Isolation, characterization, and analysis of Leymus-specific DNA sequences.

Genomic Southern hybridization using labeled total genomic DNA of Leymus mollis as probe showed intense hybridization signals on all restriction enzyme digested DNA from five species of Leymus Hochst., and four species of Psathyrostachys Nevski. Experiments using the same L. mollis probe, but with unlabeled blocking DNA from Psathyrostachys, showed no hybridization at all. These two genera evidently had the same genomic content. Southern hybridization without blocking allowed identification of DNA fragments abundant in Leymus and Psathyrostachys. Fragments potentially specific to Leymus were cloned. Five repetitive DNA clones from L. mollis and L. arenarius were characterized: pLmIs1, pLmIs44, pLmIs51, pLmIs53, and pLaIs56. These clones hybridized to both Leymus and Psathyrostachys on Southern blots - no clone hybridized to only one of these genera. Both Southern blot and fluorescence in situ hybridization (FISH) experiments showed that all the clones contained dispersed repetitive sequences. They painted all and whole chromosomes uniformly except at centromeres, telomeres, and nucleolar organiser regions. Three of these clones, i.e., pLmIs1, pLmIs44, and pLmIs53, were essentially specific to Leymus and Psathyrostachys - little or no hybridization was detected in other genera such as Triticum, Hordeum, Thinopyrum, or Elymus. Sequence analysis further revealed that the clones were part of retroelements. In particular, the clone pLmIs44 produced hybridization profiles suitable for analysis of genetic relatedness among species. The present study shows that Leymus and Psathyrostachys share the same basic genome, Ns, and therefore provides strong evidence for combining these two genera.     

Molecular cytogenetics of Leymus: Mapping the Ns genome-specific repetitive sequences

The objective of this paper is to summarize the work in my group on FISH (fluorescent in situ hybridization) mapping of Ns-specific repetitive DNA sequences fromLeymus and discuss the results in the context of classification based on the genome system currently used among Triticeae researchers. The key question here is whether the genome composition of a tetraploid Leymus species should be NsXm or NsNs (Ns₁Ns₂). Different types of Leymus-specific dispersed retroelement-like repeats have been isolated and characterized. Because the sequences occur in significantly high copy number in Leymus, based on strong hybridization signal in Southern blots, they are considered essentially specific to Leymus. They are also abundant in Psathyrostachys, the progenitor of Ns genome in Leymus. These dispersed repeats are found to distribute over the whole of all Leymus chromosomes, without any differentiation between chromosomes that have been suggested to be of different genomic origins, meaning that all genomes in Leymus are the same. GISH (genomic in situ hybridization) experiments on Leymus chromosomes using Psathyrostachys genomic DNA as probes further support the NsNs (Ns₁Ns₂) genome constitution for Leymus. The Xm genome of an unknown origin might have been there in the beginning of the allopolyploidization process, but the Ns genome-specific elements must have spread predominantly and rapidly across genomes, thus homogenizing the nuclear genomes of Leymus. I present here for the first time evidence that Ns-specific dispersed repeats can spread in a very short time, from Leymus over to wheat in Triticum × Leymus hybrids growing in artificial conditions.     

Phylogenetic Analysis of Leymus (Poaceae: Triticeae) Inferred from Nuclear rDNA ITS Sequences

To investigate the phylogenetic relationships of polyploid Leymus (Poaceae: Triticeae), sequences of the nuclear rDNA internal transcribed spacer region (ITS) were analyzed for 34 Leymus accessions representing 25 species, together with three Psathyrostachys species (Ns genome), two Pseudoroegneria (St genome) species, Lophopyrum elongatum (E(e) genome), and Thinopyrum bessarabicum (E(b) genome). The phylogenetic analyses (maximum likelihood and Bayesian inference) supported two major clades, one including 21 Leymus species and three Psathyrostachys species, the other with nine Leymus species and four diploid species. The ITS RNA secondary structure of the Leymus species was compared with that of their putative diploid donor. It is suggested that (1) the species from the same areas or neighboring geographic regions are closely related to each other; (2) L. coreanus, L. duthiei, L. duthiei var. longearistatus, and L. komarovii are closely related to other Leymus species, and it is reasonable to transfer these species from the genus Hystrix to Leymus; (3) the ITS sequences of Leymus are evolutionarily distinct; (4) the different Leymus species and different distribution of a species derived their Ns genome from different Psathyrostachys species; and (5) there is a close relationship among Leymus, Pseudoroegneria, Lophopyrum, and Thinopyrum, but it is difficult to presume that the St, E(e), and E(b) genome may be the Xm genome donor of the Leymus species.     

Phylogeny and molecular evolution of the DMC1 gene in the polyploid genus Leymus (Triticeae: Poaceae) and its diploid relatives

The level and pattern of nucleotide variation in duplicate genes provide important information on the evolutionary history of polyploids and divergent processes between homoeologous loci within lineages. Leymus, a group of allopolyploid species with the NsXm genomes, is a perennial genus with a diverse array of morphology, ecology, and distribution in Triticeae. To estimate the phylogeny and molecular evolution of a single-copy DMC1 gene in Leymus and its diploid relatives,DMC1 homoeologous sequences were isolated from the sampled Leymus species and were analyzed with those from 30 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that: (i) different Leymus species might derive their Ns genome from different Psathyrostachys species; (ii) Pseudoroegneria has contributed to the nuclear genome of some Leymus species, which might result from recurrent hybridization or incomplete lineage sorting; (iii) the Xm genome origin of Leymus could differ among species; (iv) rapid radiation and multiple origin might account for the rich diversity, numbers of species, and wide ecological adaptation of Leymus species; and (v) the DMC1 sequence diversity of the Ns genome in Leymus species was lower than that in the Psathyrostachys diploids, while the level of DMC1 sequence diversity in Leymus was higher than that in diploid Pseudoroegneria. Our results provide new insight on the evolutionary dynamics of duplicate DMC1 genes, polyploid speciation, and the phylogeny of Leymus species.     

Phylogeny of Hystrix and related genera (Poaceae: Triticeae) based on nuclear rDNA ITS sequences

The taxonomic status of Hystrix and phylogenetic relationships among Hystrix and its related genera of Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), Elymus (StH), Leymus (NsXm), Thinopyrum bessarabicum (E(b)) and Lophopyrum elongatum (E(e)) were estimated from sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The type species of Hystrix, H. patula, clustered with species of Pseudoroegneria, Hordeum, Elymus, Th. bessarabicum and Lo. elongatum, while H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii were grouped with Psathyrostachys and Leymus species. The results indicate that: (i) H. patula is distantly related to other species of Hystrix, but is closely related to Elymus species; (ii) H. duthiei ssp. duthiei, H. duthiei ssp. longearistata, H. coreana and H. komarovii have a close affinity with Psathyrostachys and Leymus species, and H. komarovii might contain the NsXm genome of Leymus; and (iii) the St, H and Ns genomes in Hystrix originate from Pseudoroegneria, Hordeum and Psathyrostachys, respectively, while the Xm in Hystrix and Leymus has a complex relationship with the E or St genomes. According to the genomic system of classification in Tiritceae, it is reasonable to treat Hystrix patula as Elymus hystrix L, and the other species of Hystrix as species of a section of Leymus, Leymus Sect. Hystrix.     

Phylogenetic relationships in Leymus (Poaceae: Triticeae) revealed by the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences

Using the nuclear ribosomal internal transcribed spacer (ITS) sequences and the chloroplasttrnL-F sequence, phylogeneic analysis was performed on 57 accessions of species in the tribe Triticeae including 13 Leymus species (N(s)) with different ploidy levels and 40 diploid species from 18 genera. The ITS sequences revealed that ployploid Leymus has close phylogentic relationships with Psathyrostachys and an undefined genus in Triticeae. The trnL-F tree demonstrated close relationships between certain Leymus species and Psathyrostachys, and other Leymus species distributed in North America were far from Psathyrostachys. Based on these results, it is unlikely that the unknown genome in Leymus species originated from one of the sampled diploid species in the present study. The maternal donor of all the Leymus species with a natural distribution in Eurasia were N(s) genome. Furthermore, Elymus californicus should be transferred from the genus Elymus to Leymus.     

Genome- and species-specific markers and genome relationships of diploid perennial species in Triticeae based on RAPD analyses.

Eight different genomes (E, H, I, P, R, St, W, and Ns) represented by 22 diploid species of the tribe Triticeae were analyzed using the random amplified polymorphic DNA (RAPD) technique. The genome relationships were obtained based on 371 RAPD fragments produced with 30 primers. The four species of the genus Psathyrostachys (having various Ns genomes) were closely related. The genomes Ee and Eb had a similarly close relationship and were distinct from all other genomes analyzed. Genomes P, R, and St were grouped in one cluster and genomes H and I in another. Genome W had a distant relationship with all other genomes. These results agree with the conclusions from studies of chromosome pairing and isozyme and DNA sequence analyses. Twenty-nine and 11 RAPD fragments are considered to be genome- and species-specific markers, respectively. One to six genome-specific markers were identified for each genome. These RAPD markers are useful in studies of genome evolution, analysis of genome composition, and genome identification.     

A study of 28 Elymus species using repetitive DNA sequences.

Four repetitive DNA sequences cloned from the barley (Hordeum vulgare) genome and common for different Triticeae species were used for a molecular study of phylogenetic relationships among 28 Elymus species. Two wild Hordeum species (H genome), two Pseudoroegneria species (S genome), Agropyron cristatum (P genome), and Australopyrum velutinum (W genome) were included as genomic representatives for the genomes that supposedly were involved in the evolution of the genus Elymus. Our results are essentially congruent with the genomic classification system. This study demonstrates that Elymus is not a monophyletic genus. Based on an analysis of Southern blot hybridization we could discriminate between SY and SH species owing to the strong specific hybridization pattern of the H genome. Hexaploid SYH species gave a hybridization pattern similar to SH species for the same reason. The results support the genomic composition of Elymus batalinii as SYP and also indicated the presence of at least one H genome in Elymus enysii with a hitherto unknown genomic constitution. Elymus erianthus had a hybridization pattern distinctly different from all other species in the investigation. Key words : Elymus, RFLP, phylogeny, repetitive DNA.     

Variations in abundance of 2 repetitive sequences in Leymus and Psathyrostachys species.

The Ns genome of the genus Psathyrostachys is a component of the polyploid genome in the genus Leymus. Using fluorescence in situ hybridization (FISH), the occurrence and abundance of 2 tandem repetitive sequences from Leymus racemosus (Lam.) Tzvelev, pLrTaiI-1 (TaiI family) and pLrPstI-1 (1 class of 350-bp family), were assayed in 4 species of the genera Psathyrostachys and Leymus. The pLrPstI-1 sequence was absent in all 4 Psathyrostachys species. While P. fragilis and P. huashanica did not have the pLrTaiI-1 sequence, 15 accessions of P. juncea and 2 accessions of P. lanuginosa had pLrTaiI-1 sites ranging in number from 7 to 16 and from 2 to 21, respectively. The numbers of pLrTaiI-1 and pLrPstI-1 sites were 1-24 and 0-30, respectively, in L. ramosus; 2-31 and 5-36 in L. racemosus; 0-4 and 0 in L. mollis; 2-9 and 24-27 in L. secalinus. The FISH assay on pLrTaiI-1 was successfully converted to a sequence-tagged-site polymerase chain reaction (STS-PCR) test using a primer pair designed from the sequence of this repetitive DNA. Seventy-three accessions representing 27 Leymus species were assayed for the abundance of pLrTaiI-1 by STS-PCR. With a few exceptions of uniformity in some accessions, nearly all Leymus species observed were heterogeneous for the abundance of pLrTaiI-1 sequence and no Leymus species was totally devoid of this repetitive sequence. These findings may have significance for the understanding of phylogeny, nature of polyploidy, adaptive ranges, and breeding potential of Leymus species.     

猬草及其近缘属植物单拷贝核Pgk1基因序列的系统发育分析

文章对禾本科小麦族猬草属及其近缘属Thinopyrum(Eb)、Lophopyrum(Ee)、拟鹅观草属(St)、新麦草属(Ns)、大麦属(H)、赖草属(NsXm)和披碱草属(StH)植物共23个类群的单拷贝核Pgk1基因序列进行系统发育分析, 探讨猬草属及其近缘属植物的系统发育关系。序列分析发现Pgk1基因序列在L. arenarius和Psa. juncea中有81 bp的Stowaway家族DNA转座元件插入, 而在Hy. duthiei、Hy. duthiei ssp. longearistata和L. akmolinensis中有29 bp Copia家族的反转录转座元件插入。最大似然和贝叶斯推断进行的系统发育分析表明: (1)猬草属模式种Hy. patula与披碱草属、拟鹅观草属和大麦属具有密切的亲缘关系; (2)猬草属的其他物种Hy. duthiei、Hy. duthiei ssp. longearistata、Hy. coreana和Hy. komarovii与新麦草属和赖草属植物亲缘关系密切。研究结果支持将Hy. patula从猬草属组合到披碱草属中, 而Hy. duthiei、Hy. duthiei ssp. longearistata、Hy. coreana和Hy. komarovii应组合到赖草属中。     

Genetic diversity and phylogeny in Hystrix (Poaceae, Triticeae) and related genera inferred from Giemsa C-banded karyotypes

The phylogenetic relationships of 15 taxa from Hystrix and the related genera Leymus (NsXm), Elymus (StH), Pseudoroegneria (St), Hordeum (H), Psathyrostachys (Ns), and Thinopyrum (E) were examined by using the Giemsa C-banded karyotype. The Hy. patula C-banding pattern was similar to those of Elymus species, whereas C-banding patterns of the other Hystrix species were similar to those of Leymus species. The results suggest high genetic diversity within Hystrix, and support treating Hy. patula as E. hystrix L., and transferring Hy. coreana, Hy. duthiei ssp. duthiei and Hy. duthiei ssp. longearistata to the genus Leymus. On comparing C-banding patterns of Elymus species with their diploid ancestors (Pseudoroegneria and Hordeum), there are indications that certain chromosomal re-arrangements had previously occurred in the St and H genomes. Furthermore, a comparison of the C-banding patterns of the Hystrix and Leymus species with the potential diploid progenitors (Psathyrostachys and Thinopyrum) suggests that Hy. coreana and some Leymus species are closely related to the Ns genome of Psathyrostachys, whereas Hy. duthiei ssp. duthiei, Hy. duthiei ssp. longearistata and some of the Leymus species have a close relationship with the E genome. The results suggest a multiple origin of the polyploid genera Hystrix and Leymus.     

Chromosomal DNA from both flagellate and non-flagellate Bordetella species contains sequences homologous to the Salmonella H1 flagellin gene

Abstract The genus Bordetella contains four species: two are non-motile, the human pathogens B. pertussis and B. parapertussis ; and two are motile, the broad host-range mammalian pathogen B. bronchiseptica , and the avian pathogen B. avium . The motility of the latter two species is due to peritrichous flagella. Here we show that strains of all four species contain DNA sequences homologous to flagellin genes. Two types of gene probe were hybridised to Bordetella chromosomal DNA in Southern blots: the structural gene for H1 flagellin of Salmonella typhimurium and an oligonucleotide derived from the conserved N-terminal amino acid sequences of various flagellin proteins. Cla I-digested DNA from all four Bordetella species hybridised with both probes in Southern blots, although each species gave a characteristic pattern of hybridisation. This indicates that the non-motile B. pertussis and B. parapertussis species contain non-expressed flagellin genes.     

Repetitive DNA, molecular cytogenetics and genome organization in the King scallop (Pecten maximus)

We studied the structure, organization and relationship of repetitive DNA sequences in the genome of the scallop, Pecten maximus, a bivalve that is important both commercially and in marine ecology. Recombinant DNA libraries were constructed after partial digestion of genomic DNA from scallop with PstI and ApaI restriction enzymes. Clones containing repetitive DNA were selected by hybridisation to labelled DNA from scallop, oyster and mussel; colonies showing strong hybridisation only to scallop were selected for analysis and sequencing. Six non-homologous tandemly repeated sequences were identified in the sequences, and Southern hybridisation with all repeat families to genomic DNA digests showed characteristic ladders of hybridised bands. Three families had monomer lengths around 40 bp while three had repeats characteristic of the length wrapping around one (170 bp), or two (326 bp) nucleosomes. In situ hybridisation to interphase nuclei showed each family had characteristic numbers of clusters indicating contrasting arrangements. Two of the repeats had unusual repetitions of bases within their sequence, which may relate to the nature of microsatellites reported in bivalves. The study of these rapidly evolving sequences is valuable to understand an important source of genomic diversity, has the potential to provide useful markers for population studies and gives a route to identify mechanisms of DNA sequence evolution.     

Cloning and characterization of repetitive DNA sequences from genomes of Oryza minuta and Oryza australiensis

The value of genome-specific repetitive DNA sequences for use as molecular markers in studying genome differentiation was investigated. Five repetitive DNA sequences from wild species of rice were cloned. Four of the clones, pOm1, pOm4, pOmA536, and pOmPB10, were isolated from Oryza minuta accession 101141 (BBCC genomes), and one clone, pOa237, was isolated from Oryza australiensis accession 100882 (EE genome). Southern blot hybridization to different rice genomes showed strong hybridization of all five clones to O. minuta genomic DNA and no cross hybridization to genomic DNA from Oryza sativa (AA genome). The pOm1 and pOmA536 sequences showed cross hybridization only to all of the wild rice species containing the C genome. However, the pOm4, pOmPB10, and pOa237 sequences showed cross hybridization to O. australiensis genomic DNA in addition to showing hybridization to the O. minuta genomic DNA.     

利用RAPD特异标记分析东北猬草染色体组成

选用5个染色体组特异的RAPD引物(St、H、Ns、Ee、Eb),对东北猬草[Hystrix komarovii (Roshev.) Ohwi]等5个猬草属及其8个近缘属物种进行PCR扩增,以探讨东北猬草的染色体组组成.结果显示:Hy.komarovii具有Ns染色体组特异的RAPD标记,而没有St、H、Ee和Eb特异的RAPD标记.表明Hy.komarovii含有Ns染色体组,而不含St和H染色体组,认为其染色体组组成可能与Hy.duthiei、Hy.coreana和Leymus arenarius一样,具有NsXm染色体组.根据染色体组分类原理,支持将东北猬草归于赖草属中.     

Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa.

DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D gneomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome.     

RPB2 sequences reveal a close phylogenetic relationship between tetraploid Hordelymus and diploid Hordeum species in Triticeae (Poaceae)

The origin of Hordelymus genome has been debated for years, and no consensus conclusion was reached. In this study, we sequenced and analyzed the RPB2 (RNA polymerase subunit II) gene from Hordelymus europaeus (L.) Harz, and its potential diploid ancestor species those were suggested in previous studies. The focus of this study was to examine the phylogenetic relationship of Hordelymus genomes with its potential donor Hordeum, Psathyrostachys, and Taeniatherum species. Two distinguishable copies of sequences were obtained from H. europaeus. The obvious difference between the two copies of sequences is a 24 bp indel (insertion/deletion). Phylogenetic analysis showed a strong affinity between Hordeum genome and Hordelymus with 85% bootstrap support. These results suggested that one genome in tetraploid H. europaeus closely related to the genome in Hordeum species. Another genome in H. europaeus is sister to the genomes in Triticeae species examined here, which corresponds well with the recently published EF-G data. No obvious relationship was found between Hordelymus and either Ta genome donor, Taeniatherum caput-medusae or Ns genome donor, Psathyrostachys juncea. Our data does not support the presence of Ta and Ns genome in H. europaeus, and further confirms that H. europaeus is allopolyploid.     

Phylogenetic relationships between Leymus (Poaceae,Triticeae) and related diploid Triticeae species based on isozyme and genome-specific random amplified polymorphic DNA (RAPD) markers

Abstract

To investigate the phylogenetic relationships between Leymus and related diploid species of the Triticeae tribe, the esterase isozyme (EST), superoxide dismutase (SOD) isozymes, and genome-specific random amplified polymorphic DNA (RAPD) markers were used to analyze for 14 Leymus species, together with two Psathyrostachys species (Ns), three Pseudoroegneria species (St), two Hordeum species (H), Lophopyrum elongatum (E^e), Australopyrum retrofractum (W), and Agropyron cristatum (P). The data were used to construct dendrograms by means of UPGMA in the NTSYS-pc computer program. The results suggested that (1) isozyme analysis can be used in the systematic studies of these perennial Triticeae; (2) there is a close relationship between Leymus, Psathyrostachys juncea, three Pseudoroegneria species, and Lophopyrum elongatum; (3) the Ns genome-specific RAPD marker was present in all 14 polyploid species of Leymus, while the E^e and P genome-specific RAPD markers were absent in 14 polyploid species of Leymus; the St, W and H genome-specific RAPD markers were present in some species of Leymus; (4) Leymus species have multiple origins, and different Leymus species derived their genomes from different donors.     

Ubiquity of the St chloroplast genome in St-containing Triticeae polyploids.

Interspecific hybridization occurs between Tritceae species in the grass family (Poaceae) giving rise to allopolyploid species. To examine bias in cytoplasmic DNA inheritance in these hybridizations, the sequence of the 3' end of the chloroplast ndhF gene was compared among 29 allopolyploid Triticeae species containing the St nuclear genome in combination with the H, I, Ns, P, W, Y, and Xm nuclear genomes. These ndhF sequences were also compared with those from diploid or allotetraploid Triticeae species having the H, I, Ns, P, W, St, and Xm genomes. The cpDNA sequences were highly similar among diploid, allotetraploid, allohexaploid, and allooctoploid Triticeae accessions containing the St nuclear genome, with 0-6-nucleotide (nt) substitutions (0-0.8%) occurring between pairs of species. Neighbor-joining analysis of the sequences showed that the ndhF DNA sequences from species containing the St nuclear genome formed a strongly supported clade. The data indicated a strong preference for cpDNA inheritance from the St nuclear genome-containing parent in hybridizations between Triticeae species. This preference was independent of the presence of the H, I, Ns, P, W, and Xm nuclear genomes, the geographic distribution of the species, and the mode of reproduction. The data suggests that hybridizations having the St-containing parent as the female may be more successful.     

Isolation and characterization of genome-specific DNA sequences in Triticeae species

Two contrasting genome-specific DNA sequences were isolated from Aegilops speltoides (wild goat grass) and Hordeum chilense (wild barley), each representing more than 1 % of the genomes. These repetitive DNA fragments were identified as being genome-specific before cloning by genomic Southern hybridization (using total genomic DNA as a probe), and hence extensive screening of clones was not required. For each fragment, up to six recombinant plasmid clones were screened and about half were genome-specific. Clone pAesKB52 from Ae. speltoides was a 763 by EcoRI fragment, physically organized in simple tandem repeats and shown to localize to sub-telomerec chromosome regions of species with the Triticeae S-genome by in situ hybridization to chromosomes. The sequence data showed an internal duplication of some 280 bp, which presumably occurred before sequence amplification and dispersion, perhaps by unequal crossing-over or reciprocal translocation. In situ hybridization showed that the sequence distribution varied between closely related (S-genome) species. Clone pHcKB6 was a 339 by DraI fragment from H. chilense, also tandemly repeated but more variable; loss of the DraI site resulting in a ladder pattern in Southern blots which had little background smear. In situ hybridization showed that the tandem repeats were present as small clusters dispersed along all chromosome arms except at a few discrete regions including the centromeres and telomeres. The clone hybridized essentially specifically to the H-genome of H. chilense and hence was able to identify the origin of chromosomes in a H. chilense x Secale africanum hybrid by in situ hybridization. It has a high A + T content (66%), small internal duplications, and a 50 by degenerate inverted repeat. We speculate that it has dispersed by retrotransposition in association with other sequences carrying coding domains. The organization and evolution of such sequences are important in understanding long-range genome organization and the types of change that can occur on evolutionary and plant breeding timescales. Genome-specific sequences are also useful as markers for alien chromatin in plant breeding.