase that uses a short sequence within its RNA moiety as the template for addition of the G-cluster teiomeric DNA strand to chromosome ends. Without replenishment of telomeric sequences, which normally requires telomerase to make up for losses caused by incomplete replication, the chromosome ends gradually recede (Figure 1). Usually, chromosomes with broken ends lacking their species-specific teiomeric DNA sequences or that fail to maintain preexisting teiomeric DNA on the end of chromosomes are not stably maintained (reviewed by Blackburn, 1991). This instability has been emphasized by recent studies in the yeast Saccharomyces cerevisiae. Sandeil and Zakian (1993) removed a telomere in a controlled way from a dispensable chromosome and watched the fate of the chromosome immediately thereafter. The short-term response of the ceil was very similar to that elicited by introducing a single break into a circular, nonessential plasmid, producing two teiomereiess ends; this response included temporary arrest of the ceil cycle (Bennett et al., 1993; Sandeii and Zakian, 1993). Subsequently, the linear chromosome lacking one teiomere was lost, although sometimes only after several ceil divisions, unless it was stabilized by acquiring ateiomere by some means (Sandeii and Zakian, 1993). Another line of evidence highlighting the need for the telomeric DNA sequence itself to maintain chromosomes stably in yeast has come from asking how cells can survive Minireview

Characterization of phosphoglycan-containing secretory products of Leishmania.

This article presents an overview on phosphoglycan-containing components secreted by the insect and mammalian stages of several species of Leishmania, the causative agents of leishmaniasis in the Old and New World. Firstly, promastigotes of all three species considered, L. mexicana, L. donovani and L. major, shed lipophosphoglycan (LPG) into the culture medium possibly by release of micelles from the cell surface. Like the cell-associated LPG, culture supernatant LPG is amphiphilic and composed of a lysoalkylphosphatidylinositol-phosphosaccharide core connected to species-specific phosphosaccharide repeats and oligosaccharide caps. Secondly, all three species release hydrophilic phosphoglycan. Thirdly, all three species appear to secrete proteins covalently modified by phosphosaccharide repeats and oligosaccharide caps. In the case of promastigotes of L. mexicana, these components are organized as two filamentous polymers released from the flagellar pocket: the secreted acid phosphatase (sAP) composed of a 100 kDa phosphoglycoprotein and a protein-containing high-molecular-weight-phosphoglycan (proteo-HMWPG) and fibrous networks likewise composed of phosphoglycan possibly linked to protein. Structural analyses and gene cloning suggest that the parasites can covalently modify protein regions rich in serine and threonine residues by the attachment of phosphosaccharide repeats capped by oligosaccharides. We propose that the networks formed in vitro correspond to fibrous material previously demonstrated in the digestive tract of infected sandflies. In the case of L. donovani, the sAP is also modified by phosphoglycans but contains neither proteo-HMWPG nor does it aggregate to filaments. Finally, L. mexicana amastigotes release proteo-HMWPG via the flagellar pocket into the parasitophorous vacuole of infected macrophages.(ABSTRACT TRUNCATED AT 250 WORDS)

Isolation of a new species-specific repetitive sequence from Thinopyrum elongatum and its use in the studies of alien translocations

A new repetitive sequence that is extremely abundant and well dispersed in the Thinopyrum elongatum genome but present in low-copy number in wheat (Triticum aestivum L.) has been isolated. This repeat and a Th. elongatum repeat isolated in another laboratory were used to identify cosmid genomic clones containing the repeats and, thus, putatively located on a Th. elongatum/T. aestivum translocation arm. Most of the selected cosmids contained single- or low-copy sequences, making them potentially useful in mapping studies. The repeats were used in deletion mapping to deduce gene order of three genes located on the Th. elongatum translocation arm. In situ hybridization studies suggested that this newly identified Th. elongatum repeat is well dispersed throughout the Thinopyrum genome but present at only one location in wheat. This raises some interesting questions about the role of such repetitive elements in the evolution of grass species.