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Caballero-López V, Lundberg M, Sokolovskis K, Bensch S. Transposable elements mark a repeat-rich region associated with migratory phenotypes of willow warblers (Phylloscopus trochilus). Mol Ecol 2021; 31:1128-1141. [PMID: 34837428 DOI: 10.1111/mec.16292] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/26/2021] [Accepted: 11/16/2021] [Indexed: 11/30/2022]
Abstract
The genetic basis of bird migration has been the focus of several studies. Two willow warbler subspecies (Phylloscopus trochilus trochilus and Phylloscopus trochilus acredula) follow different migratory routes to wintering grounds in Africa. Their breeding populations overlap in contact areas or "migratory divides" located in central Scandinavia and in eastern Poland. Earlier analyses demonstrated that the genetic differences between these two migratory phenotypes are few and cluster on chromosomes 1 and 5. In addition, an amplified fragment length polymorphism-derived biallelic marker (known as WW2) presents steep clines across both migratory divides but failed to be mapped in the genome. Here, we characterize the WW2 marker and describe its two variants (WW2 ancestral and WW2 derived) as portions of long terminal repeat retrotransposons originating from an ancient infection by an endogenous retrovirus. We used quantitative polymerase chain reaction techniques to quantify copy numbers of the WW2 derived variant in the two subspecies and their hybrids. This, together with genome analyses revealed that WW2 derived variants are much more abundant in P. t. acredula and appear embedded in a large repeat-rich region (>12 Mbp), not associated with the divergent regions of chromosomes 1 or 5. However, it might interact with genetic elements controlling migration direction. Testing this hypothesis further will require knowing the exact location of this region, such as by obtaining more complete genome assemblies preferably in combination with techniques like fluorescence in situ hybridization applied to a willow warbler karyotype, and finally to investigate the copy number of this marker in hybrids with known migratory tracks.
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Affiliation(s)
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
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2
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Pasquesi GIM, Perry BW, Vandewege MW, Ruggiero RP, Schield DR, Castoe TA. Vertebrate Lineages Exhibit Diverse Patterns of Transposable Element Regulation and Expression across Tissues. Genome Biol Evol 2021; 12:506-521. [PMID: 32271917 PMCID: PMC7211425 DOI: 10.1093/gbe/evaa068] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/02/2020] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) comprise a major fraction of vertebrate genomes, yet little is known about their expression and regulation across tissues, and how this varies across major vertebrate lineages. We present the first comparative analysis integrating TE expression and TE regulatory pathway activity in somatic and gametic tissues for a diverse set of 12 vertebrates. We conduct simultaneous gene and TE expression analyses to characterize patterns of TE expression and TE regulation across vertebrates and examine relationships between these features. We find remarkable variation in the expression of genes involved in TE negative regulation across tissues and species, yet consistently high expression in germline tissues, particularly in testes. Most vertebrates show comparably high levels of TE regulatory pathway activity across gonadal tissues except for mammals, where reduced activity of TE regulatory pathways in ovarian tissues may be the result of lower relative germ cell densities. We also find that all vertebrate lineages examined exhibit remarkably high levels of TE-derived transcripts in somatic and gametic tissues, with recently active TE families showing higher expression in gametic tissues. Although most TE-derived transcripts originate from inactive ancient TE families (and are likely incapable of transposition), such high levels of TE-derived RNA in the cytoplasm may have secondary, unappreciated biological relevance.
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Affiliation(s)
- Giulia I M Pasquesi
- Department of Biology, University of Texas at Arlington.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington
| | | | | | - Drew R Schield
- Department of Biology, University of Texas at Arlington.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington
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3
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Dennenmoser S, Sedlazeck FJ, Schatz MC, Altmüller J, Zytnicki M, Nolte AW. Genome‐wide patterns of transposon proliferation in an evolutionary young hybrid fish. Mol Ecol 2019; 28:1491-1505. [DOI: 10.1111/mec.14969] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/15/2018] [Accepted: 10/23/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Stefan Dennenmoser
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
| | | | - Michael C. Schatz
- Cold Spring Harbor Laboratory Cold Spring Harbor New York
- Departments of Computer Science and Biology Johns Hopkins University Baltimore Maryland
| | - Janine Altmüller
- Cologne Center for Genomics, and Institute of Human Genetics University of Cologne Cologne Germany
| | | | - Arne W. Nolte
- Institute for Biology and Environmental Sciences Carl von Ossietzky University Oldenburg Oldenburg Germany
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4
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Pasquesi GIM, Adams RH, Card DC, Schield DR, Corbin AB, Perry BW, Reyes-Velasco J, Ruggiero RP, Vandewege MW, Shortt JA, Castoe TA. Squamate reptiles challenge paradigms of genomic repeat element evolution set by birds and mammals. Nat Commun 2018; 9:2774. [PMID: 30018307 PMCID: PMC6050309 DOI: 10.1038/s41467-018-05279-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/25/2018] [Indexed: 12/14/2022] Open
Abstract
Broad paradigms of vertebrate genomic repeat element evolution have been largely shaped by analyses of mammalian and avian genomes. Here, based on analyses of genomes sequenced from over 60 squamate reptiles (lizards and snakes), we show that patterns of genomic repeat landscape evolution in squamates challenge such paradigms. Despite low variance in genome size, squamate genomes exhibit surprisingly high variation among species in abundance (ca. 25–73% of the genome) and composition of identifiable repeat elements. We also demonstrate that snake genomes have experienced microsatellite seeding by transposable elements at a scale unparalleled among eukaryotes, leading to some snake genomes containing the highest microsatellite content of any known eukaryote. Our analyses of transposable element evolution across squamates also suggest that lineage-specific variation in mechanisms of transposable element activity and silencing, rather than variation in species-specific demography, may play a dominant role in driving variation in repeat element landscapes across squamate phylogeny. Large-scale patterns of genomic repeat element evolution have been studied mainly in birds and mammals. Here, the authors analyze the genomes of over 60 squamate reptiles and show high variation in repeat elements compared to mammals and birds, and particularly high microsatellite seeding in snakes.
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Affiliation(s)
- Giulia I M Pasquesi
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Andrew B Corbin
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA
| | - Jacobo Reyes-Velasco
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA.,Department of Biology, New York University Abu Dhabi, Saadiyat Island, United Arab Emirates
| | - Robert P Ruggiero
- Department of Biology, New York University Abu Dhabi, Saadiyat Island, United Arab Emirates
| | - Michael W Vandewege
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, 19122, USA
| | - Jonathan A Shortt
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, 501S. Nedderman Drive, Arlington, TX, 76019, USA.
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5
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Han MJ, Xu HE, Xiong XM, Zhang HH. Evolutionary dynamics of transposable elements during silkworm domestication. Genes Genomics 2018; 40:1041-1051. [DOI: 10.1007/s13258-018-0713-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 05/31/2018] [Indexed: 11/24/2022]
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Ruggiero RP, Bourgeois Y, Boissinot S. LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis. Front Genet 2017; 8:44. [PMID: 28450881 PMCID: PMC5389967 DOI: 10.3389/fgene.2017.00044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/29/2017] [Indexed: 12/30/2022] Open
Abstract
Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies. It is unclear why vertebrate genomes harbor such drastic differences in LINE composition. To address this issue, we conducted whole genome resequencing to investigate the population genomics of LINEs across 13 genomes of the lizard Anolis carolinensis sampled from two geographically and genetically distinct populations in the Eastern Florida and the Gulf Atlantic regions of the United States. We used the Mobile Element Locator Tool to identify and genotype polymorphic insertions from five major clades of LINEs (CR1, L1, L2, RTE and R4) and the 41 subfamilies that constitute them. Across these groups we found large variation in the frequency of polymorphic insertions and the observed length distributions of these insertions, suggesting these groups vary in their activity and how frequently they successfully generate full-length, potentially active copies. Though we found an abundance of polymorphic insertions (over 45,000) most of these were observed at low frequencies and typically appeared as singletons. Site frequency spectra for most LINEs showed a significant shift toward low frequency alleles compared to the spectra observed for total genomic single nucleotide polymorphisms. Using Tajima's D, FST and the mean number of pairwise differences in LINE insertion polymorphisms, we found evidence that negative selection is acting on LINE families in a length-dependent manner, its effects being stronger in the larger Eastern Florida population. Our results suggest that a large effective population size and negative selection limit the expansion of polymorphic LINE insertions across these populations and that the probability of LINE polymorphisms reaching fixation is extremely low.
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Staton SE, Burke JM. Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance. BMC Genomics 2015; 16:623. [PMID: 26290182 PMCID: PMC4546089 DOI: 10.1186/s12864-015-1830-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/07/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The transposable element (TE) content of the genomes of plant species varies from near zero in the genome of Utricularia gibba to more than 80% in many species. It is not well understood whether this variation in genome composition results from common mechanisms or stochastic variation. The major obstacles to investigating mechanisms of TE evolution have been a lack of comparative genomic data sets and efficient computational methods for measuring differences in TE composition between species. In this study, we describe patterns of TE evolution in 14 species in the flowering plant family Asteraceae and 1 outgroup species in the Calyceraceae to investigate phylogenetic patterns of TE dynamics in this important group of plants. RESULTS Our findings indicate that TE families in the Asteraceae exhibit distinct patterns of non-neutral evolution, and that there has been a directional increase in copy number of Gypsy retrotransposons since the origin of the Asteraceae. Specifically, there is marked increase in Gypsy abundance at the origin of the Asteraceae and at the base of the tribe Heliantheae. This latter shift in genome composition has had a significant impact on the diversity and abundance distribution of TEs in a lineage-specific manner. CONCLUSIONS We show that the TE-driven expansion of plant genomes can be facilitated by just a few TE families, and is likely accompanied by the modification and/or replacement of the TE community. Importantly, large shifts in TE composition may be correlated with major of phylogenetic transitions.
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Affiliation(s)
- S Evan Staton
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
- Current address: Beaty Biodiversity Research Centre and Department of Botany, 3529-6270 University Blvd, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
| | - John M Burke
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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Tollis M, Boissinot S. Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). Genome Biol Evol 2014; 5:1754-68. [PMID: 24013105 PMCID: PMC3787681 DOI: 10.1093/gbe/evt133] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Autonomous retrotransposons lacking long terminal repeats (LTR) account for much of the variation in genome size and structure among vertebrates. Mammalian genomes contain hundreds of thousands of non-LTR retrotransposon copies, mostly resulting from the amplification of a single clade known as L1. The genomes of teleost fish and squamate reptiles contain a much more diverse array of non-LTR retrotransposon families, whereas copy number is relatively low. The majority of non-LTR retrotransposon insertions in nonmammalian vertebrates also appear to be very recent, suggesting strong purifying selection limits the accumulation of non-LTR retrotransposon copies. It is however unclear whether this turnover model, originally proposed in Drosophila, applies to nonmammalian vertebrates. Here, we studied the population dynamics of L1 in the green anole lizard (Anolis carolinensis). We found that although most L1 elements are recent in this genome, truncated insertions accumulate readily, and many are fixed at both the population and species level. In contrast, full-length L1 insertions are found at lower population frequencies, suggesting that the turnover model only applies to longer L1 elements in Anolis. We also found that full-length L1 inserts are more likely to be fixed in populations of small effective size, suggesting that the strength of purifying selection against deleterious alleles is highly dependent on host demographic history. Similar mechanisms seem to be controlling the fate of non-LTR retrotransposons in both Anolis and teleostean fish, which suggests that mammals have considerably diverged from the ancestral vertebrate in terms of how they interact with their intragenomic parasites.
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Affiliation(s)
- Marc Tollis
- Biology Department, Queens College, City University of New York, Flushing
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Blumenstiel JP, Chen X, He M, Bergman CM. An age-of-allele test of neutrality for transposable element insertions. Genetics 2014; 196:523-38. [PMID: 24336751 PMCID: PMC3914624 DOI: 10.1534/genetics.113.158147] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/06/2013] [Indexed: 01/31/2023] Open
Abstract
How natural selection acts to limit the proliferation of transposable elements (TEs) in genomes has been of interest to evolutionary biologists for many years. To describe TE dynamics in populations, previous studies have used models of transposition-selection equilibrium that assume a constant rate of transposition. However, since TE invasions are known to happen in bursts through time, this assumption may not be reasonable. Here we propose a test of neutrality for TE insertions that does not rely on the assumption of a constant transposition rate. We consider the case of TE insertions that have been ascertained from a single haploid reference genome sequence. By conditioning on the age of an individual TE insertion allele (inferred by the number of unique substitutions that have occurred within the particular TE sequence since insertion), we determine the probability distribution of the insertion allele frequency in a population sample under neutrality. Taking models of varying population size into account, we then evaluate predictions of our model against allele frequency data from 190 retrotransposon insertions sampled from North American and African populations of Drosophila melanogaster. Using this nonequilibrium neutral model, we are able to explain ∼ 80% of the variance in TE insertion allele frequencies based on age alone. Controlling for both nonequilibrium dynamics of transposition and host demography, we provide evidence for negative selection acting against most TEs as well as for positive selection acting on a small subset of TEs. Our work establishes a new framework for the analysis of the evolutionary forces governing large insertion mutations like TEs, gene duplications, or other copy number variants.
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Affiliation(s)
- Justin P. Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66049
| | - Xi Chen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66049
| | - Miaomiao He
- Faculty of Life Sciences, University of Manchester, Manchester M21 0RG, United Kingdom
| | - Casey M. Bergman
- Faculty of Life Sciences, University of Manchester, Manchester M21 0RG, United Kingdom
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Shen JJ, Dushoff J, Bewick AJ, Chain FJ, Evans BJ. Genomic dynamics of transposable elements in the western clawed frog (Silurana tropicalis). Genome Biol Evol 2013; 5:998-1009. [PMID: 23645600 PMCID: PMC3673623 DOI: 10.1093/gbe/evt065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2013] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences that can make new copies of themselves that are inserted elsewhere in a host genome. The abundance and distributions of TEs vary considerably among phylogenetically diverse hosts. With the aim of exploring the basis of this variation, we evaluated correlations between several genomic variables and the presence of TEs and non-TE repeats in the complete genome sequence of the Western clawed frog (Silurana tropicalis). This analysis reveals patterns of TE insertion consistent with gene disruption but not with the insertional preference model. Analysis of non-TE repeats recovered unique features of their genome-wide distribution when compared with TE repeats, including no strong correlation with exons and a particularly strong negative correlation with GC content. We also collected polymorphism data from 25 TE insertion sites in 19 wild-caught S. tropicalis individuals. DNA transposon insertions were fixed at eight of nine sites and at a high frequency at one of nine, whereas insertions of long terminal repeat (LTR) and non-LTR retrotransposons were fixed at only 4 of 16 sites and at low frequency at 12 of 16. A maximum likelihood model failed to attribute these differences in insertion frequencies to variation in selection pressure on different classes of TE, opening the possibility that other phenomena such as variation in rates of replication or duration of residence in the genome could play a role. Taken together, these results identify factors that sculpt heterogeneity in TE distribution in S. tropicalis and illustrate that genomic dynamics differ markedly among TE classes and between TE and non-TE repeats.
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Affiliation(s)
- Jiangshan J. Shen
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
- Present address: Department of Pathology, The University of Hong Kong, Hong Kong, China
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Adam J. Bewick
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Frédéric J.J. Chain
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Ben J. Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
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Blass E, Bell M, Boissinot S. Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback. Genome Biol Evol 2012; 4:687-702. [PMID: 22534163 PMCID: PMC3381678 DOI: 10.1093/gbe/evs044] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The diversity and abundance of non–long terminal repeat (LTR) retrotransposons (nLTR-RT) differ drastically among vertebrate genomes. At one extreme, the genome of placental mammals is littered with hundreds of thousands of copies resulting from the activity of a single clade of nLTR-RT, the L1 clade. In contrast, fish genomes contain a much more diverse repertoire of nLTR-RT, represented by numerous active clades and families. Yet, the number of nLTR-RT copies in teleostean fish is two orders of magnitude smaller than in mammals. The vast majority of insertions appear to be very recent, suggesting that nLTR-RT do not accumulate in fish genomes. This pattern had previously been explained by a high rate of turnover, in which the insertion of new elements is offset by the selective loss of deleterious inserts. The turnover model was proposed because of the similarity between fish and Drosophila genomes with regard to their nLTR-RT profile. However, it is unclear if this model applies to fish. In fact, a previous study performed on the puffer fish suggested that transposable element insertions behave as neutral alleles. Here we examined the dynamics of amplification of nLTR-RT in the three-spine stickleback (Gasterosteus aculeatus). In this species, the vast majority of nLTR-RT insertions are relatively young, as suggested by their low level of divergence. Contrary to expectations, a majority of these insertions are fixed in lake and oceanic populations; thus, nLTR-RT do indeed accumulate in the genome of their fish host. This is not to say that nLTR-RTs are fully neutral, as the lack of fixed long elements in this genome suggests a deleterious effect related to their length. This analysis does not support the turnover model and strongly suggests that a much higher rate of DNA loss in fish than in mammals is responsible for the relatively small number of nLTR-RT copies and for the scarcity of ancient elements in fish genomes. We further demonstrate that nLTR-RT decay in fish occurs mostly through large deletions and not by the accumulation of small deletions.
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Affiliation(s)
- Eryn Blass
- Department of Biology, Queens College, City University of New York, Flushing, NY, USA
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Castillo DM, Mell JC, Box KS, Blumenstiel JP. Molecular evolution under increasing transposable element burden in Drosophila: a speed limit on the evolutionary arms race. BMC Evol Biol 2011; 11:258. [PMID: 21917173 PMCID: PMC3185285 DOI: 10.1186/1471-2148-11-258] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 09/14/2011] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Genome architecture is profoundly influenced by transposable elements (TEs), and natural selection against their harmful effects is a critical factor limiting their spread. Genome defense by the piRNA silencing pathway also plays a crucial role in limiting TE proliferation. How these two forces jointly determine TE abundance is not well understood. To shed light on the nature of factors that predict TE success, we test three distinct hypotheses in the Drosophila genus. First, we determine whether TE abundance and relaxed genome-wide purifying selection on protein sequences are positively correlated. This serves to test the hypothesis that variation in TE abundance in the Drosophila genus can be explained by the strength of natural selection, relative to drift, acting in parallel against mildly deleterious non-synonymous mutations. Second, we test whether increasing TE abundance is correlated with an increased rate of amino-acid evolution in genes encoding the piRNA machinery, as might be predicted by an evolutionary arms race model. Third, we test whether increasing TE abundance is correlated with greater codon bias in genes of the piRNA machinery. This is predicted if increasing TE abundance selects for increased efficiency in the machinery of genome defense. RESULTS Surprisingly, we find neither of the first two hypotheses to be true. Specifically, we found that genome-wide levels of purifying selection, measured by the ratio of non-synonymous to synonymous substitution rates (ω), were greater in species with greater TE abundance. In addition, species with greater TE abundance have greater levels of purifying selection in the piRNA machinery. In contrast, it appears that increasing TE abundance has primarily driven adaptation in the piRNA machinery by increasing codon bias. CONCLUSIONS These results indicate that within the Drosophila genus, a historically reduced strength of selection relative to drift is unlikely to explain patterns of increased TE success across species. Other factors, such as ecological exposure, are likely to contribute to variation in TE abundances within species. Furthermore, constraints on the piRNA machinery may temper the evolutionary arms race that would drive increasing rates of evolution at the amino acid level. In the face of these constraints, selection may act primarily by improving the translational efficiency of the machinery of genome defense through efficient codon usage.
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Affiliation(s)
- Dean M Castillo
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence Kansas 66045, USA
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Joshua Chang Mell
- Life Sciences Centre (Zoology), 2350 Health Sciences Mall, University of British Columbia, Vancouver, BC, V6T 3Z4, Canada
| | - Kimberly S Box
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence Kansas 66045, USA
| | - Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence Kansas 66045, USA
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Blumenstiel JP. Evolutionary dynamics of transposable elements in a small RNA world. Trends Genet 2010; 27:23-31. [PMID: 21074888 DOI: 10.1016/j.tig.2010.10.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 10/14/2010] [Accepted: 10/18/2010] [Indexed: 12/13/2022]
Abstract
Transposable elements (TEs) are selfish elements that cause harmful mutations, contribute to the structure of regulatory networks and shape the architecture of genomes. Natural selection against their harmful effects has long been considered the dominant force limiting their spread. It is now clear that a genome defense system of RNA-mediated silencing also plays a crucial role in limiting TE proliferation. A full understanding of TE evolutionary dynamics must consider how these forces jointly determine their proliferation within genomes. Here I consider these forces from two perspectives - dynamics within populations and evolutionary games within the germline. The analysis of TE dynamics from these two perspectives promises to provide new insight into their role in evolution.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA.
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14
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Lu J, Clark AG. Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Res 2009; 20:212-27. [PMID: 19948818 DOI: 10.1101/gr.095406.109] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-interacting RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruit flies. By quantifying expression levels of 32 TE families in piRNA pathway mutants relative to wild-type fruit flies, we provide evidence that piRNAs can severely silence the activities of retrotransposons. We incorporate piRNAs into a population genetic framework for retrotransposons and perform forward simulations to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster, our simulation results indicate that (1) piRNAs can significantly reduce the fitness cost of retrotransposons; (2) retrotransposons that generate piRNAs (piRTs) are selectively more advantageous, and such retrotransposon insertions more easily attain high frequency or fixation; (3) retrotransposons that are repressed by piRNAs (targetRTs), however, also have an elevated probability of reaching high frequency or fixation in the population because their deleterious effects are attenuated. By surveying the polymorphisms of piRT and targetRT insertions across nine strains of D. melanogaster, we verified these theoretical predictions with population genomic data. Our theoretical and empirical analysis suggests that piRNAs can significantly increase the fitness of individuals that bear them; however, piRNAs may provide a shelter or Trojan horse for retrotransposons, allowing them to increase in frequency in a population by shielding the host from the deleterious consequences of retrotransposition.
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Affiliation(s)
- Jian Lu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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Novick PA, Basta H, Floumanhaft M, McClure MA, Boissinot S. The Evolutionary Dynamics of Autonomous Non-LTR Retrotransposons in the Lizard Anolis Carolinensis Shows More Similarity to Fish Than Mammals. Mol Biol Evol 2009; 26:1811-22. [DOI: 10.1093/molbev/msp090] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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The evolution of plant genomes: scaling up from a population perspective. Curr Opin Genet Dev 2009; 18:565-70. [PMID: 19131240 DOI: 10.1016/j.gde.2008.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2008] [Revised: 11/14/2008] [Accepted: 11/18/2008] [Indexed: 02/02/2023]
Abstract
Plant genomes exhibit tremendous diversity in both their size and structure, with genome sizes across land plants ranging over two to three orders of magnitude and significant variation in structural organization was observed across species (EA Kellogg, JL Bennetzen, The evolution of nuclear genome structure in seed plants, Am J Bot 2004, 91:1709-1725). Five plant genomes are now either completely sequenced or in the draft stage; the grape (O Jaillon et al., The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla, Nature 2007, 449:463-467) and papaya (R Ming et al., The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus), Nature 2008, 452:991-997) whole genome sequences were reported most recently. Moreover, sequencing of 41 additional genomes is in progress. There is now an emerging consensus that understanding genome evolution requires consideration of the population genetics of genome diversification, and that description of evolutionary forces at the level of populations and within species can help identify the features that led to plant genome diversity (M Lynch, JS Conery, The origins of genome complexity, Science 2003, 302:1401-1404). In this review we focus on advances in our understanding of the mechanisms that drive the diversification of genomes. In particular, we look at the extent to which demographic features such as effective population size changes within species can drive genome evolution, discuss population genetic models of genome diversification associated with transposable element (TE) mobilization, and describe recent studies on the evolution of gene families.
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17
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Population frequencies of transposable elements in selfing and outcrossing Caenorhabditis nematodes. Genet Res (Camb) 2008; 90:317-29. [PMID: 18840306 DOI: 10.1017/s0016672308009440] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Population genetics theory predicts that differences in breeding systems should be an important factor in the dynamics of selfish genetic elements, because of different intensities of selection on both hosts and elements. We examined population frequencies of transposable elements (TEs) in natural populations of the self-fertilizing nematode Caenorhabditis elegans and its outcrossing relative Caenorhabditis remanei. We identified a Tc1-like class of elements in the C. remanei genome with homology to the terminal inverted repeats of the C. elegans Tc1 transposon, which we name mTcre1. We measured levels of insertion polymorphism for all 32 Tc1 elements present in the genome sequence of the C. elegans N2 strain, and 16 mTcre1 elements from the genome sequence of the C. remanei PB4641 strain. We show that transposons are less polymorphic and segregate at higher frequencies in C. elegans compared with C. remanei. Estimates of the intensity of selection based on the population frequencies of polymorphic elements suggest that transposons are selectively neutral in C. elegans, but subject to purifying selection in C. remanei. These results are consistent with a reduced efficacy of natural selection against TEs in selfing populations, but may in part be explained by non-equilibrium TE dynamics.
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18
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Demography and weak selection drive patterns of transposable element diversity in natural populations of Arabidopsis lyrata. Proc Natl Acad Sci U S A 2008; 105:13965-70. [PMID: 18772373 DOI: 10.1073/pnas.0804671105] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Transposable elements (TEs) are the major component of most plant genomes, and characterizing their population dynamics is key to understanding plant genome complexity. Yet there have been few studies of TE population genetics in plant systems. To study the roles of selection, transposition, and demography in shaping TE population diversity, we generated a polymorphism dataset for six TE families in four populations of the flowering plant Arabidopsis lyrata. The TE data indicated significant differentiation among populations, and maximum likelihood procedures suggested weak selection. For strongly bottlenecked populations, the observed TE band-frequency spectra fit data simulated under neutral demographic models constructed from nucleotide polymorphism data. Overall, we propose that TEs are subjected to weak selection, the efficacy of which varies as a function of demographic factors. Thus, demographic effects could be a major factor driving distributions of TEs among plant lineages.
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19
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Uchiyama T, Saito Y, Kuwabara H, Fujino K, Kishima Y, Martin C, Sano Y. Multiple regulatory mechanisms influence the activity of the transposon, Tam3, of Antirrhinum. THE NEW PHYTOLOGIST 2008; 179:343-355. [PMID: 19086175 DOI: 10.1111/j.1469-8137.2008.02477.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In Antirrhinum, several unique regulations of the transposon, Tam3, have been described. Tam3 activity in Antirrhinum is strictly controlled by the growing temperature of plants (low-temperature-dependent transposition: LTDT), by chromosomal position of Tam3 copy and by two specific repressor genes Stabiliser (St) and New Stabiliser (NSt). Here, the effects of the St and NSt loci on Tam3 transposition are compared. In cotyledons and hypocotyls, Tam3 is active even at high growing temperatures, indicating that LTDT does not operate when these organs are developing. This developmental regulation of Tam3 activity is differentially influenced by the St and NSt loci: St permits Tam3 transposition in cotyledons and hypocotyls, whereas NSt suppresses it in these organs. The effects of these host genes on Tam3 activity at the molecular level were examined. It was found that neither of these genes inhibits the transcription of the Tam3 transposase gene nor its translation, and that the Tam3 transposase has the potential to catalyze transposition in the St and NSt lines. The differences between the effects of St and NSt imply that they regulate Tam3 activity independently. Our molecular data indicate that their influence on Tam3 transposition seems to be nonepigenetic; possible mechanisms for their activity are discussed.
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Affiliation(s)
| | | | | | - Kaien Fujino
- Laboratories of Crop Physiology, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | | | - Cathie Martin
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, Norfolk NR4 7UH, UK
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20
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Subramanian RA, Akala OO, Adejinmi JO, O'Brochta DA. Topi, an IS630/Tc1/mariner-type transposable element in the African malaria mosquito, Anopheles gambiae. Gene 2008; 423:63-71. [PMID: 18634859 DOI: 10.1016/j.gene.2008.06.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Revised: 06/10/2008] [Accepted: 06/12/2008] [Indexed: 11/19/2022]
Abstract
IS630/Tc1/mariner elements are diverse and widespread within insects. The African malaria mosquito, Anopheles gambiae, contains over 30 families of IS630/Tc1/mariner elements although few have been studied in any detail. To examine the history of Topi elements in An. gambiae populations, Topi elements (n=73) were sampled from five distinct populations of An. gambiae from eastern and western Africa and evaluated with respect to copy number, nucleotide diversity and insertion site-occupancy frequency. Topi 1 and 2 elements were abundant (10-34 per diploid genome) and highly diverse (pi=0.051). Elements from mosquitoes collected in Nigeria were Topi 2 elements and those from mosquitoes collected in Mozambique were Topi 1 elements. Of the 49 Topi transposase open reading frames sequenced none were found to be identical. Intact elements with complete transposase open reading frames were common, although based on insertion site-occupancy frequency data it appeared that genetic drift was the major force acting on these IS630/Tc1/mariner-type elements. Topi 3 elements were not recovered from any of the populations sampled in this study and appear to be rare elements in An. gambiae, possibly due to a recent introduction.
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Affiliation(s)
- Ramanand A Subramanian
- Center for Biosystems Research, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA
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21
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22
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Transposable elements as drivers of genomic and biological diversity in vertebrates. Chromosome Res 2008; 16:203-15. [DOI: 10.1007/s10577-007-1202-6] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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23
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O'Brochta DA, Subramanian RA, Orsetti J, Peckham E, Nolan N, Arensburger P, Atkinson PW, Charlwood DJ. hAT element population genetics in Anopheles gambiae s.l. in Mozambique. Genetica 2006; 127:185-98. [PMID: 16850223 DOI: 10.1007/s10709-005-3535-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Accepted: 09/26/2005] [Indexed: 10/24/2022]
Abstract
Herves is a functional Class II transposable element in Anopheles gambiae belonging to the hAT superfamily of elements. Class II transposable elements are used as gene vectors in this species and are also being considered as genetic drive agents for spreading desirable genes through natural populations as part of an effort to control malaria transmission. In this study, Herves was investigated in populations of Anopheles gambiae s.s., Anopheles arabiensis and Anopheles merus in Mozambique over a period of 2 years. The copy number of Herves within these three species was approximately 5 copies per diploid genome and did not differ among species or between years. Based on the insertion-site occupancy-frequency distribution and existing models of transposable element dynamics, Herves appears to be transpositionally active currently or, at least recently, in all species tested. Ninety-five percent of the individuals within the populations of the three species tested contained intact elements with complete Herves transposase genes and this is consistent with the idea that these elements are currently active.
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Affiliation(s)
- David A O'Brochta
- Center for Biosystems Research, University of Maryland Biotechnology Institute, Building 036/Room 5115, College Park, MD 20742, USA.
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24
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Song M, Boissinot S. Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination. Gene 2006; 390:206-13. [PMID: 17134851 DOI: 10.1016/j.gene.2006.09.033] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 09/27/2006] [Accepted: 09/28/2006] [Indexed: 11/25/2022]
Abstract
LINE-1 (L1) retrotransposons constitute the most successful family of autonomous retroelements in mammals and they represent at least 17% of the size of the human genome. L1 insertions have occasionally been recruited to perform a beneficial function but the vast majority of L1 inserts are either neutral or deleterious. The basis for the deleterious effect of L1 remains a matter of debate and three possible mechanisms have been suggested: the direct effect of L1 inserts on gene activity, genetic rearrangements caused by L1-mediated ectopic recombination, or the retrotransposition process per se. We performed a genome-wide analysis of the distribution of L1 retrotransposons relative to the local recombination rate and the age and length of the elements. The proportion of L1 elements that are longer than 1.2 Kb is higher in low-recombining regions of the genome than in regions with a high recombination rate, but the genomic distributions of full-length elements (i.e. elements capable of retrotransposition) and long truncated elements were indistinguishable. We also found that the intensity of selection against long elements is proportional to the replicative success of L1 families. This suggests that the deleterious effect of L1 elements results principally from their ability to mediate ectopic recombination.
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Affiliation(s)
- Mingzhou Song
- Department of Computer Science, New Mexico State University, Las Cruces, New Mexico 88003, USA
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25
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Johnson PLF, Slatkin M. Inference of population genetic parameters in metagenomics: a clean look at messy data. Genes Dev 2006; 16:1320-7. [PMID: 16954540 PMCID: PMC1581441 DOI: 10.1101/gr.5431206] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Accepted: 07/17/2006] [Indexed: 12/21/2022]
Abstract
Metagenomic projects generate short, overlapping fragments of DNA sequence, each deriving from a different individual. We report a new method for inferring the scaled mutation rate, theta = 2Neu, and the scaled exponential growth rate, R = Ner, from the site-frequency spectrum of these data while accounting for sequencing error via Phred quality scores. After obtaining maximum likelihood parameter estimates for theta and R, we calculate empirical Bayes quality scores reflecting the posterior probability that each apparently polymorphic site is truly polymorphic; these scores can then be used for other applications such as SNP discovery. For realistic parameter ranges, analytic and simulation results show our estimates to be essentially unbiased with tight confidence intervals. In contrast, choosing an arbitrary quality score cutoff (e.g., trimming reads) and ignoring further quality information during inference yields biased estimates with greater variance. We illustrate the use of our technique on a new project analyzing activated sludge from a lab-scale bioreactor seeded by a wastewater treatment plant.
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Affiliation(s)
- Philip L F Johnson
- Biophysics Graduate Group, University of California, Berkeley, California 94720, USA.
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26
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Abrusán G, Krambeck HJ. Competition may determine the diversity of transposable elements. Theor Popul Biol 2006; 70:364-75. [PMID: 16814337 DOI: 10.1016/j.tpb.2006.05.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 04/21/2006] [Accepted: 05/03/2006] [Indexed: 11/23/2022]
Abstract
Transposable elements are genomic parasites that replicate independently from their hosts. They harm their hosts by causing mutations or genomic rearrangements, and most organisms have evolved various mechanisms to suppress their activity. The evolutionary dynamics of transposons in insects, fish, birds and mammals are dramatically different. Mammalian genomes contain few, very abundant but relatively inactive transposon strains, while Drosophila and fish species harbour diverse strains, which typically have low abundance but are much more virulent. We hypothesise that the variation in the diversity and activity of transposable elements between various animal genomes is caused by the differences in the host defence mechanisms against transposon activity. In recent years RNAi, a mechanism capable of gene, virus and transposon silencing has been discovered. We model RNAi as a density dependant mechanism of defence, which can cause competition among transposons depending on its specificity, and test its predictions using the complete Caenorhabditis elegans, Drosophila melanogaster, Fugu rubripes, chicken, mouse, rat and human genome sequences.
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Affiliation(s)
- György Abrusán
- Department of Ecophysiology, Max-Planck institute for Limnology, August-Thienemann str.2 24302 Plön, Germany.
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27
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Abstract
As is the case with mammals in general, primate genomes are inundated with repetitive sequence. Although much of this repetitive content consists of "molecular fossils" inherited from early mammalian ancestors, a significant portion of this material comprises active mobile element lineages. Despite indications that these elements played a major role in shaping the architecture of the genome, there remain many unanswered questions surrounding the nature of the host-element relationship. Here we review advances in our understanding of the host-mobile element dynamic and its overall impact on primate evolution.
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Affiliation(s)
- Dale J Hedges
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, LA 70803, USA
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