Our knowledge of the structure and composition of genomes is rapidly progressing in pace with their sequencing. The emerging data show that a significant portion of eukaryotic genomes is composed of transposable elements (TEs). Given the abundance and diversity of TEs and the speed at which large quantities of sequence data are emerging, identification and annotation of TEs presents a significant challenge. Here we propose the first unified hierarchical classification system, designed on the basis of the transposition mechanism, sequence similarities and structural relationships, that can be easily applied by non-experts. The system and nomenclature is kept up to date at the WikiPoson web site.

A unified classification system for eukaryotic transposable elements

Microsatellites are a ubiquitous class of simple repetitive DNA sequence. An excess of such repetitive tracts has been described in all eukaryotes analyzed and is thought to result from the mutational effects of replication slippage1. Large-scale genomic and EST sequencing provides the opportunity to evaluate the abundance and relative distribution of microsatellites2 between transcribed and nontranscribed regions and the relationship of these features to haploid genome size. Although this has been studied in microbial and animal genomes3,4,5,6, information in plants is limited. We assessed microsatellite frequency in plant species with a 50-fold range in genome size that is mostly attributable to the recent amplification of repetitive DNA7. Among species, the overall frequency of microsatellites was inversely related to genome size and to the proportion of repetitive DNA but remained constant in the transcribed portion of the genome. This indicates that most microsatellites reside in regions pre-dating the recent genome expansion in many plants. The microsatellite frequency was higher in transcribed regions, especially in the untranslated portions, than in genomic DNA. Contrary to previous reports suggesting a preferential mechanism for the origin of microsatellites from repetitive DNA in both animals8,9 and plants10, our findings show a significant association with the low-copy fraction of plant genomes.

Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes.

Many enzymes in plants have isozymes because the same catalytic reaction is often present in several subcellular compartments, most frequently the plastids and the cytosol. The number and subcellular locations of the isozymes appear to be highly conserved in plant evolution. However, gene duplication in diploid species and the addition of genomes in polyploid species have increased the number of isozymes.

https://science.sciencemag.org/content/sci/216/4544/373.full.pdf

Conservation and duplication of isozymes in plants.

A molecular description of telomeric heterochromatin in Secale species.

In Situ Localization of Parental Genomes in a Wide Hybrid

The effect of DNA fragment size on the extent of hybridisation that occurs between repeated sequence DNAs from oats, barley, wheat and rye has been investigated. The extent of hybridisation is very dependent on fragment size, at least over the range of 200 to 1000 nucleotides. This is because only a fraction of each fragment forms duplex DNA during renaturation. From these results estimates of the proportions of repeated sequences of each of the cereal genomes that are homologous with repeated sequences in the other species have been determined and a phylogenetic tree of cereal evolution constructed on the basis of the repeated sequence DNA homologies. It is proposed that wheat and rye diverged after their common ancestor had diverged from the ancestor of barley. This was preceded by the divergence of the common ancestor of wheat, rye and barley and the ancestor of oats. Once introduced in Gramineae evolution most families of repeated sequences appear to have been maintained in all subsequently diverging species. — The repeated sequences of oats, barley, wheat and rye have been divided into Groups based upon their presence or absence in different species. Repeated sequences of related families are more closely related to one another within a species than between species. It is suggested that this is because repeated sequences have been involved in many rounds of amplification or quantitative change via unequal crossing over during species divergence in cereal evolution.

Repeated sequence DNA relationships in four cereal genomes

Sequence organisation analysis of the wheat and rye genomes by interspecies DNA/DNA hybridisation.

The organisation of the repeated and non-repeated sequences in barley and oats genomes has been investigated using the repeated sequences of the wheat, oats, barley and rye genomes as DNA probes. Labelled barley and oats fragments of different lengths (200 to > 7000 nucleotides were hybridised to the repeated sequence probes and the proportions of the labelled fragments re-naturing with the probe DNAs were determined. The average spacings of these sequences through the barley and oats genomes were inferred from the results together with the proportions of the genomes in which the renatured sequences are concentrated. Over 70 per cent of barley and oats DNAs belong to families of repeated sequences. The few copy or non-repeated sequences in these genomes have a mean length of around 700 nucleotide pairs and are interspersed between repeated sequences. These findings have enabled schematic maps of the barley and oats genomes to be drawn. Both genomes appear to be constructed mostly of short sequences with neighbouring sequences being distinguished by their repetition frequency (repeated or non-repeated) or their homology with different repeated sequence probes. Short non-repeated sequences interspersed with short repeated sequences are concentrated in regions occupying 50 to 60 per cent of the barley genome and 40 to 50 per cent of the oats genome. Most of the remaining DNA consists of tandemly arranged repeated sequences of different evolutionary origins. It is postulated that much of this complex repeated sequence DNA could have arisen from amplification of compound sequences each containing repeated and non-repeated sequences.

/pdf/sequence-organisation-in-barley-and-oats-chromosomes-is3en8juq9.pdf

Sequence organisation in barley and oats chromosomes revealed by interspecies DNA/DNA hybridisation.

The repeated sequences in oats DNA have been used to study chromosomal repeated sequence organisation in wheat. Approximately 75% of the wheat genome consists of repeated sequences but only approximately 20% will form heteroduplexes with repeated sequences from oats DNA at 60 degrees C in 0.18 M Na+. The proportion of wheat DNA that forms heteroduplexes with oats DNA is shown to be independent of the wheat DNA fragment length. However, the proportion of wheat DNA that is retained with the heteroduplexes when fractionated on hydroxyapatite is very dependent upon the wheat fragment length up to 3500 nucleotides. This is because more non-renatured wheat DNA is attached to the heteroduplexes with longer fragments. The results indicate that the repeated sequences in the wheat genome homologous to repeated sequences in oats are not clustered in the chromosomes but distributed amongst other repeated and possible non-repeated sequences.

Interspersion of different repeated sequences in the wheat genome revealed by interspecies DNA/DNA hybridisation.

Wheat lines carrying homologous pairs of complete or telocentric rye chromosomes have been used to investigate the detection of rye chromosomes or chromosome fragments in a wheat genetic background, by nucleic acid hybridisation. Three different radioactive rye probes were used: (1) the most highly repeated DNA sequences made radioactive in vitro by “nick translation”, (2) the whole complement of repeated sequences radioactively labelled in vivo and (3) 25s and 18s ribosomal RNAs radioactively labelled in vivo. Radioactive highly repeated sequence DNA was hybridised to unlabelled DNAs from wheat-rye chromosome addition lines immobilised on nitrocellulose filters. Rye-specific highly repeated sequences were detected in all the lines, illustrating that rye-specific highly repeated sequences reside on all chromosome arms. The effect of the size of the radioactive probe DNA was investigated by hybridising labelled rye repeated sequences to unlabelled DNAs from wheat-rye chromosome addition lines in solution. Short fragments round 300 nucleotides long detected rye-specific repeated sequences in all the unlabelled DNAs. Longer fragments, greater than 2000 nucleotides, were used to show that some of these rye-specific repeated sequences are in chromosomal regions which lack repeated sequences related to repeated sequences in wheat. The regions are probably considerably longer than 10,000 base pairs. Saturating concentrations of 25s and 18s ribosomal RNAs were hybridised to DNAs from Holdfast wheat-King II rye chromosome addition lines bound to nitrocellulose filters. The results showed that chromosome 1R of King II possesses the major cluster of ribosomal RNA genes of rye. However with DNAs from Chinese Spring wheat-Imperial rye chromosome addition lines, those with rye chromosome 1R and chromosome 5R had considerably more ribosomal RNA genes than Chinese Spring wheat. Using labelled barley repeated sequences as probe DNA it was shown in wheat-barley DNA mixtures that it was possible to detect 0.05 per cent barley DNA, i.e. 5 parts in 10,000, by incubating the DNAs to C0t 100 at 70°C in 0.12-M phosphate buffer. It is concluded that these sorts of experiments should be of considerable use for detecting the presence of alien chromosome segments in wheat and other plant species.

Jürgen Rimpau

Papers

Repeated sequence DNA relationships in four cereal genomes

Sequence organisation analysis of the wheat and rye genomes by interspecies DNA/DNA hybridisation.

Sequence organisation in barley and oats chromosomes revealed by interspecies DNA/DNA hybridisation.

Interspersion of different repeated sequences in the wheat genome revealed by interspecies DNA/DNA hybridisation.

Biochemical detection of alien DNA incorporated into wheat by chromosome engineering