Plant Genome Evolution Research Articles

Plant retrotransposons.

Retrotransposons are mobile genetic elements that transpose through reverse transcription of an RNA intermediate. Retrotransposons are ubiquitous in plants and play a major role in plant gene and genome evolution. In many cases, retrotransposons comprise over 50% of nuclear DNA content, a situation that can arise in just a few million years. Plant retrotransposons are structurally and functionally similar to the retrotransposons and retroviruses that are found in other eukaryotic organisms. However, there are important differences in the genomic organization of retrotransposons in plants compared to some other eukaryotes, including their often-high copy numbers, their extensively heterogeneous populations, and their chromosomal dispersion patterns. Recent studies are providing valuable insights into the mechanisms involved in regulating the expression and transposition of retrotransposons. This review describes the structure, genomic organization, expression, regulation, and evolution of retrotransposons, and discusses both their contributions to plant genome evolution and their use as genetic tools in plant biology.

Multiple ribosomal RNA gene loci in the genome of the homosporous fernCeratopteris richardii

The genomes of homosporous ferns are largely uncharacterized, but they appear to differ from gymnosperms and angiosperms in key aspects, such as high chromosome numbers at the diploid level, and thus provide a unique perspective on plant genome structure and evolution. Using the model homosporous fern Ceratopteris richardii, loci encoding ribosomal RNA sequences (rDNA genes) were detected using fluorescent in situ hybridization. At least two major rDNA loci were visible in all cases, and six or more weakly hybridizing signals were observed in most cytological preparations. These results are consistent with models of homosporous fern evolution via cycles of polyploidy followed by gene silencing. They are also consistent with other models of fern genome evolution. With the exception of the weakly hybridizing signals, these data are similar to analogous reports of one or two major rDNA loci in diploid angiosperms. These results suggest that the gross morphology of rDNA loci are similar between diploid homosporous ferns and angiosperms, but that important clues to rDNA gene and chromosome evolution in homosporous ferns may reside in the analysis of their minor rDNA sequences.Key words: rDNA, in situ hybridization, homosporous ferns, evolution, gene silencing, polyploidy.

Integrated pararetroviral sequences define a unique class of dispersed repetitive DNA in plants.

Although integration of viral DNA into host chromosomes occurs regularly in bacteria and animals, there are few reported cases in plants, and these involve insertion at only one or a few sites. Here, we report that pararetrovirus-like sequences have integrated repeatedly into tobacco chromosomes, attaining a copy number of approximately 10(3). Insertion apparently occurred by illegitimate recombination. From the sequences of 22 independent insertions recovered from a healthy plant, an 8-kilobase genome encoding a previously uncharacterized pararetrovirus that does not contain an integrase function could be assembled. Preferred boundaries of the viral inserts may correspond to recombinogenic gaps in open circular viral DNA. An unusual feature of the integrated viral sequences is a variable tandem repeat cluster, which might reflect defective genomes that preferentially recombine into plant DNA. The recurrent invasion of pararetroviral DNA into tobacco chromosomes demonstrates that viral sequences can contribute significantly to plant genome evolution.

Identification and analysis of homoeologous segments of the genomes of rice andArabidopsis thaliana

Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved framework of genes identified is interspersed with non-conserved genes, indicating that mechanisms beyond segmental inversions and translocations need to be invoked to fully explain plant genome evolution, and that the benefits of comparative genomics over such large taxonomic distances may be limited.

Repetitive DNA Elements as a Major Component of Plant Genomes

A major part of the nuclear genome of most plants is composed of different repetitive DNA elements. Studying these sequence elements is essential for our understanding of the nature and consequences of genome size variation between different species, and for studying the large-scale organization and evolution of plant genomes. Sugar beet ( Beta vulgarisL.) is an important crop and a suitable model for such investigations: with a genome size of 0.8 pg 1C (760 Mbp) it contains significant amounts of all major groups of repetitive sequences among its nine chromosome pairs, but analysis is not complicated by polyploidy or the huge size of some genomes, and there are valuable genetic data, recombinant DNA libraries and wild relatives to complement studies of sequence contribution to genome size in sugar beet. A sophisticated understanding of the structure of the genome will provide valuable data about the major factors responsible for genome size variation, useful aids in the development of a molecular understanding of genome evolution, and perhaps indicate strategies for crop improvement. Using molecular and cytological approaches, we have characterized a range of differentially organized repetitive DNA sequence elements from the genomes of cultivated and wild beet species, leading to an extensive model of the repetitive DNA, its organization and evolution.

Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton.

Polyploid formation has played a major role in the evolution of many plant and animal genomes; however, surprisingly little is known regarding the subsequent evolution of DNA sequences that become newly united in a common nucleus. Of particular interest is the repetitive DNA fraction, which accounts for most nuclear DNA in higher plants and animals and which can be remarkably different, even in closely related taxa. In one recently formed polyploid, cotton (Gossypium barbadense L.; AD genome), 83 non-cross-hybridizing DNA clones contain dispersed repeats that are estimated to comprise about 24% of the nuclear DNA. Among these, 64 (77%) are largely restricted to diploid taxa containing the larger A genome and collectively account for about half of the difference in DNA content between Old World (A) and New World (D) diploid ancestors of cultivated AD tetraploid cotton. In tetraploid cotton, FISH analysis showed that some A-genome dispersed repeats appear to have spread to D-genome chromosomes. Such spread may also account for the finding that one, and only one, D-genome diploid cotton, Gossypium gossypioides, contains moderate levels of (otherwise) A-genome-specific repeats in addition to normal levels of D-genome repeats. The discovery of A-genome repeats in G. gossypioides adds genome-wide support to a suggestion previously based on evidence from only a single genetic locus that this species may be either the closest living descendant of the New World cotton ancestor, or an adulterated relic of polyploid formation. Spread of dispersed repeats in the early stages of polyploid formation may provide a tag to identify diploid progenitors of a polyploid. Although most repetitive clones do not correspond to known DNA sequences, 4 correspond to known transposons, most contain internal subrepeats, and at least 12 (including 2 of the possible transposons) hybridize to mRNAs expressed at readily discernible levels in cotton seedlings, implicating transposition as one possible mechanism of spread. Integration of molecular, phylogenetic, and cytogenetic analysis of dispersed repetitive DNA may shed new light on evolution of other polyploid genomes, as well as providing valuable landmarks for many aspects of genome analysis.

Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes.

To study genome evolution in allopolyploid plants, we analyzed polyploid wheats and their diploid progenitors for the occurrence of 16 low-copy chromosome- or genome-specific sequences isolated from hexaploid wheat. Based on their occurrence in the diploid species, we classified the sequences into two groups: group I, found in only one of the three diploid progenitors of hexaploid wheat, and group II, found in all three diploid progenitors. The absence of group II sequences from one genome of tetraploid wheat and from two genomes of hexaploid wheat indicates their specific elimination from these genomes at the polyploid level. Analysis of a newly synthesized amphiploid, having a genomic constitution analogous to that of hexaploid wheat, revealed a pattern of sequence elimination similar to the one found in hexaploid wheat. Apparently, speciation through allopolyploidy is accompanied by a rapid, nonrandom elimination of specific, low-copy, probably noncoding DNA sequences at the early stages of allopolyploidization, resulting in further divergence of homoeologous chromosomes (partially homologous chromosomes of different genomes carrying the same order of gene loci). We suggest that such genomic changes may provide the physical basis for the diploid-like meiotic behavior of polyploid wheat.

Molecular cytogenetics of the genes encoding 18s-5.8s-26s rRNA and 5s rRNA in two species of spruce (Picea)

Molecular cytogenetics is a convenient tool to investigate the organization and evolution of plant genomes. In coniferous trees of the Pinaceae, cytogenetic data is rudimentary since individual chromosomes are difficult to distinguish and karyotypes of related species are poorly differentiated. We determined the chromosomal locations of ribosomal RNA genes in white spruce (Picea glauca) and Sitka spruce (Picea sitchensis) using fluorescence in situ hybridization. The biotin-labeled DNA probes consisted of the 5s ribosomal DNA (rDNA) amplified from white spruce using the polymerase chain reaction and a heterologous 18s-5.8s-26s rDNA sequence. The 5s rDNA was present only on chromosome 5 at a single locus and near to an 18s-5.8s-26s rDNA locus in both species. Additional 18s-5.8s-26s rDNA loci were found at interstitial sites on six and four chromosomes of white and Sitka spruce, respectively, providing potentially useful interspecific differences. Progress in karyotyping both species is presented. A molecular analysis of 5s rDNA of white spruce revealed the presence of two classes of repeating units, one of 221 bp corresponding to the PCR amplification product, and another of approximately 600 bp. The nucleotide sequence and copy number of the 221-bp class is reported.

The maize transposable element Ac induces recombination between the donor site and an homologous ectopic sequence.

The prominent repair mechanism of DNA double-strand breaks formed upon excision of the maize Ac transposable element is via nonhomologous end joining. In this work we have studied the role of homologous recombination as an additional repair pathway. To this end, we developed an assay whereby beta-Glucuronidase (GUS) activity is restored upon recombination between two homologous ectopic (nonallelic) sequences in transgenic tobacco plants. One of the recombination partners carried a deletion at the 5' end of GUS and an Ac or a Ds element inserted at the deletion site. The other partner carried an intact 5' end of the GUS open reading frame and had a deletion at the 3' end of the gene. Based on GUS reactivation data, we found that the excision of Ac induced recombination between ectopic sequences by at least two orders of magnitude. Recombination events, visualized by blue staining, were detected in seedlings, in pollen and in protoplasts. DNA fragments corresponding to recombination events were recovered exclusively in crosses with Ac-carrying plants, providing physical evidence for Ac-induced ectopic recombination. The occurrence of ectopic recombination following double-strand breaks is a potentially important factor in plant genome evolution.

LTR-retrotransposons and MITEs: important players in the evolution of plant genomes

Retrotransposons are an abundant and ancient component of plant genomes, yet recent evidence indicates that element activity in many modern plants is restricted to times of stress. Stress activation of plant retrotransposons may be a significant factor in somaclonal variation, in addition to providing an important means to isolate new active elements. Long terminal repeat retrotransposons and a second class of elements we have called miniature inverted-repeat transposable elements (MITEs) have recently been found to be associated with the genes of diverse plants where some contribute regulatory sequences. Because of their sequence diversity and small size, MITEs may be a valuable evolutionary tool for altering patterns of gene expression.

Plant Genomes: A Current Molecular Description

A major advance in plant genome analysis has been the development of molecular marker maps. These, in combination with repeated sequence analysis, have given considerable insight into the organization and evolution of many plant genomes. Physical mapping and sequencing of the genomes of the model plant species Arabidopsis thaliana and rice are progressing rapidly. The physical maps facilitate the isolation of genes by map-based cloning and will enable the organization of whole chromosomes to be analyzed. Comparative mapping studies between related plant species, using common sets of molecular markers, have revealed extensive collinearity over short chromosomal segments or whole chromosomes. Thus, in the future, collinearity as well as homology may be used to clone genes from many plant species, maximally exploiting the A. thaliana or rice physical maps.

Plant Genomes: A Current Molecular Description

A major advance in plant genome analysis has been the development of molecular marker maps. These, in combination with repeated sequence analysis, have given considerable insight into the organization and evolution of many plant genomes. Physical mapping and sequencing of the genomes of the model plant species Arabidopsis thaliana and rice are progressing rapidly. The physical maps facilitate the isolation of genes by map-based cloning and will enable the organization of whole chromosomes to be analyzed. Comparative mapping studies between related plant species, using common sets of molecular markers, have revealed extensive collinearity over short chromosomal segments or whole chromosomes. Thus, in the future, collinearity as well as homology may be used to clone genes from many plant species, maximally exploiting the A. thaliana or rice physical maps.

Comparative RFLP mapping of Hordeum vulgare and Triticum tauschii

Hordeum vulgare (barley) and Triticum tauschii are related, but sexually incompatible, species. This study was conducted to determine the extent of homology between the genomes of barley and T. tauschii using a common set of restriction fragment length polymorphism (RFLP) markers. Results showed that >95% of low-copy sequences are shared, but 42% of the conserved sequences showed copy-number differences. Sixty-three loci were mapped in T. tauschii using RFLP markers previously mapped in barley. A comparison of RFLP marker order showed that, in general, barley and T. tauschii have conserved linkage groups, with markers in the same linear orders. However, six of the seven linkage groups of T. tauschii contained markers which mapped to unrelated (i.e., non-homoeologous) barley chromosomes. Additionally, four of the T. tauschii linkage groups contained markers that were switched in order with respect to barley. All the chromosome segments differing between T. tauschii and barley contained markers that were detected by multi-copy probes. The results suggest that the observed differences between the T. tauschii and barley genomes were brought about by duplications or deletions of segments in one or both species. The implications of these findings for genetic mapping, breeding, and plant genome evolution are discussed.

Nucleotide distribution in gymnosperm nuclear sequences suggests a model for GC-content change in land-plant nuclear genomes

Nuclear protein coding sequences from gymnosperms are currently scarce. We have determined 4 kb of nuclear protein coding sequences from gynosperms and have collected and analyzed > 60 kb of nuclear sequences from gymnosperms and nonspermatophytes in order to better understand processes influencing genome evolution in plants. We show that conifers possess both biased and nonbiased genes with respect to GC content, as found in monocots, suggesting that the common ancestor of conifers and monocots may have possessed both biased and nonbiased genes. The lack of biased genes in dicots is suggested to be a derived character for this lineage. We present a simple but speculative model of land-plant genome evolution which considers changes in GC bias and CpG frequency, respectively, as independent processes and which can account for several puzzling aspects of observed nucleotide frequencies in plant genes.

SYMPOSIUM: Genome Structure and Evolution in Cultivated Plants and Relatives

American Journal of BotanyVolume 81, Issue S6 p. 77-79 Genetics Section SYMPOSIUM: Genome Structure and Evolution in Cultivated Plants and Relatives First published: 01 June 1994 https://doi.org/10.1002/j.1537-2197.1994.tb15534.xAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume81, IssueS6June 1994Pages 77-79 RelatedInformation

Genome-specific repetitive sequences in the genus Oryza

Repetitive DNA sequences are useful molecular markers for studying plant genome evolution and species divergence. In this paper, we report the isolation and characterization of four genome-type specific repetitive DNA sequences in the genus Oryza. Sequences specific to the AA, CC, EE or FF genome types are described. These genome-type specific repetitive sequences will be useful in classifying unknown species of wild or domestic rice, and in studying genome evolution at the molecular level. Using an AA genome-specific repetitive DNA sequence (pOs48) as a hybridization probe, considerable differences in its copy number were found among different varieties of Asian-cultivated rice (O. sativa) and other related species within the AA genome type. Thus, the relationship among some of the members of AA genome type can be deduced based on the degree of DNA sequence similarity of this repetitive sequence.