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Domingues DS, Cruz GMQ, Metcalfe CJ, Nogueira FTS, Vicentini R, de S Alves C, Van Sluys MA. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns. BMC Genomics 2012; 13:137. [PMID: 22507400 PMCID: PMC3352295 DOI: 10.1186/1471-2164-13-137] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 04/16/2012] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. RESULTS Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. CONCLUSIONS Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.
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Affiliation(s)
- Douglas S Domingues
- GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil
- Plant Biotechnology Laboratory, Instituto Agronômico do Paraná, Rod. Celso Garcia Cid (PR-445), km375, 86047-902 Londrina, Brazil
| | - Guilherme MQ Cruz
- GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil
| | - Cushla J Metcalfe
- GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil
| | - Fabio TS Nogueira
- Depto. de Genética, Inst. de Biociências, Universidade Estadual Paulista, campus de Botucatu, Distrito de Rubião Jr., s/n, 18618-000 Botucatu, Brazil
| | - Renato Vicentini
- Systems Biology Laboratory, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Av. Cândido Rondon, 400, 13083-875 Campinas, Brazil
| | - Cristiane de S Alves
- Depto. de Genética, Inst. de Biociências, Universidade Estadual Paulista, campus de Botucatu, Distrito de Rubião Jr., s/n, 18618-000 Botucatu, Brazil
| | - Marie-Anne Van Sluys
- GaTE Lab, Depto. de Botânica, Inst. de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090 São Paulo, Brazil
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152
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Boutin TS, Le Rouzic A, Capy P. How does selfing affect the dynamics of selfish transposable elements? Mob DNA 2012; 3:5. [PMID: 22394388 PMCID: PMC3395816 DOI: 10.1186/1759-8753-3-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 03/07/2012] [Indexed: 02/02/2023] Open
Abstract
Background Many theoretical models predicting the dynamics of transposable elements (TEs) in genomes, populations, and species have already been proposed. However, most of them only focus on populations of sexual diploid individuals, and TE dynamics in populations partly composed by autogamous individuals remains poorly investigated. To estimate the impact of selfing on TE dynamics, the short- and long-term evolution of TEs was simulated in outcrossing populations with various proportions of selfing individuals. Results Selfing has a deep impact on TE dynamics: the higher the selfing rate, the lower the probability of invasion. Already known non-equilibrium dynamics (complete loss, domestication, cyclical invasion of TEs) can all be described whatever the mating system. However, their pattern and their respective frequencies greatly depend on the selfing rate. For instance, in cyclical dynamics resulting from interactions between autonomous and non-autonomous copies, cycles are faster when the selfing rate increases. Interestingly, an abrupt change in the mating system from sexuality to complete asexuality leads to the loss of all the elements over a few hundred generations. In general, for intermediate selfing rates, the transposition activity remains maintained. Conclusions Our theoretical results evidence that a clear and systematic contrast in TE content according to the mating system is expected, with a smooth transition for intermediate selfing rates. Several parameters impact the TE copy number, and all dynamics described in allogamous populations can be also observed in partly autogamous species. This study thus provides new insights to understand the complex signal from empirical comparison of closely related species with different mating systems.
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Affiliation(s)
- Thibaud S Boutin
- LEGS, CNRS UPR9034, IDEEV FR3284, Avenue de la terrasse, Bat 13, 91198 Gif-sur-Yvette, France.
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153
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Eagle SH, Crease TJ. Copy number variation of ribosomal DNA and Pokey transposons in natural populations of Daphnia. Mob DNA 2012; 3:4. [PMID: 22390386 PMCID: PMC3315735 DOI: 10.1186/1759-8753-3-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 03/05/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite their ubiquity and high diversity in eukaryotic genomes, DNA transposons are rarely encountered in ribosomal DNA (rDNA). In contrast, R-elements, a diverse group of non-LTR retrotransposons, specifically target rDNA. Pokey is a DNA transposon that targets a specific rDNA site, but also occurs in many other genomic locations, unlike R-elements. However, unlike most DNA transposons, Pokey has been a stable component of Daphnia genomes for over 100 million years. Here we use qPCR to estimate the number of 18S and 28S ribosomal RNA genes and Pokey elements in rDNA (rPokey), as well as other genomic locations (gPokey) in two species of Daphnia. Our goals are to estimate the correlation between (1) the number of 18S and 28S rRNA genes, (2) the number of 28S genes and rPokey, and (3) the number of rPokey and gPokey. In addition, we ask whether Pokey number and distribution in both genomic compartments are affected by differences in life history between D. pulex and D. pulicaria. RESULTS We found differences in 18S and 28S gene number within isolates that are too large to be explained by experimental variation. In general, Pokey number within isolates is modest (< 20), and most are gPokey. There is no correlation between the number of rRNA genes and rPokey, or between rPokey and gPokey. However, we identified three isolates with unusually high numbers of both rPokey and gPokey, which we infer is a consequence of recent transposition. We also detected other rDNA insertions (rInserts) that could be degraded Pokey elements, R- elements or the divergent PokeyB lineage recently detected in the Daphnia genome sequence. Unlike rPokey, rInserts are positively correlated with rRNA genes, suggesting that they are amplified by the same mechanisms that amplify rDNA units even though rPokey is not. Overall, Pokey frequency and distribution are similar in D. pulex and D. pulicaria suggesting that differences in life history have no impact on Pokey. CONCLUSIONS The possibility that many rDNA units do not contain a copy of both 18S and 28S genes suggests that rDNA is much more complicated than once thought, and warrants further study. In addition, the lack of correlation between rPokey, gPokey and rDNA unit numbers suggests that Pokey transposition rate is generally very low, and that recombination, in combination with natural selection, eliminates rPokey much faster than gPokey. Our results suggest that further research to determine the mechanisms by which Pokey has escaped complete inactivation by its host (the usual fate of DNA transposons), would provide important insights into transposon biology.
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Affiliation(s)
- Shannon Hc Eagle
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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de Setta N, Metcalfe CJ, Cruz GMQ, Ochoa EA, Van Sluys MA. Noise or Symphony: Comparative Evolutionary Analysis of Sugarcane Transposable Elements with Other Grasses. PLANT TRANSPOSABLE ELEMENTS 2012. [DOI: 10.1007/978-3-642-31842-9_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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157
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Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 2011; 13:36-46. [PMID: 22124482 DOI: 10.1038/nrg3117] [Citation(s) in RCA: 1066] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Repetitive DNA sequences are abundant in a broad range of species, from bacteria to mammals, and they cover nearly half of the human genome. Repeats have always presented technical challenges for sequence alignment and assembly programs. Next-generation sequencing projects, with their short read lengths and high data volumes, have made these challenges more difficult. From a computational perspective, repeats create ambiguities in alignment and assembly, which, in turn, can produce biases and errors when interpreting results. Simply ignoring repeats is not an option, as this creates problems of its own and may mean that important biological phenomena are missed. We discuss the computational problems surrounding repeats and describe strategies used by current bioinformatics systems to solve them.
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158
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Farré M, Bosch M, López-Giráldez F, Ponsà M, Ruiz-Herrera A. Assessing the role of tandem repeats in shaping the genomic architecture of great apes. PLoS One 2011; 6:e27239. [PMID: 22076140 PMCID: PMC3208591 DOI: 10.1371/journal.pone.0027239] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
Background Ancestral reconstructions of mammalian genomes have revealed that evolutionary breakpoint regions are clustered in regions that are more prone to break and reorganize. What is still unclear to evolutionary biologists is whether these regions are physically unstable due solely to sequence composition and/or genome organization, or do they represent genomic areas where the selection against breakpoints is minimal. Methodology and Principal Findings Here we present a comprehensive study of the distribution of tandem repeats in great apes. We analyzed the distribution of tandem repeats in relation to the localization of evolutionary breakpoint regions in the human, chimpanzee, orangutan and macaque genomes. We observed an accumulation of tandem repeats in the genomic regions implicated in chromosomal reorganizations. In the case of the human genome our analyses revealed that evolutionary breakpoint regions contained more base pairs implicated in tandem repeats compared to synteny blocks, being the AAAT motif the most frequently involved in evolutionary regions. We found that those AAAT repeats located in evolutionary regions were preferentially associated with Alu elements. Significance Our observations provide evidence for the role of tandem repeats in shaping mammalian genome architecture. We hypothesize that an accumulation of specific tandem repeats in evolutionary regions can promote genome instability by altering the state of the chromatin conformation or by promoting the insertion of transposable elements.
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Affiliation(s)
- Marta Farré
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | - Francesc López-Giráldez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
| | - Montserrat Ponsà
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Aurora Ruiz-Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- * E-mail:
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Jurka J, Bao W, Kojima KK. Families of transposable elements, population structure and the origin of species. Biol Direct 2011; 6:44. [PMID: 21929767 PMCID: PMC3183009 DOI: 10.1186/1745-6150-6-44] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/19/2011] [Indexed: 11/23/2022] Open
Abstract
Background Eukaryotic genomes harbor diverse families of repetitive DNA derived from transposable elements (TEs) that are able to replicate and insert into genomic DNA. The biological role of TEs remains unclear, although they have profound mutagenic impact on eukaryotic genomes and the origin of repetitive families often correlates with speciation events. We present a new hypothesis to explain the observed correlations based on classical concepts of population genetics. Presentation of the hypothesis The main thesis presented in this paper is that the TE-derived repetitive families originate primarily by genetic drift in small populations derived mostly by subdivisions of large populations into subpopulations. We outline the potential impact of the emerging repetitive families on genetic diversification of different subpopulations, and discuss implications of such diversification for the origin of new species. Testing the hypothesis Several testable predictions of the hypothesis are examined. First, we focus on the prediction that the number of diverse families of TEs fixed in a representative genome of a particular species positively correlates with the cumulative number of subpopulations (demes) in the historical metapopulation from which the species has emerged. Furthermore, we present evidence indicating that human AluYa5 and AluYb8 families might have originated in separate proto-human subpopulations. We also revisit prior evidence linking the origin of repetitive families to mammalian phylogeny and present additional evidence linking repetitive families to speciation based on mammalian taxonomy. Finally, we discuss evidence that mammalian orders represented by the largest numbers of species may be subject to relatively recent population subdivisions and speciation events. Implications of the hypothesis The hypothesis implies that subdivision of a population into small subpopulations is the major step in the origin of new families of TEs as well as of new species. The origin of new subpopulations is likely to be driven by the availability of new biological niches, consistent with the hypothesis of punctuated equilibria. The hypothesis also has implications for the ongoing debate on the role of genetic drift in genome evolution. Reviewers This article was reviewed by Eugene Koonin, Juergen Brosius and I. King Jordan.
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Affiliation(s)
- Jerzy Jurka
- Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA 94043, USA.
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