A molecular description of telometic heterochromatin in secale species

Physical mapping of repetitive DNA sequences and 5S and 18S-26S rDNA in five wild species of the genus Hordeum

The genetic relationships between several wild species and subspecies of the genus Hordeum were assessed using fluorescence in situ hybridization (FISH). Plant material included natural populations of wild barley growing in Spain of the annual species, H. marinum ssp. marinum (2n = 14) and gussoneanum (2n = 14), and H. murinum ssp. murinum (2n = 28), and leporinum (2n = 28) and the perennial species H. bulbosum (2n = 14) and H. secalinum (2n = 28), plus the South American perennial species H. chilense (2n = 14). FISH was used to locate the chromosomal sites of two rDNA multigene families 5S and 18S-26S (pTa71 and pTa794) and three repetitive DNA sequences (pSc119.2, pAs1 and pHch950) isolated from different species and genera. The seven chromosomes of the diploid species were readily distinguished by their external morphology and hybridization patterns to pTa71, pTa794, pSc119.2 and pAs1. These DNA probes were also useful for the identification of homologous chromosomes and in differentiating these from unidentified chromosomes in the tetraploid taxa. The use of the probe pHch950 permitted intergenomic differentiation in tetraploids and supports the diphyletic origin of H. murinum and H. secalinum. The in situ experiments yielded the following conclusions: (1) differences between the sub-species marinum and gussoneanum; (2) close relationships between the subspecies murinum and leporinum; and (3) major differences in physical mapping between H. bulbosum and the remaining taxa. The genomic and phylogenetic relationships between taxa, as inferred from the results, are discussed.

Adult-type splenocytes of Xenopus induce apoptosis of histocompatible larval tail cells in vitro

Larval cells of the anuran tadpole are replaced by adult cells in the corresponding tissues of the frog during metamorphosis; tissues of the tail, which have no counterpart in the adult, are completely eliminated during metamorphosis. We have previously demonstrated that young adults of the major histocompatibility complex (MHC) homozygous inbred J strain of Xenopus laevis reject skin grafts from larvae of the same strain, showing that there is histoincompatibility between larval and adult skin tissues [19]. Thus, we postulated that some immunological recognition might be involved in this specific elimination of the tail tissue and set out to test the idea. Using in vitro assays, we detected a significant increase in proliferation of splenocytes derived from adult and metamorphic climax animals co-cultured with larval tail tissue. This response was shown to be thymus-dependent. However, the degeneration of larval tissues was not observed in such co-cultures under our standard culture conditions. To detect the possible cytotoxicity of splenocytes, the culture conditions were modified by supplementing with 10% heat-inactivated adult Xenopus serum instead of 10% fetal calf serum (FCS). After this modification, the degeneration of larval tissues was observable macroscopically and microscopically with co-cultured adult splenocytes, but not tadpole ones. The nuclear fragmentation of the epidermal cells was seen by light and electron microscopy. Apoptosis was evidenced by the demonstration of the "ladder pattern" upon electrophoresis of genomic DNA obtained from the degenerating larval tissues. Surprisingly, this response was thymus independent. Moreover, it was shown that this response was not observed when the larval tissues were cultured with adult thymocytes or adult epidermal cells. In vivo, migration of T cells into the epidermis of tail tissues at the late climax of metamorphosis was demonstrated immunohistochemically using a monoclonal antibody against Xenopus T cells, even in the early thymectomized tadpoles. Considering these results, we propose that populations of adult-type non-T leukocytes might participate in the specific detection and elimination of larval type cells during metamorphosis.

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5'-TTTAGGG-3'. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31 digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature.

Identification and distribution of seven classes of middle-repetitive DNA in the Arabidopsis thaliana genome

In order to analyse further the genomic distribution of repetitive sequences in the Arabidopsis genome, we have identified and characterized seven novel repetitive sequences. Analysis of genomic representation, genomic location and DNA sequence divided the seven repeated sequences into two classes. The first was represented by three cosmid subclones (182A, 74A, 191A) carrying sequences that hybridised to up to 20 genomic fragments and showed sequence homology to the genes, Arabidopsis CCR2, Arabidopsis MYB and to various ATP-binding transport proteins. These multigene families mapped to various positions within the genome, as judged by hybridization to YAC clones constituting the Arabidopsis physical map. The second class was represented by four cosmid subclones (106B, 164A, 163A, 278A) that hybridised to between 20 and 300 genomic fragments. One of these, 106B, is a diverged, partial copy of the LTR of the Arabidopsis retrotransposon Athila. The other three sequences showed no homology to known genes or proteins. The distribution of these sequences on chromosome 4 was analysed and sequences hybridizing to 106B, 164A and 163A were found exclusively at the centromeric region of this chromosome. Their detailed arrangement at the centromeric region of chromosome 4, relative to other repeated sequence families and single copy sequences, was determined.

Genome and chromosome identification in cultivated barley and related species of the Triticeae (Poaceae) by in situ hybridization with the GAA-satellite sequence

The satellite sequence studied was primarily composed of GAA repeats organized in long tracts of heterochromatic DNA. Fluorescent in situ hybridization (FISH) with the GAA satellite (GAA banding) to the chromosomes of barley, wheat, rye, and other Triticeae species produced banding patterns similar to those obtained by N-banding. The GAA-banding patterns of barley are described in detail and those of 12 other Triticeae species are described briefly. In situ hybridization with the GAA-satellite sequence permits identification of all the chromosomes of barley. It is a valuable alternative to other banding techniques, especially in connection with physical gene mapping by FISH. The application of the GAA-satellite sequence for the characterization of genomes in phylogenetic studies of genera containing the sequence is discussed.

Cloning and characterization of the majority of repetitive DNA in cotton (Gossypium L.)

Repetitive DNA elements representing 60-70% of the total repetitive DNA in tetraploid cotton (Gossypium barbadense L.) and comprising 30-36% of the tetraploid cotton genome were isolated from a genomic library of DNA digested with a mixture of four blunt-end cutting restriction enzymes. A total of 313 clones putatively containing nuclear repetitive sequences were classified into 1103 families, based on cross hybridization and Southern blot analysis. The 103 families were characterized in terms of genome organization, methylation pattern, abundance, and DNA variation. As in many other eukaryotic genomes, interspersed repetitive elements are the most abundant class of repetitive DNA in the cotton genome. Paucity of tandem repeat families with high copy numbers (>10(4)) may be a unique feature of the cotton genome as compared with other higher plant genomes. Interspersed repeats tend to be methylated, while tandem repeats seem to be largely unmethylated in the cotton genome. Minimal variation in repertoire and overall copy number of repetitive DNA elements among different tetraploid cotton species is consistent with the hypothesis of a relatively recent origin of tetraploid cottons.

Molecular and cytological characterization of a highly repeated DNA sequence in Raphanus sativus

A highly repeated DNA sequence with a repeat unit of ca. 180 bp was found in genomic DNA HindIII-digests of Raphanus sativus. The repeating units of six isolated, independent clones were sequenced. These units have 177 or 178 bp, are 36% G+C in their DNA base composition, and show 90% sequence homology. The copy number of this 180-bp repeat unit is about 0.5 x 10(6) per diploid genome. In situ hybridization analysis with the repeating units as the probe and C-banding analysis indicated that the repeated DNA sequence of R. sativus is closely associated with the major C-heterochromatins in the proximal regions of all 18 chromosomes at mitotic metaphase.

Analysis of rye B-chromosome structure using fluorescence in situ hybridization (FISH)

Fluorescence in situ hybridization (FISH) has been used to analyse the structure of the rye B chromosome. Genomic in situ hybridization (GISH) demonstrates the high level of overall similarity between A and B chromosomes of rye, as well as the presence of a number of specific sequences. The B-specific repeat families D1100 and E3900 have been analysed in terms of their physical location and possible contiguity. Rye Bs contain members of the rye-specific dispersed repetitive family R173, as well as centromeric regions similar to those of the As. The B chromosomes analysed in our study lack detectable rDNA sequences. Anomalous results have been obtained with a number of subtelomeric repetitive probes from rye. Bs usually lack these sequences, but evidence is presented that in some cases A-B translocation events may relocate such sequences from the As to the Bs. These data are discussed in the context of current models for the origin of the B chromosome.

DNA organization and polymorphism of a wild-type Drosophila telomere region

Telomeres at the ends of linear chromosomes of eukaryotes protect the chromosome termini from degradation and fusion. While telomeric replication/elongation mechanisms have been studied extensively, the functions of subterminal sequences are less well understood. In general, subterminal regions can be quite polymorphic, varying in size from organism to organism, and differing among chromosomes within an organism. The subterminal regions of Drosophila melanogaster are not well characterized today, and it is not known which and how many different components they contain. Here we present the molecular characterization of DNA components and their organization in the subterminal region of the left arm of chromosome 2 of the Oregon RC wild-type strain of D. melanogaster, including a minisatellite with a 457bp repeat length. Two distinct polymorphic arrangements at 2L were found and analyzed, supporting the Drosophila telomere elongation model by retrotransposition. The high incidence of terminal chromosome deficiencies occurring in natural Drosophila populations is discussed in view of the telomere structure at 2L.

Variation in highly repetitive DNA composition of heterochromatin in rye studied by fluorescence in situ hybridization

The molecular characterization of heterochromatin in six lines of rye has been performed using fluorescence in situ hybridization (FISH). The highly repetitive rye DNA sequences pSc 119.2, pSc74, and pSc34, and the probes pTa71 and pSc794 containing the 25S–5.8S–18S rDNA (NOR) and the 5S rDNA multigene families, respectively, were used. This allowed the individual identification of all seven rye chromosomes and most chromosome arms in all lines. All varieties showed similar but not identical patterns. A standard in situ hybridization map was constructed following the nomenclature system recommended for C-bands. All FISH sites observed appeared to correspond well with C-band locations, but not all C-banding sites coincided with hybridization sites of the repetitive DNA probes used. Quantitative and qualitative differences between different varieties were found for in situ hybridization response at corresponding sites. Variation between plants and even between homologous chromosomes of the same plant was found in open-pollinated lines. In inbred lines, the in situ pattern of the homologues was practically identical and no variation between plants was detected. The observed quantitative and qualitative differences are consistent with a corresponding variation for C-bands detected both within and between cultivars.Key words: fluorescence in situ hybridization, repetitive DNA, rye, Secale cereale, polymorphism.

Genomic organization and evolution of the soybean SB92 satellite sequence

Repetitive DNA sequences comprise a large percentage of plant genomes, and their characterization provides information about both species and genome evolution. We have isolated a recombinant clone containing a highly repeated DNA element (SB92) that is homologous to ca. 0.9% of the soybean genome or about 10(5) copies. This repeated sequence is tandemly arranged and is found in four or five major genomic locations. FISH analysis of metaphase chromosomes suggests that two of these locations are centromeric. We have determined the sequence of two cloned repeats and performed genomic sequencing to obtain a consensus sequence. The consensus repeat size was 92 bp and exhibited an average of 10% nucleotide substitution relative to the two cloned repeats. This high level of sequence diversity suggests an ancient origin but is inconsistent with the limited phylogenetic distribution of SB92, which is found at high copy number only in the annual soybeans. It therefore seems likely that this sequence is undergoing very rapid evolution.

Refined physical mapping of theSec-1locus on the satellite of chromosome 1R of rye (Secale cereale)

The Sec-1 locus (ω-secalin) of rye (Secale cereale L.) was mapped in the satellite of the short arm of chromosome 1R using fluorescence in situ hybridization and a genomic probe called pSec2B. Sec-1 is located in the middle of the satellite at the junction of the proximal euchromatic and the distal heterochromatic regions. Double hybridization experiments using rDNA and pSec2B showed that the NOR spans over the secondary constriction of the short arm of chromosome 1R and that there is a clearly visible gap between the NOR and Sec-1. Heterologous hybridization of pSec2B to barley visualized the B-hordein locus on chromosome 1H.Key words: fluorescence in situ hybridization, physical mapping, genetic mapping, secalin, rye, B-hordein, rDNA.

Molecular characterization and chromosome location of repeated DNA sequences in Hordeum species and in the amphiploid tritordeum (x Tritordeum Ascherson et Graebner)

Genomic DNA from 19 species and subspecies representing the four basic genomes (H, I, X, and Y) of Hordeum was restricted with HaeIII and hybridized with two repeated DNA sequences of Hordeum chilense. The potential use of repeated sequences in ascertaining genomic affinities within the genus Hordeum was studied by comparing restriction fragment patterns. The study demonstrated the following: (i) species that shared a basic genome showed more similar hybridization fragment patterns than species with different genomes, whether with pHch1 or pHch3; (ii) hybridization with pHch1 revealed the presence of certain fragments limited to the species with a H genome; and (iii) the alloploid nature of species like H. jubatum was confirmed. The chromosomal distribution of the two repeated sequences was studied in species representing each basic genome and in the amphiploid tritordeum using fluorescent in situ hybridization. No interspecific differences were found between the diploid species. In situ experiments indicated the alloploid nature of H. depressum. Both sequences allow H. chilense chromatin to be distinguished from wheat chromosomes in tritordeum.

Fluorescent in situ hybridization and C-banding analyses of highly repetitive DNA sequences in the heterochromatin of rye (Secale montanum Guss.) and wheat incorporating S. montanum chromosome segments

The molecular characterization of C-banded regions of Secale montanum Guss. by means of in situ hybridization was performed in order to provide new information about their chromosome structure relative to cultivated rye, Secale cereale L. Accurate identification of individual chromosomes was achieved using simultaneous and (or) successive fluorescent in situ hybridization (FISH) and C-banding. FISH identification was performed using total rye DNA, three highly repetitive rye DNA sequences (pSc119.2, pSc74, and pSc34), and the ribosomal RNA probes pTa71 (18S, 5.8S, and 26S rDNA) and pTa794 (5S rDNA). FISH was also used to identify the chromosome segment involved in two spontaneous translocation lines recovered from a 'Chinese Spring'--S. montanum wheat-rye addition line. FISH analysis revealed the exact translocation breakpoints and allowed the identification of the transferred rye segments. The value of this type of analysis is discussed.

Barley telomeres are associated with two different types of satellite DNA sequences

The genomic organization of two different types of satellite DNA sequences was analysed by means of fluorescence in situ hybridization (FISH) and pulsed-field gel electrophoresis (PFGE) in barley. Satellite HvT01 was detected at all chromosome ends except the long arms of chromosomes 2 and 7. The unrelated satellite pAS1 was found at all chromosome ends except the long arm of chromosome 7 and at two interstitial sites, both located on the long arm of chromosome 4 on the standard karyotype. Southern and in situ hybridization further indicate that pAS1 also occurs interspersed in the barley genome. For most chromosome ends, the linear order of HvT01 and pAS1 could not be determined by in situ hybridization except at the short arms of chromosomes 2 and 6, where HvT01 is more distal than pAS1. This is confirmed by PFGE analysis, HvT01 being frequently associated with the telomeric repeat but not pAS1. Furthermore, we found that HvT01 occurred in clusters up to 1000 kb in size, whereas the pAS1 cluster had a maximum size of 500 kb. Sequence comparison revealed that both satellites are completely unrelated and differ considerably in their G + C contents.

Chromosome localization and characterization of a family of long interspersed repetitive DNA elements from the genus Zea

This paper describes the characterization and chromosomal distribution of new long repetitive sequences present in all species of the genus Zea. These sequences constitute a family of moderately repetitive elements ranging approximately from 1350 to 1700 copies per haploid genome in modern maize (Zea mays ssp. mays) and teosinte (Zea diploperennis), respectively. The elements are long, probably larger than 9 kb, and they show a highly conserved internal organization among Zea subspecies and species. The elements are present in all maize chromosomes in an interspersed pattern of distribution, are absent from centromeric and pericentric heterochromatin, and with some clustering in the distal regions of chromosome arms.

A chromosome 5-specific repetitive DNA sequence in rice (Oryza sativa L)

Repetitive DNA sequences in the rice genome comprise more than half of the nuclear DNA. The isolation and characterization of these repetitive DNA sequences should lead to a better understanding of rice chromosome structure and genome organization. We report here the characterization and chromosome localization of a chromosome 5-specific repetitive DNA sequence. This repetitive DNA sequence was estimated to have at least 900 copies. DNA sequence analysis of three genomic clones which contain the repeat unit indicated that the DNA sequences have two sub-repeat units of 37 bp and 19 bp, connected by 30-to 90-bp short sequences with high similarity. RFLP mapping and physical mapping by fluorescence in situ hybridization (FISH) indicated that almost all copies of the repetitive DNA sequence are located in the centromeric heterochromatic region of the long arm of chromosome 5. The strategy for cloning such repetitive DNA sequences and their uses in rice genome research are discussed.

Characterization of a highly repeated DNA component of perennial oats (Helictotrichon, Poaceae) with sequence similarity to a A-genome-specific satellite DNA of rice (Oryza)

The taxonomic relationships among perennial oats (Helictotrichon Besser ex Schultes & Schultes, Aveninae, Aveneae, Poaceae) have been studied using highly repeated satellite DNA as a molecular marker. Highly repetitive sequences were isolated from restriction endonuclease digests of nuclear DNA of Helictotrichon convolutum, and satellite repeats (approximately 365 bp in length) were cloned, sequenced and compared among each other. They exhibited an intraspecific sequence variability of 6-9%. This satellite DNA, CON1, is differentially distributed within the genus Helictotrichon. In species of the subgenus Helictotrichon a high copy number is detectable, whereas in representatives of the subgenera Pratavenastrum and Pubavenastrum the number of copies per genome is rather low. Surprisingly, the satellite DNA repeat CON1 shows 74% sequence similarity to an A-genome specific repetitive DNA of Oryza (rice).

Molecular characterization of a tandem repeat, Afa family, and its distribution among Triticeae

We have characterized a so-called D genome specific repetitive DNA sequence (pAs1) of Aegilops squarrosa L. (2n = 14, genome DD) with respect to its DNA sequence and its distribution among Triticeae species. The clone consisted of three units of a repetitive DNA sequence of 336 or 337 base pairs, and was AT rich (65.2%). DNA analyses revealed the presence of the pAs1-like sequences in other genomes of Triticeae species, although the repetition was greatly (as much as 100-fold) variable among the genomes. The repetitive sequences from 10 diploid species were amplified using PCR with specific primers, and the sequential variability was analyzed by the digestion pattern obtained with five restriction enzymes. Since the AfaI site was the most conservatively present in the unit of the repetitive sequences, we named them "Afa family." The analysis clearly displayed the variation of the repetitive sequences regardless of the uniformity of the size of the amplified product. These results indicated that plural amplification events of these repetitive sequences happened independently in the genome evolution of Triticeae.

Chromosomal distribution of a repeated DNA sequence from C-genome heterochromatin and the identification of a new ribosomal DNA locus in the Avena genus

Satellite DNA specific to the oat C genome was sequenced and located on chromosomes of diploid, tetraploid, and hexaploid Avena ssp. using in situ hybridization. The sequence was present on all seven C genome chromosome pairs and hybridized to the entire length of each chromosome, with the exception of the terminal segments of some chromosome pairs. Three chromosome pairs belonging to the A genome showed hybridization signals near the telomeres of their long arms. The existence of intergenomic chromosome rearrangements and the deletions of the repeated units are deduced from these observations. The number of rDNA loci (18S-5.8S-26S rDNA) was determined for the tetraploid and hexaploid oat species. Simultaneous in situ hybridization with the satellite and rDNA probes was used to assign the SAT chromosomes of these species to their correct genomes.

A major satellite DNA of soybean is a 92-base pairs tandem repeat

We report the cloning, sequencing and analysis of the major repetitive DNA of soybean (Glycine max). The repeat, SB92, was cloned as several monomers and trimers produced by digestion with XhoI. The deduced consensus sequence of the repeat is 92 base pairs long. Genomic sequences do not fluctuate in length. Their average homology to the consensus sequence is 92%. The consensus of SB92 contains slightly degenerated homologies for several 6-cutters. Therefore, many of them generate a ladder of 92-bp oligomers. The distribution of bands seems to be random, but the occurrence of sites for different 6-cutters varies widely. There is no obvious correlation between the sequences of the neighboring units of SB92 in cloned trimers. Also, there are none of the internal repetitive blocks reported for many satellite DNAs from other species. The SB92 repeat makes up 0.7% of total soybean DNA. This is equivalent to 8×10(4) copies, or 7 megabases. The repeat is organized in giant tandem blocks over 1 Mb in length, and there are fewer blocks than chromosomes. The polymorphism of these blocks is extremely high. The SB92 repeat is present in identical arrangement and number of copies in the ancestral subspecies Glycine soja. There are 10 times fewer copies of the repeat in a related species Vigna unguiculata (cowpea), and no homologies in several other more distant leguminous plants studied.

BamHI and HindIII repetitive DNA families in the rice genome

In this paper we describe a novel method of cloning representative members of different repetitive DNA families based on the screening of a rice (Oryza sativa) genomic library using DNA from different C0t fractions as probes. Two genomic clones, which represent two different repetitive DNA families in rice, were isolated by this method and have been characterized. Their nucleotide sequences, copy numbers, distributions in major rice genome types, methylation patterns, and chromosomal localizations were determined.

Isolation, characterization and application of a species-specific repeated sequence from Haynaldia villosa

A species-specific repeated sequence, pHvNAU62, was cloned from Haynaldia villosa, a wheat relative of great importance. It strongly hybridized to H. villosa, but not to wheat. In situ hybridization localized this sequence to six of seven H. villosa chromosome pairs in telomeric or sub-telomeric regions. Southern hybridization to whea-H. villosa addition lines showed that chromosomes 1V through 6V gave strong signals in ladders while chromosome 7V escaped detection. In addition to H. villosa, several Triticeae species were identified for a high abundance of the pHvNAU62 repeated sequence, among which Thinopyrum bassarabicum and Leymus racemosus produced the strongest signals. Sequence analysis indicated that the cloned fragment was 292 bp long, being AT rich (61%), and showed 67% homology of pSc7235, a rye repeated sequence. Isochizomer analysis suggested that the present repeated sequence was heavily methylated at the cytosine of the CpG dimer in the genome of H. villosa.It was also demonstrated that pHvNAU62 is useful in tagging the introduced 6VS chromosome arm, which confers a resistance gene to wheat powdery mildew, in the segregating generations.

Nucleotide sequence of a highly repeated DNA sequence and its chromosomal localization in Allium fistulosum

A highly repeated DNA sequence with a repeating unit of approximately 380bp was found in EcoRV digests of the total genomic DNA of Allium fistulosum. Three independent clones containing this unit were isolated, and their repeating units sequenced. These units showed more than 94% sequence homology, and the copy number was estimated to be about 2.8×10(6) per haploid genome. In situ hybridization, with the repeating unit as a probe, and C-banding analyses indicated that the repeated DNA sequence of A. fistulosum is closely associated with the major C-heterochromatin in the terminal regions of all 16 chromosomes at mitotic metaphase. The characters of the repeating unit are similar to those of the A. cepa unit, which is taxonomically closely related to A. fistulosum.

Analysis of a repetitive DNA family from Arabidopsis arenosa and relationships between Arabidopsis species

We have analysed a family of highly repetitive DNA from Arabidopsis arenosa (L.) Lawalrée [syn. Cardaminopsis arenosa (L.) Hayck] composed of AT-rich tandem repeats of 166-179 bp in head to tail organization. Sequence comparison between several repeat units revealed a high level of divergence of 4.5% to 25%. The sequence family shows more than 58% homology to satellite sequences described in Arabidopsis thaliana (L.) Heynh. but no homology to other satellite repeats in the Cruciferae. Within the genus Arabidopsis the satellite sequence was found to be present in A. thaliana and Arabidopsis suecica (Fries) Norrlin, but not in Arabidopsis griffithiana (Boiss.) N. Busch and Arabidopsis pumila (Stephan) N. Busch. In situ hybridization to metaphase chromosomes of A. arenosa (2n = 4x = 32) showed the sequence to be localized at the centromeres of all 32 chromosomes with substantial hybridization along the chromosome arms. Using Southern hybridization and in situ hybridization, we give evidence that A. suecica is a hybrid of A. thaliana and A. arenosa. A considerable reorganization of the A. thaliana satellite sequence pAL1 occurred in the hybrid genome while no molecular change of the A. arenosa repeat was observed in the hybrid. Analysis of related repeats enabled differentiation between closely related genomes and are useful for the investigation of hybrid genomes.

Pulsed-field gel analysis of 5S and satellite DNA in barley

Pulsed-field gel electrophoresis was used to study the variability of clustered tandemly repeated sequences in barley. Twelve spring barley cultivars were investigated with a heterologous 5S DNA probe and the 118 base pair barley satellite DNA probe HVT01. On a per fragment basis, the 5S probe was 5 times and the barley satellite probe 6.7 times more variable than single- or low-copy RFLP markers, demonstrating their usefulness for cultivar distinction.

Isolation, characterization and RFLP linkage mapping of a DNA repeat family of Solanum spegazzinii by which chromosome ends can be localized on the genetic map of potato

In a random sample of 2263 cloned genomic DNA fragments of the wild potato species Solanum spegazzinii six related, highly repetitive fragments (SPG repeat family) were identified that were present in much higher copy numbers in S. spegazzinii when compared with the closely related cultivated potato S. tuberosum. The SPG repeat family was organized in long arrays of multiple copies. Cross hybridization experiments with 29 wild and cultivated Solanum species and with the related tomato showed specificity of the SPG repeat family for tuber-bearing Solanum species. Among tuber bearing Solanum species a high degree of variation was observed for restriction fragment length and copy number. The variation in copy number was not correlated with established taxonomic relationships between tuber-bearing Solanum species. DNA sequence analysis revealed a subrepeat structure of 120-140 base pairs embedded in longer repeat units of variable length. Length polymorphisms between highly repeated restriction fragments detected by the SPG probes were used for segregation- and linkage analysis in four mapping populations of potato, for which RFLP maps had been constructed. Twelve loci were identified, eleven of which mapped to the distal ends of nine linkage groups. All the evidence suggested that the SPG repeat family represents a satellite repeat members of which are localized in the subtelomeric region of potato chromosomes. The SPG repeat family could be used, therefore, for completing the genetic map of potato.

Physical mapping of 5S and 18S–25S rDNA and repetitive DNA sequences in Aegilops umbellulata

An accurate physical map of the location of the 5S and the 18S–5.8S–25S rRNA genes and a repetitive DNA sequence has been produced on Aegilops umbellulata Zhuk., (2n = 2x = 14) chromosomes by in situ hybridization. Chromosome morphology together with the hybridization pattern of pSc119.2, a DNA sequence from rye, allowed identification and discrimination of different chromosomes; pSc119.2 hybridizes with all Ae. umbellulata chromosomes at the telomeres, except for the short arm of chromosome 6U, and shows intercalary sites on the long arms of chromosomes 6U and 7U. The 5S and 18S–25S rDNA have been mapped physically only on the short arms of chromosomes 1U and 5U. On chromosome 1U the order of the genes is 5S rDNA subterminal and 18S–25S rDNA more proximal, while on chromosome 5U the position of the genes is reversed. The relative order of the genes, together with the hybridization pattern of the pSc119.2, is useful in identifying whole chromosomes or chromosome segments from Ae. umbellulata in recombinant or addition lines with wheat. The data help link the physical organization of chromosomes to the genetic map. Other members of the Triticeae vary in the presence and order of the 5S and 18S–25S rDNA sequences on groups 1 and 5, indicating multiple and complex evolutionary rearrangements of the chromosome arms.Key words: Triticum umbellulatum.

Chromosome painting in plants: in situ hybridization with a DNA probe from a specific microdissected chromosome arm of common wheat

We report here on the successful painting of a specific plant chromosome within its own genome. Isochromosomes for the long arm of chromosome 5 of the wheat B genome (5BL) were microdissected from first meiotic metaphase spreads of a monoisosomic 5BL line of the common wheat Triticum aestivum cv. Chinese Spring. The dissected isochromosomes were amplified by degenerate oligonucleotide-primed PCR in a single tube reaction. The amplified DNA was used as a complex probe mixture for fluorescent in situ hybridization on first meiotic metaphase spreads of lines carrying 5BL as a distinctive marker. Hybridization signals were observed, specifically, along the entire 5BL. In some of the cells, labeling was also detected in two bivalents, presumably those of the 5B "homoeologues" (partial homologues) found in common wheat (5A and 5D). The probe also revealed discrete domains in tapetal nuclei at interphase, further supporting the probe's high specificity. These data suggest that chromosome and homoeologous group-specific sequences are more abundant in 5BL than genome-specific sequences. Chromosome-painting probes, such as the one described here for 5BL, can facilitate the study of chromosome evolution in polyploid wheat.

Genomic organization of the canrep repetitive DNA in Brassica juncea

Canrep is a heterogeneous, tandemly repeated, 176 bp nucleotide sequence that contains a single Hind III site and is present in high copy numbers in the genomes of many Brassica species. Complete clusters of repeats of this DNA were cloned from the nuclear DNA of Brassica juncea. Restriction-fragment dimers and higher multimers of the 176 bp sequence have arisen by mutations within the Hind III recognition sequence. Adjacent repeats from within the same cluster usually have different nucleotide sequences with features indicating that diversity is generated by a mechanism that causes site-specific base substitutions. While most of the units of canrep DNA are clustered in long arrays of tandem repeats, some are dispersed throughout the genome as isolated copies or in small clusters. Regardless of the size of the arrays, each cluster begins and ends with a variable-length, truncated repeat and is flanked by inverted copies of the sequence 5'-ATCTCAT3'-, which is not part of the basic sequence of the canrep family of DNAs. Furthermore, some clusters are located close to nucleotide sequences related to those of known plant transposons. Thus, canrep elements may be dispersed by transposition. There are two distinct subfamilies of canrep sequences in B. juncea, and one of these is closely related to one of the two subfamilies of this type of DNA from B. napus, indicating that it originated from B. campestris, the common diploid ancestor of both amphidiploid species. Neither the repetitive DNA nor nucleotide sequences flanking canrep clusters are transcribed in seedlings, suggesting that even small arrays of repeats are located in heterochromatic regions and might be involved in chromatin condensation and/or chromosome segregation.

Transcribed repetitive DNA sequences in telomeric regions of rice (Oryza sativa)

We have isolated and characterized from rice three repetitive DNA sequences, Os48, Osc-567, and OsG3-430. Our results indicate that these repetitive sequences are highly transcribed, and transcripts complementary to both strands of the Os48 family of sequences account for up to 3% of the total cellular RNA. Pulsed-field gel electrophoresis, restriction mapping, and DNA sequence analyses have revealed a complex pattern of structural organization of the three families of repetitive sequences. Os48 and Osc-567 are organized in long tandem arrays, whereas copies of the OsG3-340 sequence are interspersed with other sequences including arrays of the Os48 and Osc567 families. Interestingly, the three families of repetitive sequences are closely linked not only to each other, but also to telomeric sequences of rice, suggesting that transcription of these repetitive sequences may occur in regions very close to telomeres in rice.

Determination of the frequency of wheat-rye chromosome pairing in wheat x rye hybrids with and without chromosome 5B

Genomic in-situ hybridization (GISH) was used to determine the amount of wheat-rye chromosome pairing in wheat (Triticum aestivum) x rye (Secale cereale) hybrids having chromosome 5B present, absent, or replaced by an extra dose of chromosome 5D. The levels of overall chromosome pairing were similar to those reported earlier but the levels of wheat-rye pairing were higher than earlier determinations using C-banding. Significant differences in chromosome pairing were found between the three genotypes studied. Both of the chromosome-5B-deficient hybrid genotypes showed much higher pairing than the euploid wheat hybrid. However, the 5B-deficient hybrid carrying an extra chromosome 5D had significantly less wheat-rye pairing than the simple 5B-deficient genotype, indicating the presence of a suppressing factor on chromosome 5D. Non-homologous/non-homoeologous chromosome pairing was observed in all three hybrid genotypes. The value of GISH for assessing the level of wheat-alien chromosome pairing in wheat/alien hybrids and the effectiveness of wheat genotypes that affect homoeologous chromosome pairing is demonstrated.

Organization of a Solatium brevidens repetitive sequence related to the TGRI subtelomeric repeats of Lycopersicon esculentum

A species-specific repetitive DNA fragment has been isolated from a genomic library of Solanum brevidens. Sequence analysis revealed a regular organization of three non-homologous subrepeats forming tandemly-arranged composite repetitive units. Interpretation of Southern hybridization patterns based on the known sequence data suggests that the isolated sequence element represents an abundant organization type, although the presence of simple tandem arrays of the subrepeats is also indicated. Seventy-four percent sequence similarity was found between one of the S. brevidens subrepeats (Sb4AX) and a satellite DNA (TGRI) localized as a subtelomeric repeat on almost all Lycopersicon esculentum chromosomes. Insitu hybridization indicated that, similarly to TGRI, the S. brevidens-specific repeats are located at the ends of the arms of several chromosomes. On the basis of the data obtained, a common ancestral sequence can be proposed for the tomato (TGRI) and the S. brevidens (Sb4AX) repeat however, the molecular organization of this element in these two species evolved in a basically different manner.

Physical mapping of 5S rDNA reveals a new locus on 3R and unexpected complexity in a rye translocation used in chromosome mapping

Using fluorescence in situ hybridization (FISH) with probe pScT7, three different 5S rDNA loci were detected in the satellite of rye chromosome 1R (5SDna-R1) and in the short arms of chromosomes 3R (5SDna-R3) and 5R (5SDna-R2) respectively. All three loci showed polymorphism for the hybridization signal intensity. In order to determine the localization of these rye 5S rDNA multigene loci with higher precision within the corresponding chromosome arms, the probe pScT7 was physically mapped by FISH in relation to the following five translocations (Wageningen Tester Set): T850W (1RS/4RL), T248W (1RS/6RS), T273W (1RS/5RL), T305W (2RS/5RS) and T240W (3RS/5RL). Accurate physical maps of the translocation breakpoints had previously been made using electron microscope analysis of spread pachytene synaptonemal complexes of heterozygotes for the different translocations. The results indicate that locus 5SDna-R3 is located between the breakpoint of translocation T240W and the telomere, whereas locus 5SDna-R2 is located between the breakpoint of translocation T305W and the centromere, the hybridization of probe pScT7 on T305W translocated chromosomes demonstrating the complex nature of this translocation. On the other hand, the simultaneous detection of probes pScT7 and pTA71 (18S-5.8S-26S rDNA) with two different fluorochromes, indicated that the breakpoints of translocations T850W and T248W are located between loci Nor-R1 and 5SDna-R1.

Molecular and physical organization of highly repetitive, undermethylated DNA from Pennisetum glaucum

A HaeIII monomer of a repetitive DNA family from Pennisetum glaucum (L.) R. Br. cv. Massue has been cloned and characterized. The repeat is 137 bp long and is organized in head-to-tail orientation in tandem arrays. The HaeIII monomer contains 55% A+T residues. The distribution of this highly repetitive sequence in different Pennisetum species and in other cereals was investigated. The HaeIII satellite is present in all Pennisetum species investigated but absent from other genera examined. In situ hybridization revealed a centromeric localization of this sequence on all seven chromosome pairs and indicated chromosome-specific differences in copy number. Methylation was investigated by comparative restriction enzyme analysis (MspI/HpaII) which showed a greater extent of methylation of the internal C of the enzyme recognition site 5'-CCGG. A South-Western analysis, using an anti-methylcytosine antibody to examine the methylation status in P. glaucum confirmed that the sequence is not highly methylated.

Analysis of genome-specific sequences inPhleum species: Identification and use for study of genomic relationships

Sau3AI "shot gun" cloning and colony hybridization with total genomic probes were used to isolate genome-specific sequences inPhleum species. The total DNA isolated from diploid speciesP. alpinum andP. bertolonii was partially digested withSau3AI and cloned using pUC19 as a vector to anE. coli strain DH5αmcr. A partial genomic DNA library consisting of 3030 colonies for the genome ofP. alpinum and one consisting of 3240 colonies for the genome ofP. bertolonii were constructed. Twelve hundred and thirty colonies from the DNA library ofP. alpinum and 1320 from that ofP. bertolonii were respectively blotted to membrane filters and hybridized to the total genomic probes from these two species. Eight clones specific toP. alpinum and 13 specific toP. bertolonii were isolated through colony hybridization and further dot-blot hybridization. Most of these clones may carry highly or moderately repetitive sequences. Three sequences specific toP. alpinum and 3 specific toP. bertolonii were used as probes to hybridize theEcoRI-digested DNA samples from four species,P. alpinum,P. bertolonii,P. pratense andP. montanum, on Southern blot. The results from these hybridization experiments showed that all 3P. bertolonii-specific probes and 2 of the 3P. alpinum-specific probes hybridized to the DNA ofP. pratense, thus confirming the conclusion of the close relationships between the cultivated timothy and its two wild relatives that was drawn in our previous study using the C-banding technique.

Mapping and organization of highly-repeated DNA sequences by means of simultaneous and sequential FISH and C-banding in 6x-triticale

Three families of highly repeated sequences from rye and the rRNA multigenes (NOR and 5S) have been mapped by FISH and C-banding, in chromosomes of triticale. The pSc119.2 probe showed interstitial hybridization in chromosome arms 1RS, 1RL, 4RL, 5RL, 6RS, 6RL, 7RS and 7RL, and is very effective for chromosome identification of rye chromosomes in triticale. This sequence also hybridizes to the 4A, 5A and the seven B-genome wheat chromosomes. Simultaneous hybridization with the pSc119.2 and pTa794 (5S rRNA) is very useful to distinguish the metacentric chromosomes 2R and 3R. The pSc74 probe appears at interstitial sites in the long arm of the most heterobrachial chromosomes (5R and 6R). The three repetitive sequences of 120 bp, 480 bp, and 610 bp hybridize to telomeric regions in rye chromosomes. Different arrangements and complex organizations consisting of arrays of three or more family sequences were found. The results demonstrate a great variation in the relative arrangement of the repetitive sequences in the telomeres of the rye chromosomes. There were quantitative differences in each cytological marker between triticale lines in both in situ labelling and C-banding, probably as the result of differences in the number and/or kind of repeat sequence.

New 18S.26S ribosomal RNA gene loci: chromosomal landmarks for the evolution of polyploid wheats

Three new 18S.26S rRNA gene loci were identified in common wheat by sequential N-banding and in situ hybridization (ISH) analysis. Locus Nor-A7 is located at the terminal area of the long arm of 5A in both diploid and polyploid wheats. Locus Nor-B6 is located in N-band 1BL2.5 of the long arm of chromosome 1B in Triticum turgidum and Triticum aestivum. ISH sites, similar to Nor-B6, were also detected on the long arms of chromosomes 1G in Triticum timopheevii and 1S in Aegilops speltoides, but their locations on the chromosomes were different from that of Nor-B6, indicating possible chromosome rearrangements in 1GL and 1BL during evolution. The third new locus, Nor-D8, was only found on the short arm of chromosome 3D in the common wheat Wichita. The loss of rRNA gene locus Nor-A3 and gain of repetitive DNA sequence pSc119 on the terminal part of 5AS suggest a structural modification of 5AS. Comparative studies of the location of the 18S.26S rRNA gene loci in polyploid wheats and putative A and B (G) genome progenitor species support the idea that: (1) Triticum monococcum subsp. urartu is the donor of both the A and A(t) genome of polyploid wheats. (2) Ae. speltoides is closer to the B and G genome of polyploid wheats than Aegilops longissima and is the most probable progenitor of these two genomes.

Different species-specific chromosome translocations in Triticum timopheevii and T. turgidum support the diphyletic origin of polyploid wheats

Triticum timopheevii ssp. timopheevii and T. timopheevii ssp. araraticum were analysed by sequential N-banding and genomic in situ hybridization. Three chromosomes, 6At, 1G and 4G, were involved in At-G intergenomic translocations in all six lines analysed. These chromosomes may be derived from a cyclic translocation that is species-specific to T. timopheevii. In contrast, Triticum turgidum has a species-specific cyclic translocation involving chromosomes 4A, 5A and 7B. The discovery of different species-specific chromosome translocations supports the diphyletic hypothesis of the evolution of tetraploid wheats. The results from genomic blocking analysis also revealed that the chromosomes of Aegilops speltoides are closer to the G genome than the B genome chromosomes. The possible role of species-specific translocations in the evolution of wheat is discussed.

Genes encoding two isocitrate dehydrogenase isozymes of a psychrophilic bacterium, Vibrio sp. strain ABE-1

The genes coding for two structurally different isocitrate dehydrogenase isozymes (IDH-I and IDH-II) of a psychrophilic bacterium, Vibrio sp. strain ABE-1, were cloned and sequenced. Open reading frames of the genes (icdI and icdII) are 1,248 and 2,229 bp in length, respectively. The amino acid sequences predicted from the open reading frames of icdI and icdII corresponded to the N-terminal amino acid sequences of the purified IDH-I and IDH-II, respectively. No homology was found between the deduced amino acid sequences of the isozymes; however, the IDH-I, a dimeric enzyme, had a high amino acid sequence identity (74.3%) to the Escherichia coli IDH. The deduced amino acid sequence of the IDH-II, a monomeric enzyme, was not related to any known sequence. However, the IDH-II had an amino acid sequence homologous to that of a cyanogen bromide-cleaved peptide containing a putative active-site methionyl residue of the monomeric IDH of Azotobacter vinelandii. The two genes (icdlI and icdII) were found to be tandemly located in the same orientation. Northern (RNA) blot analyses showed that the two genes are transcribed independently. Primer extension experiments located single transcriptional start sites 39 and 96 bp upstream of the start codons of icdI and icdII, respectively. The amount of icdI transcript but not icdII increased when Vibrio sp. strain ABE-1 cells were cultured in acetate minimal medium.

PFGE analysis of the rice genome: estimation of fragment sizes, organization of repetitive sequences and relationships between genetic and physical distances

Pulsed-field gel electrophoresis (PFGE) has been applied to analyze the rice nuclear genome. Probing 56 RFLP probes selected from the 12 rice chromosomes to PFGE blots of nine rare-cutting restriction enzymes revealed that there are relatively high numbers of 'rare-cutting' restriction sites in the rice genome. The average sizes of restriction fragments detected by single-copy probes are smaller than 200 kb for all of the rare-cutting restriction enzymes examined. Sizes of fragments detected by repetitive probes are variable, depending on the probes analyzed. By using PFGE, a tandemly repeated sequence, Os48, was found to be tightly linked to telomeric tandem repeats but not physically linked to r5s genes with which sequence homology had been observed. Relationships between genetic and physical distances have been established for three different chromosomal segments. In these regions 1 cm corresponds to ca. 260 kb on average. Analysis of a cluster of RFLP markers on chromosome 3 revealed that genetically clustered RFLP markers are also physically closely linked, suggesting that clustering of genetic markers may result in part from uneven distribution of single-copy sequences.

Genetic and physical mapping of telomeres and macrosatellites of rice

Telomeres and telomere-associated satellites of rice were genetically and physically analyzed by pulsed-field gel electrophoresis (PFGE) using Arabidopsis telomeric DNA and rice satellite sequences as probes. We demonstrate that Arabidopsis telomeric sequences hybridize to rice telomeres under the conditions of high stringency. Using the Arabidopsis probe, multiple, discrete telomeric fragments could be identified on pulsed-field gel blots of rice DNAs digested with rare-cutting restriction enzymes. Most of the telomeric bands larger than 300 kb are physically linked with satellite bands as revealed by PFGE. Some of the telomeric and satellite bands segregate in a Mendelian fashion and are highly reproducible. Three such telomeric bands have been mapped to the distal ends of RFLP linkage groups: Telsm-1 on chromosome 8, Telsa-1 on chromosome 9 and Telsm-3 on chromosome 11. One segregating satellite band was mapped to an internal region of chromosome 10. Telomeric fragments were shown not only to be genetically linked to but also physically linked (based on PFGE) to the terminal RFLP markers. The physical distance from telomeric sequences to a distal RFLP marker, r45s gene, on chromosome 9, is 200 kb while the distance from telomeric sequences to RG98, a terminal RFLP marker on chromosome 11, is 260 kb. Physical maps of the telomere regions of chromosome 9 and chromosome 11 are presented.

A structural and evolutionary analysis of a dispersed repetitive sequence

A family of dispersed repetitive sequences (Hch1) which is present in the genome of the wild barley Hordeum chilense was studied in detail. Hch1 sequences are found both as part of short tandem arrays and dispersed throughout the H. chilense chromosomes. Subcloning of sections of the sequence reveals that it is composed of unrelated classes of sequences which can also be found separately in other genomic locations. Analysis of these sequences in the genomes of wheat and two other wild barley species strongly suggests that specific amplifications and arrangements of the repeated sequences have taken place during speciation. Nucleotide sequence analysis fails to detect, in their entirety, the features shown by plant transposons.

Repetitive sequences in the genome of Anemone blanda: identification of tandem arrays and of dispersed repeats

A tandemly repetitive sequence family (AbS1) and a repetitive sequence (Hd) forming part of a larger dispersed element (dorf-1) of Anemone blanda were characterised. The AbS1 satellite sequence family is located in all 4',6-diamidino-2-phenylindole (DAPI) positive intercalary heterochromatic bands and in the DAPI positive heterochromatic terminal region of chromosome 3, while the dispersed Hd homologous sequences are preferentially associated with euchromatic chromosome regions. The major component of the AbS1 satellite is AbS1-H1 with a basic repeat unit of 1640 bp; a minor fraction (AbS1-H5) consists of 320 bp units. A subsection of the AbS1-H1 repeat unit exhibits homologies to the 25S rRNA gene of flowering plants suggesting that the 1.64 kb satellite was generated by amplification of a precursor satellite and/or single copy sequence together with an rDNA fragment. The rDNA homologous region is considered to evolve at a rate similar to pseudogenes and thus the age of this satellite DNA fraction can be roughly estimated as about 27 million years. The dispersed repeated sequence Hd (about 1300 bp) is associated with the 8 kb element dorf-1. A. blanda dorf-1 constitutes about 0.2% of the genome (3 x 10(4) copies), is bounded by identical long terminal repeats, and exhibits partial homology to the Lilium gypsy-type element del1, but has yet to be confirmed as a retrotransposon. In contrast to the AbS1 satellite sequence family, Hd homologous sequences were found not only in A. apennina, the closest relative of A. blanda, but also in A. nemorosa and A. ranunculoides indicating that a progenitor sequence of dorf-1 was present in a common ancestor before speciation occurred.

Genetic and physical mapping of barley telomeres

Barley (Hordeum vulgare L.) telomeres were investigated by means of pulsed field gel electrophoresis (PFGE) and in situ hybridization. In situ hybridization showed that a tandemly repeated satellite sequence has a subtelomeric location, and is present at thirteen of the fourteen chromosome ends. PFGE revealed that this satellite sequence is physically close to the telomeric repeat. Pulsed field gel electrophoresis was then used for segregation analysis and linkage mapping of several telomeric and satellite loci in a segregating doubled-haploid population. The telomeric repeat displayed a hypervariable segregation pattern with new alleles occurring in the progeny. Eight satellite and telomeric sites were mapped on an restriction fragment length polymorphism (RFLP)-map of barley, defining the ends of chromosome arms 1L, 2S, 3L, 4S, 4L, 5S and 6. One satellite locus mapped to an interstitial site on the long arm of chromosome 3. The physical location of this locus was confirmed by in situ hybridization to wheat/barley addition line 3.