Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel's anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel's early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.

• Keywords
• FISH, NGS, TRAP, eukaryotic tree of life, interstitial telomere sequences, retroelements, satellite, subtelomere structure, telomerase RNA, telomere evolution,
• MeSH
• DNA MeSH
• Humans MeSH
• Repetitive Sequences, Nucleic Acid MeSH
• DNA, Satellite * MeSH
• Base Sequence MeSH
• Telomere * genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH
• Names of Substances
• DNA MeSH
• DNA, Satellite * MeSH

Satellite repeats are major sequence constituents of centromeres in many plant and animal species. Within a species, a single family of satellite sequences typically occupies centromeres of all chromosomes and is absent from other parts of the genome. Due to their common origin, sequence similarities exist among the centromere-specific satellites in related species. Here, we report a remarkably different pattern of centromere evolution in the plant tribe Fabeae, which includes genera Pisum, Lathyrus, Vicia, and Lens. By immunoprecipitation of centromeric chromatin with CENH3 antibodies, we identified and characterized a large and diverse set of 64 families of centromeric satellites in 14 species. These families differed in their nucleotide sequence, monomer length (33-2,979 bp), and abundance in individual species. Most families were species-specific, and most species possessed multiple (2-12) satellites in their centromeres. Some of the repeats that were shared by several species exhibited promiscuous patterns of centromere association, being located within CENH3 chromatin in some species, but apart from the centromeres in others. Moreover, FISH experiments revealed that the same family could assume centromeric and noncentromeric positions even within a single species. Taken together, these findings suggest that Fabeae centromeres are not shaped by the coevolution of a single centromeric satellite with its interacting CENH3 proteins, as proposed by the centromere drive model. This conclusion is also supported by the absence of pervasive adaptive evolution of CENH3 sequences retrieved from Fabeae species.

• Keywords
• CENH3, ChIP-seq, centromere evolution, plant chromosomes, satellite DNA,
• MeSH
• Centromere chemistry   MeSH
• Species Specificity MeSH
• Fabaceae genetics   MeSH
• Genetic Variation * MeSH
• DNA, Satellite chemistry   MeSH
• Selection, Genetic MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Names of Substances
• DNA, Satellite MeSH

We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

• MeSH
• Chromosomes, Plant genetics   MeSH
• Fabaceae classification   genetics   MeSH
• Phenotype MeSH
• Phylogeny MeSH
• Genetic Variation MeSH
• Genome, Plant * MeSH
• Genomics MeSH
• Pisum sativum genetics   MeSH
• Quantitative Trait Loci * MeSH
• Chromosome Mapping MeSH
• Evolution, Molecular * MeSH
• Reference Standards MeSH
• Gene Expression Regulation, Plant MeSH
• Repetitive Sequences, Nucleic Acid MeSH
• Plant Proteins genetics   MeSH
• Whole Genome Sequencing MeSH
• Seed Storage Proteins genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Plant Proteins MeSH
• Seed Storage Proteins MeSH

BACKGROUND: The centromeric and pericentromeric regions of plant chromosomes are colonized by Ty3/gypsy retrotransposons, which, on the basis of their reverse transcriptase sequences, form the chromovirus CRM clade. Despite their potential importance for centromere evolution and function, they have remained poorly characterized. In this work, we aimed to carry out a comprehensive survey of CRM clade elements with an emphasis on their diversity, structure, chromosomal distribution and transcriptional activity. RESULTS: We have surveyed a set of 190 CRM elements belonging to 81 different retrotransposon families, derived from 33 host species and falling into 12 plant families. The sequences at the C-terminus of their integrases were unexpectedly heterogeneous, despite the understanding that they are responsible for targeting to the centromere. This variation allowed the division of the CRM clade into the three groups A, B and C, and the members of each differed considerably with respect to their chromosomal distribution. The differences in chromosomal distribution coincided with variation in the integrase C-terminus sequences possessing a putative targeting domain (PTD). A majority of the group A elements possess the CR motif and are concentrated in the centromeric region, while members of group C have the type II chromodomain and are dispersed throughout the genome. Although representatives of the group B lack a PTD of any type, they appeared to be localized preferentially in the centromeres of tested species. All tested elements were found to be transcriptionally active. CONCLUSIONS: Comprehensive analysis of the CRM clade elements showed that genuinely centromeric retrotransposons represent only a fraction of the CRM clade (group A). These centromeric retrotransposons represent an active component of centromeres of a wide range of angiosperm species, implying that they play an important role in plant centromere evolution. In addition, their transcriptional activity is consistent with the notion that the transcription of centromeric retrotransposons has a role in normal centromere function.

• Publication type
• Journal Article MeSH

BACKGROUND: Satellite repeats represent one of the most dynamic components of higher plant genomes, undergoing rapid evolutionary changes of their nucleotide sequences and abundance in a genome. However, the exact molecular mechanisms driving these changes and their eventual regulation are mostly unknown. It has been proposed that amplification and homogenization of satellite DNA could be facilitated by extrachromosomal circular DNA (eccDNA) molecules originated by recombination-based excision from satellite repeat arrays. While the models including eccDNA are attractive for their potential to explain rapid turnover of satellite DNA, the existence of satellite repeat-derived eccDNA has not yet been systematically studied in a wider range of plant genomes. RESULTS: We performed a survey of eccDNA corresponding to nine different families and three subfamilies of satellite repeats in ten species from various genera of higher plants (Arabidopsis, Oryza, Pisum, Secale, Triticum and Vicia). The repeats selected for this study differed in their monomer length, abundance, and chromosomal localization in individual species. Using two-dimensional agarose gel electrophoresis followed by Southern blotting, eccDNA molecules corresponding to all examined satellites were detected. EccDNA occurred in the form of nicked circles ranging from hundreds to over eight thousand nucleotides in size. Within this range the circular molecules occurred preferentially in discrete size intervals corresponding to multiples of monomer or higher-order repeat lengths. CONCLUSION: This work demonstrated that satellite repeat-derived eccDNA is common in plant genomes and thus it can be seriously considered as a potential intermediate in processes driving satellite repeat evolution. The observed size distribution of circular molecules suggests that they are most likely generated by molecular mechanisms based on homologous recombination requiring long stretches of sequence similarity.

• MeSH
• Electrophoresis, Gel, Two-Dimensional MeSH
• DNA, Plant genetics   MeSH
• Genetic Markers MeSH
• Genome, Plant MeSH
• Cloning, Molecular MeSH
• DNA, Circular genetics   MeSH
• Molecular Sequence Data MeSH
• Plants genetics   MeSH
• DNA, Satellite genetics   MeSH
• Base Sequence MeSH
• Sequence Alignment MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA, Plant MeSH
• Genetic Markers MeSH
• DNA, Circular MeSH
• DNA, Satellite MeSH

BACKGROUND: Extraordinary size variation of higher plant nuclear genomes is in large part caused by differences in accumulation of repetitive DNA. This makes repetitive DNA of great interest for studying the molecular mechanisms shaping architecture and function of complex plant genomes. However, due to methodological constraints of conventional cloning and sequencing, a global description of repeat composition is available for only a very limited number of higher plants. In order to provide further data required for investigating evolutionary patterns of repeated DNA within and between species, we used a novel approach based on massive parallel sequencing which allowed a comprehensive repeat characterization in our model species, garden pea (Pisum sativum). RESULTS: Analysis of 33.3 Mb sequence data resulted in quantification and partial sequence reconstruction of major repeat families occurring in the pea genome with at least thousands of copies. Our results showed that the pea genome is dominated by LTR-retrotransposons, estimated at 140,000 copies/1C. Ty3/gypsy elements are less diverse and accumulated to higher copy numbers than Ty1/copia. This is in part due to a large population of Ogre-like retrotransposons which alone make up over 20% of the genome. In addition to numerous types of mobile elements, we have discovered a set of novel satellite repeats and two additional variants of telomeric sequences. Comparative genome analysis revealed that there are only a few repeat sequences conserved between pea and soybean genomes. On the other hand, all major families of pea mobile elements are well represented in M. truncatula. CONCLUSION: We have demonstrated that even in a species with a relatively large genome like pea, where a single 454-sequencing run provided only 0.77% coverage, the generated sequences were sufficient to reconstruct and analyze major repeat families corresponding to a total of 35-48% of the genome. These data provide a starting point for further investigations of legume plant genomes based on their global comparative analysis and for the development of more sophisticated approaches for data mining.

• MeSH
• Chromosomes, Plant MeSH
• DNA, Plant * classification   MeSH
• Genome, Plant * MeSH
• Gene Dosage MeSH
• Glycine max genetics   MeSH
• Pisum sativum genetics   MeSH
• In Situ Hybridization, Fluorescence MeSH
• Contig Mapping MeSH
• Medicago truncatula genetics   MeSH
• Metaphase MeSH
• Repetitive Sequences, Nucleic Acid * MeSH
• Retroelements genetics   MeSH
• Sequence Analysis, DNA MeSH
• Sequence Homology, Nucleic Acid MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Names of Substances
• DNA, Plant * MeSH
• Retroelements MeSH

Amplification and eventual elimination of dispersed repeats, especially those of the retroelement origin, account for most of the profound size variability observed among plant genomes. In most higher plants investigated so far, differential accumulation of various families of elements contributes to these differences. Here we report the identification of giant Ty3/gypsy-like retrotransposons from the legume plant Vicia pannonica, which alone make up approximately 38% of the genome of this species. These retrotransposons have structural features of the Ogre elements previously identified in the genomes of pea and Medicago. These features include extreme size (25 kb), the presence of an extra ORF upstream of the gag-pol region, and a putative intron dividing the prot and rt coding sequences. The Ogre elements are evenly dispersed on V. pannonica chromosomes except for terminal regions containing satellite repeats, their individual copies show extraordinary sequence similarity, and at least part of them are transcriptionally active, which suggests their recent amplification. Similar elements were also detected in several other Vicia species but in most cases in significantly lower numbers. However, there was no obvious correlation of the abundance of Ogre sequences with the genome size of these species.

• MeSH
• Gene Amplification MeSH
• DNA, Plant genetics   MeSH
• Species Specificity MeSH
• Fabaceae genetics   MeSH
• Genome, Plant * MeSH
• Gene Dosage MeSH
• In Situ Hybridization, Fluorescence MeSH
• Introns MeSH
• Conserved Sequence MeSH
• Molecular Sequence Data MeSH
• Open Reading Frames MeSH
• Retroelements genetics   MeSH
• Plant Proteins genetics   MeSH
• Base Sequence MeSH
• Vicia genetics   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Names of Substances
• DNA, Plant MeSH
• Retroelements MeSH
• Plant Proteins MeSH

Fast and efficient DNA fingerprinting of crop cultivars and individuals is frequently used in both theoretical population genetics and in practical breeding. Numerous DNA marker technologies exist and the ratio of speed, cost and accuracy are of importance. Therefore even in species where highly accurate and polymorphic marker systems are available, such as microsatellite SSR (simple sequence repeats), also alternative methods may be of interest. Thanks to their high abundance and ubiquity, temporary mobile retrotransposable elements come into recent focus. Their properties, such as genome wide distribution and well-defined origin of individual insertions by descent, predetermine them for use as molecular markers. In this study, several Ty3-gypsy type retrotransposons have been developed and adopted for the inter-retrotransposon amplified polymorphism (IRAP) method, which is suitable for fast and efficient pea cultivar fingerprinting. The method can easily distinguish even between genetically closely related pea cultivars and provide high polymorphic information content (PIC) in a single PCR analysis.

• MeSH
• Breeding methods   MeSH
• DNA Fingerprinting methods   MeSH
• DNA Primers MeSH
• Electrophoresis, Polyacrylamide Gel MeSH
• Pisum sativum genetics   MeSH
• Polymorphism, Genetic * MeSH
• Retroelements genetics   MeSH
• Cluster Analysis MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Geographicals
• Czech Republic MeSH
• Names of Substances
• DNA Primers MeSH
• Retroelements MeSH

Plant LTR retrotransposons of the envelope class define a new branch in the Metaviridae family. They differ from other LTR retrotransposons mainly by the presence of an additional ORF downstream of the gag-pol region which has been hypothesized to be equivalent to the envelope gene of retroviruses. Here we present a newly identified element from pea (Pisum sativum), named PIGY, that has all the features characteristic of this group of LTR retrotransposons. In addition to the potential coding sequence downstream of the gag-pol region, PIGY has a primer binding site complementary to tRNA(asp) and a polypurine tract with a TGGGG motif and is of large size (13,645 bp). The relationship between PIGY and other retrotransposons of the env-class was confirmed by a phylogenetic analysis of their reverse transcriptase domains. One distinctive feature of PIGY is that its env-like region is actually composed of two similar ORFs, each of which encodes a protein with similarity to the Athila envelope-like protein. PIGY is present in the pea genome in 1-5x10(3) copies and is transcriptionally active, suggesting that some of these elements may still be capable of active transposition. Another new env-class retrotransposon similar to PIGY was also identified among genomic sequences of Medicago truncatula.

• MeSH
• DNA Primers MeSH
• Phylogeny * MeSH
• Genes, env genetics   MeSH
• Pisum sativum genetics   virology   MeSH
• In Situ Hybridization, Fluorescence MeSH
• Terminal Repeat Sequences genetics   MeSH
• Evolution, Molecular MeSH
• Molecular Sequence Data MeSH
• Base Pairing MeSH
• Reverse Transcriptase Polymerase Chain Reaction MeSH
• Retroelements genetics   MeSH
• RNA Viruses genetics   MeSH
• Amino Acid Sequence MeSH
• Base Sequence MeSH
• Sequence Analysis, DNA MeSH
• Sequence Alignment MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Comparative Study MeSH
• Names of Substances
• DNA Primers MeSH
• Retroelements MeSH

We have isolated and characterized a novel giant retroelement, named Ogre, which is over 22 kb long and makes up at least 5% of the pea (Pisum sativum L.) genome. This element can be classified as a Ty3/gypsy-like LTR retrotransposon based on the presence of long terminal repeats (LTRs) and the order of the domains coding for typical retrotransposon proteins. In addition to its extreme length, it has several features which make it unique among the retroelements described so far: (1) the sequences coding for gag and prot proteins are separated from the rt/rh-int domains by several stop codons; (2) the region containing these stop codons is removed from the element transcripts by splicing which results in reconstitution of the complete gag-pol coding sequence; (3) only a part of the transcripts is spliced which probably determines the ratio of translated proteins; (4) the element contains an extra ORF located upstream the gag-pol coding sequences, potentially coding for a protein of 546-562 amino acids with unknown function. The transcriptional activity of the Ogre elements has been detected in all organs tested (leaves, roots, flowers) as well as in wounded leaves and protoplasts. Considering this retroelement's constitutive expression and observed high mutual similarity of the element genomic sequences, it is possible to speculate about its recent amplification in the genomes of pea and other legume plants.

• MeSH
• Alternative Splicing * MeSH
• DNA, Plant chemistry   genetics   MeSH
• Fabaceae genetics   MeSH
• Transcription, Genetic * MeSH
• Genome, Plant MeSH
• Pisum sativum genetics   MeSH
• Molecular Sequence Data MeSH
• Open Reading Frames genetics   MeSH
• Gene Expression Regulation, Plant MeSH
• Retroelements genetics   MeSH
• Base Sequence MeSH
• Sequence Analysis, DNA MeSH
• Sequence Homology, Nucleic Acid MeSH
• Sequence Alignment MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• DNA, Plant MeSH
• Retroelements MeSH