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Poikela N, Laetsch DR, Hoikkala V, Lohse K, Kankare M. Chromosomal Inversions and the Demography of Speciation in Drosophila montana and Drosophila flavomontana. Genome Biol Evol 2024; 16:evae024. [PMID: 38482698 PMCID: PMC10972691 DOI: 10.1093/gbe/evae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 04/01/2024] Open
Abstract
Chromosomal inversions may play a central role in speciation given their ability to locally reduce recombination and therefore genetic exchange between diverging populations. We analyzed long- and short-read whole-genome data from sympatric and allopatric populations of 2 Drosophila virilis group species, Drosophila montana and Drosophila flavomontana, to understand if inversions have contributed to their divergence. We identified 3 large alternatively fixed inversions on the X chromosome and one on each of the autosomes 4 and 5. A comparison of demographic models estimated for inverted and noninverted (colinear) chromosomal regions suggests that these inversions arose before the time of the species split. We detected a low rate of interspecific gene flow (introgression) from D. montana to D. flavomontana, which was further reduced inside inversions and was lower in allopatric than in sympatric populations. Together, these results suggest that the inversions were already present in the common ancestral population and that gene exchange between the sister taxa was reduced within inversions both before and after the onset of species divergence. Such ancestrally polymorphic inversions may foster speciation by allowing the accumulation of genetic divergence in loci involved in adaptation and reproductive isolation inside inversions early in the speciation process, while gene exchange at colinear regions continues until the evolving reproductive barriers complete speciation. The overlapping X inversions are particularly good candidates for driving the speciation process of D. montana and D. flavomontana, since they harbor strong genetic incompatibilities that were detected in a recent study of experimental introgression.
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Affiliation(s)
- Noora Poikela
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Ville Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Jyväskylä, Finland
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2
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Smeds L, Huson LSA, Ellegren H. Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration. Evol Appl 2024; 17:e13652. [PMID: 38333557 PMCID: PMC10848878 DOI: 10.1111/eva.13652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024] Open
Abstract
When populations decrease in size and may become isolated, genomic erosion by loss of diversity from genetic drift and accumulation of deleterious mutations is likely an inevitable consequence. In such cases, immigration (genetic rescue) is necessary to restore levels of genetic diversity and counteract inbreeding depression. Recent work in conservation genomics has studied these processes focusing on the genetic diversity of single nucleotide polymorphisms. In contrast, our knowledge about structural genomic variation (insertions, deletions, duplications and inversions) in endangered species is limited. We analysed whole-genome, short-read sequences from 212 wolves from the inbred Scandinavian population and from neighbouring populations in Finland and Russia, and detected >35,000 structural variants (SVs) after stringent quality and genotype frequency filtering; >26,000 high-confidence variants remained after manual curation. The majority of variants were shorter than 1 kb, with a distinct peak in the length distribution of deletions at 190 bp, corresponding to insertion events of SINE/tRNA-Lys elements. The site frequency spectrum of SVs in protein-coding regions was significantly shifted towards rare alleles compared to putatively neutral variants, consistent with purifying selection. The realized genetic load of SVs in protein-coding regions increased with inbreeding levels in the Scandinavian population, but immigration provided a genetic rescue effect by lowering the load and reintroducing ancestral alleles at loci fixed for derived SVs. Our study shows that structural variation comprises a common type of in part deleterious mutations in endangered species and that establishing gene flow is necessary to mitigate the negative consequences of loss of diversity.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Lars S. A. Huson
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Evolutionary BiologyUppsala UniversityUppsalaSweden
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3
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Oliveira DS, Fablet M, Larue A, Vallier A, Carareto CA, Rebollo R, Vieira C. ChimeraTE: a pipeline to detect chimeric transcripts derived from genes and transposable elements. Nucleic Acids Res 2023; 51:9764-9784. [PMID: 37615575 PMCID: PMC10570057 DOI: 10.1093/nar/gkad671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 07/25/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Transposable elements (TEs) produce structural variants and are considered an important source of genetic diversity. Notably, TE-gene fusion transcripts, i.e. chimeric transcripts, have been associated with adaptation in several species. However, the identification of these chimeras remains hindered due to the lack of detection tools at a transcriptome-wide scale, and to the reliance on a reference genome, even though different individuals/cells/strains have different TE insertions. Therefore, we developed ChimeraTE, a pipeline that uses paired-end RNA-seq reads to identify chimeric transcripts through two different modes. Mode 1 is the reference-guided approach that employs canonical genome alignment, and Mode 2 identifies chimeras derived from fixed or insertionally polymorphic TEs without any reference genome. We have validated both modes using RNA-seq data from four Drosophila melanogaster wild-type strains. We found ∼1.12% of all genes generating chimeric transcripts, most of them from TE-exonized sequences. Approximately ∼23% of all detected chimeras were absent from the reference genome, indicating that TEs belonging to chimeric transcripts may be recent, polymorphic insertions. ChimeraTE is the first pipeline able to automatically uncover chimeric transcripts without a reference genome, consisting of two running Modes that can be used as a tool to investigate the contribution of TEs to transcriptome plasticity.
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Affiliation(s)
- Daniel S Oliveira
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
| | - Marie Fablet
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
- Institut Universitaire de France (IUF), Paris, Île-de-FranceF-75231, France
| | - Anaïs Larue
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Agnès Vallier
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Claudia M A Carareto
- São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil
| | - Rita Rebollo
- Univ Lyon, INRAE, INSA-Lyon, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR5558, Villeurbanne, Rhone-Alpes, 69100, France
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4
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Oggenfuss U, Croll D. Recent transposable element bursts are associated with the proximity to genes in a fungal plant pathogen. PLoS Pathog 2023; 19:e1011130. [PMID: 36787337 PMCID: PMC9970103 DOI: 10.1371/journal.ppat.1011130] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/27/2023] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The activity of transposable elements (TEs) contributes significantly to pathogen genome evolution. TEs often destabilize genome integrity but may also confer adaptive variation in pathogenicity or resistance traits. De-repression of epigenetically silenced TEs often initiates bursts of transposition activity that may be counteracted by purifying selection and genome defenses. However, how these forces interact to determine the expansion routes of TEs within a pathogen species remains largely unknown. Here, we analyzed a set of 19 telomere-to-telomere genomes of the fungal wheat pathogen Zymoseptoria tritici. Phylogenetic reconstruction and ancestral state estimates of individual TE families revealed that TEs have undergone distinct activation and repression periods resulting in highly uneven copy numbers between genomes of the same species. Most TEs are clustered in gene poor niches, indicating strong purifying selection against insertions near coding sequences, or as a consequence of insertion site preferences. TE families with high copy numbers have low sequence divergence and strong signatures of defense mechanisms (i.e., RIP). In contrast, small non-autonomous TEs (i.e., MITEs) are less impacted by defense mechanisms and are often located in close proximity to genes. Individual TE families have experienced multiple distinct burst events that generated many nearly identical copies. We found that a Copia element burst was initiated from recent copies inserted substantially closer to genes compared to older copies. Overall, TE bursts tended to initiate from copies in GC-rich niches that escaped inactivation by genomic defenses. Our work shows how specific genomic environments features provide triggers for TE proliferation in pathogen genomes.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- * E-mail:
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5
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Rogers RL, Grizzard SL, Garner JT. Strong, Recent Selective Sweeps Reshape Genetic Diversity in Freshwater Bivalve Megalonaias nervosa. Mol Biol Evol 2023; 40:7026026. [PMID: 36738170 PMCID: PMC9976758 DOI: 10.1093/molbev/msad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Freshwater Unionid bivalves have recently faced ecological upheaval through pollution, barriers to dispersal, harvesting, and changes in fish-host prevalence. Currently, over 70% of species in North America are threatened, endangered or extinct. To characterize the genetic response to recent selective pressures, we collected population genetic data for one successful bivalve species, Megalonaias nervosa. We identify megabase-sized regions that are nearly monomorphic across the population, signals of strong, recent selection reshaping diversity across 73 Mb total. These signatures of selection are greater than is commonly seen in population genetic models. We observe 102 duplicate genes with high dN/dS on terminal branches among regions with sweeps, suggesting that gene duplication is a causative mechanism of recent adaptation in M. nervosa. Genes in sweeps reflect functional classes important for Unionid survival, including anticoagulation genes important for fish host parasitization, detox genes, mitochondria management, and shell formation. We identify sweeps in regions with no known functional impacts, suggesting mechanisms of adaptation that deserve greater attention in future work on species survival. In contrast, polymorphic transposable elements (TEs) appear to be detrimental and underrepresented among regions with sweeps. TE site frequency spectra are skewed toward singleton variants, and TEs among regions with sweeps are present at low frequency. Our work suggests that duplicate genes are an essential source of genetic novelty that has helped this species succeed in environments where others have struggled. These results suggest that gene duplications deserve greater attention in non-model population genomics, especially in species that have recently faced sudden environmental challenges.
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Affiliation(s)
- Rebekah L Rogers
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
| | | | - Jeffrey T Garner
- Division of Wildlife and Freshwater Fisheries, Alabama Department of Conservation and Natural Resources, Florence, AL, USA
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6
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Han S, Dias GB, Basting PJ, Viswanatha R, Perrimon N, Bergman C. Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line. Nucleic Acids Res 2022; 50:e124. [PMID: 36156149 PMCID: PMC9757076 DOI: 10.1093/nar/gkac794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/21/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022] Open
Abstract
Animal cell lines often undergo extreme genome restructuring events, including polyploidy and segmental aneuploidy that can impede de novo whole-genome assembly (WGA). In some species like Drosophila, cell lines also exhibit massive proliferation of transposable elements (TEs). To better understand the role of transposition during animal cell culture, we sequenced the genome of the tetraploid Drosophila S2R+ cell line using long-read and linked-read technologies. WGAs for S2R+ were highly fragmented and generated variable estimates of TE content across sequencing and assembly technologies. We therefore developed a novel WGA-independent bioinformatics method called TELR that identifies, locally assembles, and estimates allele frequency of TEs from long-read sequence data (https://github.com/bergmanlab/telr). Application of TELR to a ∼130x PacBio dataset for S2R+ revealed many haplotype-specific TE insertions that arose by transposition after initial cell line establishment and subsequent tetraploidization. Local assemblies from TELR also allowed phylogenetic analysis of paralogous TEs, which revealed that proliferation of TE families in vitro can be driven by single or multiple source lineages. Our work provides a model for the analysis of TEs in complex heterozygous or polyploid genomes that are recalcitrant to WGA and yields new insights into the mechanisms of genome evolution in animal cell culture.
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Affiliation(s)
| | | | - Preston J Basting
- Institute of Bioinformatics, University of Georgia, 120 E. Green St., Athens, GA, USA
| | - Raghuvir Viswanatha
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, USA,Howard Hughes Medical Institute, Boston, MA, USA
| | - Casey M Bergman
- To whom correspondence should be addressed. Tel: +1 706 542 1764; Fax: +1 706 542 3910;
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7
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Huang Y, Shukla H, Lee YCG. Species-specific chromatin landscape determines how transposable elements shape genome evolution. eLife 2022; 11:81567. [PMID: 35997258 PMCID: PMC9398452 DOI: 10.7554/elife.81567] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022] Open
Abstract
Transposable elements (TEs) are selfish genetic parasites that increase their copy number at the expense of host fitness. The ‘success’, or genome-wide abundance, of TEs differs widely between species. Deciphering the causes for this large variety in TE abundance has remained a central question in evolutionary genomics. We previously proposed that species-specific TE abundance could be driven by the inadvertent consequences of host-direct epigenetic silencing of TEs—the spreading of repressive epigenetic marks from silenced TEs into adjacent sequences. Here, we compared this TE-mediated local enrichment of repressive marks, or ‘the epigenetic effect of TEs’, in six species in the Drosophila melanogaster subgroup to dissect step-by-step the role of such effect in determining genomic TE abundance. We found that TE-mediated local enrichment of repressive marks is prevalent and substantially varies across and even within species. While this TE-mediated effect alters the epigenetic states of adjacent genes, we surprisingly discovered that the transcription of neighboring genes could reciprocally impact this spreading. Importantly, our multi-species analysis provides the power and appropriate phylogenetic resolution to connect species-specific host chromatin regulation, TE-mediated epigenetic effects, the strength of natural selection against TEs, and genomic TE abundance unique to individual species. Our findings point toward the importance of host chromatin landscapes in shaping genome evolution through the epigenetic effects of a selfish genetic parasite. All the instructions required for life are encoded in the set of DNA present in a cell. It therefore seems natural to think that every bit of this genetic information should serve the organism. And yet most species carry parasitic ‘transposable’ sequences, or transposons, whose only purpose is to multiply and insert themselves at other positions in the genome. It is possible for cells to suppress these selfish elements. Chemical marks can be deposited onto the DNA to temporarily ‘silence’ transposons and prevent them from being able to move and replicate. However, this sometimes comes at a cost: the repressive chemical modifications can spread to nearby genes that are essential for the organism and perturb their function. Strangely, the prevalence of transposons varies widely across the tree of life. These sequences form the majority of the genome of certain species – in fact, they represent about half of the human genetic information. But their abundance is much lower in other organisms, forming a measly 6% of the genome of puffer fish for instance. Even amongst fruit fly species, the prevalence of transposable elements can range between 2% and 25%. What explains such differences? Huang et al. set out to examine this question through the lens of transposon silencing, systematically comparing how this process impacts nearby regions in six species of fruit flies. This revealed variations in the strength of the side effects associated with transposon silencing, resulting in different levels of perturbation on neighbouring genes. A stronger impact was associated with the species having fewer transposons in its genome, suggesting that an evolutionary pressure is at work to keep the abundance of transposons at a low level in these species. Further analyses showed that the genes which determine how silencing marks are distributed may also be responsible for the variations in the impact of transposon silencing. They could therefore be the ones driving differences in the abundance of transposons between species. Overall, this work sheds light on the complex mechanisms shaping the evolution of genomes, and it may help to better understand how transposons are linked to processes such as aging and cancer.
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Affiliation(s)
- Yuheng Huang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Harsh Shukla
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
| | - Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, United States
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8
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Smith RD, Puzey JR, Conradi Smith GD. Population genetics of transposable element load: A mechanistic account of observed overdispersion. PLoS One 2022; 17:e0270839. [PMID: 35834543 PMCID: PMC9282655 DOI: 10.1371/journal.pone.0270839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022] Open
Abstract
In an empirical analysis of transposable element (TE) abundance within natural populations of Mimulus guttatus and Drosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 300). To obtain insight regarding the evolutionary genetic mechanisms that underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analyses of population distributions of TE load reveal that overdispersion is likely to arise via copy-and-paste proliferation dynamics, especially when the elementary processes of proliferation and excision are approximately balanced. Parameter studies and analytic work confirm this result and further suggest that overdispersed population distributions of TE abundance are probably not a consequence of purifying selection on total element load.
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Affiliation(s)
- Ronald D. Smith
- Department of Applied Science, William & Mary, Williamsburg, VA, United States of America
| | - Joshua R. Puzey
- Department of Biology, William & Mary, Williamsburg, VA, United States of America
| | - Gregory D. Conradi Smith
- Department of Applied Science, William & Mary, Williamsburg, VA, United States of America
- * E-mail:
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9
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Han S, Dias GB, Basting PJ, Nelson MG, Patel S, Marzo M, Bergman CM. Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines. Genetics 2022; 221:iyac077. [PMID: 35536183 PMCID: PMC9252272 DOI: 10.1093/genetics/iyac077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cultured cells are widely used in molecular biology despite poor understanding of how cell line genomes change in vitro over time. Previous work has shown that Drosophila cultured cells have a higher transposable element content than whole flies, but whether this increase in transposable element content resulted from an initial burst of transposition during cell line establishment or ongoing transposition in cell culture remains unclear. Here, we sequenced the genomes of 25 sublines of Drosophila S2 cells and show that transposable element insertions provide abundant markers for the phylogenetic reconstruction of diverse sublines in a model animal cell culture system. DNA copy number evolution across S2 sublines revealed dramatically different patterns of genome organization that support the overall evolutionary history reconstructed using transposable element insertions. Analysis of transposable element insertion site occupancy and ancestral states support a model of ongoing transposition dominated by episodic activity of a small number of retrotransposon families. Our work demonstrates that substantial genome evolution occurs during long-term Drosophila cell culture, which may impact the reproducibility of experiments that do not control for subline identity.
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Affiliation(s)
- Shunhua Han
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Guilherme B Dias
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Preston J Basting
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Michael G Nelson
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Sanjai Patel
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Mar Marzo
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Casey M Bergman
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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10
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Wei KHC, Mai D, Chatla K, Bachtrog D. Dynamics and Impacts of Transposable Element Proliferation in the Drosophila nasuta Species Group Radiation. Mol Biol Evol 2022; 39:msac080. [PMID: 35485457 PMCID: PMC9075770 DOI: 10.1093/molbev/msac080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transposable element (TE) mobilization is a constant threat to genome integrity. Eukaryotic organisms have evolved robust defensive mechanisms to suppress their activity, yet TEs can escape suppression and proliferate, creating strong selective pressure for host defense to adapt. This genomic conflict fuels a never-ending arms race that drives the rapid evolution of TEs and recurrent positive selection of genes involved in host defense; the latter has been shown to contribute to postzygotic hybrid incompatibility. However, how TE proliferation impacts genome and regulatory divergence remains poorly understood. Here, we report the highly complete and contiguous (N50 = 33.8-38.0 Mb) genome assemblies of seven closely related Drosophila species that belong to the nasuta species group-a poorly studied group of flies that radiated in the last 2 My. We constructed a high-quality de novo TE library and gathered germline RNA-seq data, which allowed us to comprehensively annotate and compare TE insertion patterns between the species, and infer the evolutionary forces controlling their spread. We find a strong negative association between TE insertion frequency and expression of genes nearby; this likely reflects survivor bias from reduced fitness impact of TEs inserting near lowly expressed, nonessential genes, with limited TE-induced epigenetic silencing. Phylogenetic analyses of insertions of 147 TE families reveal that 53% of them show recent amplification in at least one species. The most highly amplified TE is a nonautonomous DNA element (Drosophila INterspersed Element; DINE) which has gone through multiple bouts of expansions with thousands of full-length copies littered throughout each genome. Across all TEs, we find that TEs expansions are significantly associated with high expression in the expanded species consistent with suppression escape. Thus, whereas horizontal transfer followed by the invasion of a naïve genome has been highlighted to explain the long-term survival of TEs, our analysis suggests that evasion of host suppression of resident TEs is a major strategy to persist over evolutionary times. Altogether, our results shed light on the heterogenous and context-dependent nature in which TEs affect gene regulation and the dynamics of rampant TE proliferation amidst a recently radiated species group.
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Affiliation(s)
- Kevin H.-C. Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Dat Mai
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Kamalakar Chatla
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Doris Bachtrog
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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11
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Rech GE, Radío S, Guirao-Rico S, Aguilera L, Horvath V, Green L, Lindstadt H, Jamilloux V, Quesneville H, González J. Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila. Nat Commun 2022; 13:1948. [PMID: 35413957 PMCID: PMC9005704 DOI: 10.1038/s41467-022-29518-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/15/2022] [Indexed: 12/16/2022] Open
Abstract
High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve. Even in well-studied species, there is still substantial natural genetic variation that has not been characterized. Here, the authors use long read sequencing to discover transposable elements in the Drosophila genome not detected by short read sequencing, and link them to gene expression.
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Affiliation(s)
- Gabriel E Rech
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Santiago Radío
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Sara Guirao-Rico
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Laura Aguilera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Vivien Horvath
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Llewellyn Green
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | - Hannah Lindstadt
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain
| | | | | | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003, Barcelona, Spain.
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12
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Mariyappa D, Rusch DB, Han S, Luhur A, Overton D, Miller DFB, Bergman CM, Zelhof AC. A novel transposable element-based authentication protocol for Drosophila cell lines. G3 (BETHESDA, MD.) 2022; 12:6440050. [PMID: 34849844 PMCID: PMC9210319 DOI: 10.1093/g3journal/jkab403] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 11/11/2021] [Indexed: 11/23/2022]
Abstract
Drosophila cell lines are used by researchers to investigate various cell biological phenomena. It is crucial to exercise good cell culture practice. Poor handling can lead to both inter- and intra-species cross-contamination. Prolonged culturing can lead to introduction of large- and small-scale genomic changes. These factors, therefore, make it imperative that methods to authenticate Drosophila cell lines are developed to ensure reproducibility. Mammalian cell line authentication is reliant on short tandem repeat (STR) profiling; however, the relatively low STR mutation rate in Drosophila melanogaster at the individual level is likely to preclude the value of this technique. In contrast, transposable elements (TEs) are highly polymorphic among individual flies and abundant in Drosophila cell lines. Therefore, we investigated the utility of TE insertions as markers to discriminate Drosophila cell lines derived from the same or different donor genotypes, divergent sub-lines of the same cell line, and from other insect cell lines. We developed a PCR-based next-generation sequencing protocol to cluster cell lines based on the genome-wide distribution of a limited number of diagnostic TE families. We determined the distribution of five TE families in S2R+, S2-DRSC, S2-DGRC, Kc167, ML-DmBG3-c2, mbn2, CME W1 Cl.8+, and ovarian somatic sheath Drosophila cell lines. Two independent downstream analyses of the next-generation sequencing data yielded similar clustering of these cell lines. Double-blind testing of the protocol reliably identified various Drosophila cell lines. In addition, our data indicate minimal changes with respect to the genome-wide distribution of these five TE families when cells are passaged for at least 50 times. The protocol developed can accurately identify and distinguish the numerous Drosophila cell lines available to the research community, thereby aiding reproducible Drosophila cell culture research.
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Affiliation(s)
- Daniel Mariyappa
- Biology Department, Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B Rusch
- Biology Department, Center for Genetics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Shunhua Han
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Arthur Luhur
- Biology Department, Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA
| | - Danielle Overton
- Biology Department, Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA
| | - David F B Miller
- Biology Department, Center for Genetics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Casey M Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Andrew C Zelhof
- Biology Department, Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA
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13
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Said I, McGurk MP, Clark AG, Barbash DA. Patterns of piRNA Regulation in Drosophila Revealed through Transposable Element Clade Inference. Mol Biol Evol 2022; 39:msab336. [PMID: 34921315 PMCID: PMC8788220 DOI: 10.1093/molbev/msab336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) are self-replicating "genetic parasites" ubiquitous to eukaryotic genomes. In addition to conflict between TEs and their host genomes, TEs of the same family are in competition with each other. They compete for the same genomic niches while experiencing the same regime of copy-number selection. This suggests that competition among TEs may favor the emergence of new variants that can outcompete their ancestral forms. To investigate the sequence evolution of TEs, we developed a method to infer clades: collections of TEs that share SNP variants and represent distinct TE family lineages. We applied this method to a panel of 85 Drosophila melanogaster genomes and found that the genetic variation of several TE families shows significant population structure that arises from the population-specific expansions of single clades. We used population genetic theory to classify these clades into younger versus older clades and found that younger clades are associated with a greater abundance of sense and antisense piRNAs per copy than older ones. Further, we find that the abundance of younger, but not older clades, is positively correlated with antisense piRNA production, suggesting a general pattern where hosts preferentially produce antisense piRNAs from recently active TE variants. Together these findings suggest a pattern whereby new TE variants arise by mutation and then increase in copy number, followed by the host producing antisense piRNAs that may be used to silence these emerging variants.
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Affiliation(s)
- Iskander Said
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Michael P McGurk
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Daniel A Barbash
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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14
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Taming, Domestication and Exaptation: Trajectories of Transposable Elements in Genomes. Cells 2021; 10:cells10123590. [PMID: 34944100 PMCID: PMC8700633 DOI: 10.3390/cells10123590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
During evolution, several types of sequences pass through genomes. Along with mutations and internal genetic tinkering, they are a useful source of genetic variability for adaptation and evolution. Most of these sequences are acquired by horizontal transfers (HT), but some of them may come from the genomes themselves. If they are not lost or eliminated quickly, they can be tamed, domesticated, or even exapted. Each of these processes results from a series of events, depending on the interactions between these sequences and the host genomes, but also on environmental constraints, through their impact on individuals or population fitness. After a brief reminder of the characteristics of each of these states (taming, domestication, exaptation), the evolutionary trajectories of these new or acquired sequences will be presented and discussed, emphasizing that they are not totally independent insofar as the first can constitute a step towards the second, and the second is another step towards the third.
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15
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Tusso S, Suo F, Liang Y, Du LL, Wolf JBW. Reactivation of transposable elements following hybridization in fission yeast. Genome Res 2021; 32:324-336. [PMID: 34907076 PMCID: PMC8805722 DOI: 10.1101/gr.276056.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/09/2021] [Indexed: 11/29/2022]
Abstract
Hybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of the parental hosts. Here, we provide evidence for this “genomic shock hypothesis” in the fission yeast Schizosaccharomyces pombe. In this species, two divergent lineages (Sp and Sk) have experienced recent, likely human-induced, hybridization. We used long-read sequencing data to assemble genomes of 37 samples derived from 31 S. pombe strains spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. Sequence analysis of active full-length elements, as well as solo LTRs, revealed a complex history of homologous recombination. Population genetic analyses of syntenic sequences placed insertion of many solo LTRs before the split of the Sp and Sk lineages. Most full-length elements were inserted more recently, after hybridization. With the exception of a single full-length element with signs of positive selection, both solo LTRs and, in particular, full-length elements carry signatures of purifying selection indicating effective removal by the host. Consistent with reactivation upon hybridization, the number of full-length LTR retrotransposons, varying extensively from zero to 87 among strains, significantly increases with the degree of genomic admixture. This study gives a detailed account of global TE diversity in S. pombe, documents complex recombination histories within TE elements, and provides evidence for the “genomic shock hypothesis.”
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Affiliation(s)
| | - Fang Suo
- National Institute of Biological Sciences
| | - Yue Liang
- National Institute of Biological Sciences
| | - Li-Lin Du
- National Institute of Biological Sciences
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16
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Xu H, Ye X, Yang Y, Yang Y, Sun YH, Mei Y, Xiong S, He K, Xu L, Fang Q, Li F, Ye G, Lu Z. Comparative Genomics Sheds Light on the Convergent Evolution of Miniaturized Wasps. Mol Biol Evol 2021; 38:5539-5554. [PMID: 34515790 PMCID: PMC8662594 DOI: 10.1093/molbev/msab273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Miniaturization has occurred in many animal lineages, including insects and vertebrates, as a widespread trend during animal evolution. Among Hymenoptera, miniaturization has taken place in some parasitoid wasp lineages independently, and may have contributed to the diversity of species. However, the genomic basis of miniaturization is little understood. Diverged approximately 200 Ma, Telenomus wasps (Platygastroidea) and Trichogramma wasps (Chalcidoidea) have both evolved to a highly reduced body size independently, representing a paradigmatic example of convergent evolution. Here, we report a high-quality chromosomal genome of Telenomus remus, a promising candidate for controlling Spodoptera frugiperda, a notorious pest that has recently caused severe crop damage. The T. remus genome (129 Mb) is characterized by a low density of repetitive sequence and a reduction of intron length, resulting in the shrinkage of genome size. We show that hundreds of genes evolved faster in two miniaturized parasitoids Trichogramma pretiosum and T. remus. Among them, 38 genes exhibit extremely accelerated evolutionary rates in these miniaturized wasps, possessing diverse functions in eye and wing development as well as cell size control. These genes also highlight potential roles in body size regulation. In sum, our analyses uncover a set of genes with accelerated evolutionary rates in Tri. pretiosum and T. remus, which might be responsible for their convergent adaptations to miniaturization, and thus expand our understanding on the evolutionary basis of miniaturization. Additionally, the genome of T. remus represents the first genome resource of superfamily Platygastroidea, and will facilitate future studies of Hymenoptera evolution and pest control.
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Affiliation(s)
- Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
- Shanghai Institute for Advanced Study, Zhejiang University, Shanghai, China
- Institute of Artificial Intelligence, College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Yajun Yang
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yu H Sun
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Kang He
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Le Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhongxian Lu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agroproducts, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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17
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Lee YCG. Synergistic epistasis of the deleterious effects of transposable elements. Genetics 2021; 220:6458331. [PMID: 34888644 DOI: 10.1093/genetics/iyab211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/10/2021] [Indexed: 11/12/2022] Open
Abstract
The replicative nature and generally deleterious effects of transposable elements (TEs) raise an outstanding question about how TE copy number is stably contained in host populations. Classic theoretical analyses predict that, when the decline in fitness due to each additional TE insertion is greater than linear, or when there is synergistic epistasis, selection against TEs can result in a stable equilibrium of TE copy number. While several mechanisms are predicted to yield synergistic deleterious effects of TEs, we lack empirical investigations of the presence of such epistatic interactions. Purifying selection with synergistic epistasis generates repulsion linkage between deleterious alleles. We investigated this population genetic signal in the likely ancestral Drosophila melanogaster population and found evidence supporting the presence of synergistic epistasis among TE insertions, especially TEs expected to exert large fitness impacts. Even though synergistic epistasis of TEs has been predicted to arise through ectopic recombination and TE-mediated epigenetic silencing mechanisms, we only found mixed support for the associated predictions. We observed signals of synergistic epistasis for a large number of TE families, which is consistent with the expectation that such epistatic interaction mainly happens among copies of the same family. Curiously, significant repulsion linkage was also found among TE insertions from different families, suggesting the possibility that synergism of TEs' deleterious fitness effects could arise above the family level and through mechanisms similar to those of simple mutations. Our findings set the stage for investigating the prevalence and importance of epistatic interactions in the evolutionary dynamics of TEs.
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Affiliation(s)
- Yuh Chwen G Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
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18
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Han S, Basting PJ, Dias GB, Luhur A, Zelhof AC, Bergman CM. Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture. Genetics 2021; 219:6321957. [PMID: 34849875 PMCID: PMC8633141 DOI: 10.1093/genetics/iyab113] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022] Open
Abstract
Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabeling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here, we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of long-terminal repeat retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.
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Affiliation(s)
- Shunhua Han
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Preston J Basting
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Guilherme B Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Arthur Luhur
- Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Andrew C Zelhof
- Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Casey M Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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19
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Oggenfuss U, Badet T, Wicker T, Hartmann FE, Singh NK, Abraham L, Karisto P, Vonlanthen T, Mundt C, McDonald BA, Croll D. A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen. eLife 2021; 10:e69249. [PMID: 34528512 PMCID: PMC8445621 DOI: 10.7554/elife.69249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Genome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations, but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogen's center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-SaclayOrsayFrance
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Petteri Karisto
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Tiziana Vonlanthen
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Christopher Mundt
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
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20
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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21
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Transposon-mediated insertional mutagenesis unmasks recessive insecticide resistance in the aphid Myzus persicae. Proc Natl Acad Sci U S A 2021; 118:2100559118. [PMID: 34074777 PMCID: PMC8201860 DOI: 10.1073/pnas.2100559118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The evolution of resistance to insecticides threatens the sustainable control of many of the world's most damaging insect crop pests and disease vectors. To effectively combat resistance, it is important to understand its underlying genetic architecture, including the type and number of genetic variants affecting resistance and their interactions with each other and the environment. While significant progress has been made in characterizing the individual genes or mutations leading to resistance, our understanding of how genetic variants interact to influence its phenotypic expression remains poor. Here, we uncover a mechanism of insecticide resistance resulting from transposon-mediated insertional mutagenesis of a genetically dominant but insecticide-susceptible allele that enables the adaptive potential of a previously unavailable recessive resistance allele to be unlocked. Specifically, we identify clones of the aphid pest Myzus persicae that carry a resistant allele of the essential voltage-gated sodium channel (VGSC) gene with the recessive M918T and L1014F resistance mutations, in combination with an allele lacking these mutations but carrying a Mutator-like element transposon insertion that disrupts the coding sequence of the VGSC. This results in the down-regulation of the dominant susceptible allele and monoallelic expression of the recessive resistant allele, rendering the clones resistant to the insecticide bifenthrin. These findings are a powerful example of how transposable elements can provide a source of evolutionary potential that can be revealed by environmental and genetic perturbation, with applied implications for the control of highly damaging insect pests.
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22
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Nandolo W, Mészáros G, Wurzinger M, Banda LJ, Gondwe TN, Mulindwa HA, Nakimbugwe HN, Clark EL, Woodward-Greene MJ, Liu M, Liu GE, Van Tassell CP, Rosen BD, Sölkner J. Detection of copy number variants in African goats using whole genome sequence data. BMC Genomics 2021; 22:398. [PMID: 34051743 PMCID: PMC8164248 DOI: 10.1186/s12864-021-07703-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/11/2021] [Indexed: 12/21/2022] Open
Abstract
Background Copy number variations (CNV) are a significant source of variation in the genome and are therefore essential to the understanding of genetic characterization. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. Results A total of 253,553 CNV (244,876 deletions and 8677 duplications) were identified, corresponding to an overall average of 1393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. Conclusions This study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07703-1.
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Affiliation(s)
- Wilson Nandolo
- University of Natural Resources and Life Sciences, Vienna, Austria.,Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Gábor Mészáros
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria Wurzinger
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Liveness J Banda
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Timothy N Gondwe
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | | | | | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland, UK
| | - M Jennifer Woodward-Greene
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.,National Agricultural Library, USDA-ARS, Beltsville, MD, USA
| | - Mei Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - George E Liu
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA
| | | | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, USA.
| | - Johann Sölkner
- University of Natural Resources and Life Sciences, Vienna, Austria
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23
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Mérel V, Gibert P, Buch I, Rada VR, Estoup A, Gautier M, Fablet M, Boulesteix M, Vieira C. The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions. Mol Biol Evol 2021; 38:4252-4267. [PMID: 34021759 PMCID: PMC8476158 DOI: 10.1093/molbev/msab155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we characterized the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo, and found that TEs occupy 47% of the genome and are mostly located in gene poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied variation of TE abundance in genomic data from 16 invasive and six native populations of D. suzukii. We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity θ̂w a proxy of effective population size. We did not find any correlation between TE contents and bioclimatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 2,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g. transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.
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Affiliation(s)
- Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Patricia Gibert
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Inessa Buch
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Valentina Rodriguez Rada
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Arnaud Estoup
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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24
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Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ. Evolution of genome structure in the Drosophila simulans species complex. Genome Res 2021; 31:380-396. [PMID: 33563718 PMCID: PMC7919458 DOI: 10.1101/gr.263442.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022]
Abstract
The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Ching-Ho Chang
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Danielle E Khost
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
- FAS Informatics and Scientific Applications, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jeffrey R Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | | | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
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25
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Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM. Transposable Element Landscape in Drosophila Populations Selected for Longevity. Genome Biol Evol 2021; 13:6141024. [PMID: 33595657 PMCID: PMC8355499 DOI: 10.1093/gbe/evab031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) inflict numerous negative effects on health and fitness as they replicate by integrating into new regions of the host genome. Even though organisms employ powerful mechanisms to demobilize TEs, transposons gradually lose repression during aging. The rising TE activity causes genomic instability and was implicated in age-dependent neurodegenerative diseases, inflammation, and the determination of lifespan. It is therefore conceivable that long-lived individuals have improved TE silencing mechanisms resulting in reduced TE expression relative to their shorter-lived counterparts and fewer genomic insertions. Here, we test this hypothesis by performing the first genome-wide analysis of TE insertions and expression in populations of Drosophila melanogaster selected for longevity through late-life reproduction for 50–170 generations from four independent studies. Contrary to our expectation, TE families were generally more abundant in long-lived populations compared with nonselected controls. Although simulations showed that this was not expected under neutrality, we found little evidence for selection driving TE abundance differences. Additional RNA-seq analysis revealed a tendency for reducing TE expression in selected populations, which might be more important for lifespan than regulating genomic insertions. We further find limited evidence of parallel selection on genes related to TE regulation and transposition. However, telomeric TEs were genomically and transcriptionally more abundant in long-lived flies, suggesting improved telomere maintenance as a promising TE-mediated mechanism for prolonging lifespan. Our results provide a novel viewpoint indicating that reproduction at old age increases the opportunity of TEs to be passed on to the next generation with little impact on longevity.
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Affiliation(s)
- Daniel K Fabian
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
- Corresponding author: E-mail:
| | - Handan Melike Dönertaş
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Matías Fuentealba
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
| | - Linda Partridge
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, United Kingdom
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Janet M Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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Chakraborty M, Ramaiah A, Adolfi A, Halas P, Kaduskar B, Ngo LT, Jayaprasad S, Paul K, Whadgar S, Srinivasan S, Subramani S, Bier E, James AA, Emerson JJ. Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biol 2021; 19:28. [PMID: 33568145 PMCID: PMC7876825 DOI: 10.1186/s12915-021-00963-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vector's genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution. RESULTS To access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element (TE) families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y chromosome in any mosquito. By tracking full-length mRNA for > 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively throughout male development and adulthood, suggesting an important role. CONCLUSION Collectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate the development of genetic control strategies of malaria transmission.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Arunachalam Ramaiah
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Adriana Adolfi
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Paige Halas
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Bhagyashree Kaduskar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Luna Thanh Ngo
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Suvratha Jayaprasad
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Kiran Paul
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Saurabh Whadgar
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Subhashini Srinivasan
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Suresh Subramani
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093-0322, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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27
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de Oliveira DS, Rosa MT, Vieira C, Loreto ELS. Oxidative and radiation stress induces transposable element transcription in Drosophila melanogaster. J Evol Biol 2021; 34:628-638. [PMID: 33484011 DOI: 10.1111/jeb.13762] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/27/2020] [Accepted: 12/06/2020] [Indexed: 12/20/2022]
Abstract
It has been shown that stressors are capable of activating transposable elements (TEs). Currently, there is a hypothesis that stress activation of TEs may be involved in adaptive evolution, favouring the increase in genetic variability when the population is under adverse conditions. However, TE activation under stress is still poorly understood. In the present study, we estimated the fraction of differentially expressed TEs (DETEs) under ionizing radiation (144, 360 and 864 Gy) and oxidative stress (dioxin, formaldehyde and toluene) treatments. The stress intensity of each treatment was estimated by measuring the number of differentially expressed genes, and we show that several TEs families are activated by stress whereas others are repressed. The proportion of DETEs was positively related to stress intensity. However, even under the strongest stress, only a small fraction of TE families were activated (9.28%) and 17.72% were repressed. Considering all treatments together, the activated proportion was 19.83%. Nevertheless, as several TEs are incomplete or degenerated, only 10.55% of D. melanogaster mobilome is, at same time, activated by the stressors and able to transpose or at least code a protein. Thus, our study points out that although stress activates TEs, it is not a generalized activation process, and for some families, the stress induces repression.
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Affiliation(s)
- Daniel Siqueira de Oliveira
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, 1- Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Marcos Trindade Rosa
- PPG Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, 1- Université de Lyon, Université Lyon 1, CNRS, Villeurbanne, France
| | - Elgion L S Loreto
- Dep de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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28
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Abstract
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.
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29
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Gilbert C, Peccoud J, Cordaux R. Transposable Elements and the Evolution of Insects. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:355-372. [PMID: 32931312 DOI: 10.1146/annurev-ento-070720-074650] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.
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Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France;
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France
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30
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Woodruff GC, Teterina AA. Degradation of the Repetitive Genomic Landscape in a Close Relative of Caenorhabditis elegans. Mol Biol Evol 2020; 37:2549-2567. [PMID: 32359146 PMCID: PMC7475029 DOI: 10.1093/molbev/msaa107] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The abundance, diversity, and genomic distribution of repetitive elements is highly variable among species. These patterns are thought to be driven in part by reproductive mode and the interaction of selection and recombination, and recombination rates typically vary by chromosomal position. In the nematode Caenorhabditis elegans, repetitive elements are enriched at chromosome arms and depleted on centers, and this mirrors the chromosomal distributions of other genomic features such as recombination rate. How conserved is this genomic landscape of repeats, and what evolutionary forces maintain it? To address this, we compared the genomic organization of repetitive elements across five Caenorhabditis species with chromosome-level assemblies. As previously reported, repeat content is enriched on chromosome arms in most Caenorhabditis species, and no obvious patterns of repeat content associated with reproductive mode were observed. However, the fig-associated C. inopinata has experienced repetitive element expansion and reveals no association of global repeat density with chromosome position. Patterns of repeat superfamily specific distributions reveal this global pattern is driven largely by a few repeat superfamilies that in C. inopinata have expanded in number and have weak associations with chromosome position. Additionally, 15% of predicted protein-coding genes in C. inopinata align to transposon-related proteins. When these are excluded, C. inopinata has no enrichment of genes in chromosome centers, in contrast to its close relatives who all have such clusters. Forward evolutionary simulations reveal that chromosomal heterogeneity in recombination rate alone can generate structured repetitive genomic landscapes when insertions are weakly deleterious, whereas chromosomal heterogeneity in the fitness effects of transposon insertion can promote such landscapes across a variety of evolutionary scenarios. Thus, patterns of gene density along chromosomes likely contribute to global repetitive landscapes in this group, although other historical or genomic factors are needed to explain the idiosyncrasy of genomic organization of various transposable element taxa within C. inopinata. Taken together, these results highlight the power of comparative genomics and evolutionary simulations in testing hypotheses regarding the causes of genome organization.
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Affiliation(s)
- Gavin C Woodruff
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
| | - Anastasia A Teterina
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR
- Center of Parasitology, Severtsov Institute of Ecology and Evolution RAS, Moscow, Russia
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31
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Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Mol Biol Evol 2020; 37:2661-2678. [PMID: 32413142 PMCID: PMC7475034 DOI: 10.1093/molbev/msaa120] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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Affiliation(s)
- Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Maite G Barrón
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - R Axel W Wiberg
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Clément Goubert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige, Italy
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - María Bogaerts-Márquez
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Annabelle Haudry
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Lena Waidele
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine
| | - Elena G Pasyukova
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genome Variation, Institute of Molecular Genetics of RAS, Moscow, Russia
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Svitlana Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patricia Gibert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Damiano Porcelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Animal and Plant Sciences, Sheffield, United Kingdom
| | - Nico Posnien
- The European Drosophila Population Genomics Consortium (DrosEU)
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Universität Göttingen, Göttingen, Germany
| | - Alejandro Sánchez-Gracia
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Élio Sucena
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Alan O Bergland
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Maria Pilar Garcia Guerreiro
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Lain Guio
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Bart Deplancke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Bio-engineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Cristina Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
| | - Bas J Zwaan
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Eran Tauber
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paul Schmidt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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32
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Choi JY, Lee YCG. Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements. PLoS Genet 2020; 16:e1008872. [PMID: 32673310 PMCID: PMC7365398 DOI: 10.1371/journal.pgen.1008872] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Transposable elements (TEs) are genomic parasites that selfishly replicate at the expense of host fitness. Fifty years of evolutionary studies of TEs have concentrated on the deleterious genetic effects of TEs, such as their effects on disrupting genes and regulatory sequences. However, a flurry of recent work suggests that there is another important source of TEs’ harmful effects—epigenetic silencing. Host genomes typically silence TEs by the deposition of repressive epigenetic marks. While this silencing reduces the selfish replication of TEs and should benefit hosts, a picture is emerging that the epigenetic silencing of TEs triggers inadvertent spreading of repressive marks to otherwise expressed neighboring genes, ultimately jeopardizing host fitness. In this Review, we provide a long-overdue overview of the recent genome-wide evidence for the presence and prevalence of TEs’ epigenetic effects, highlighting both the similarities and differences across mammals, insects, and plants. We lay out the current understanding of the functional and fitness consequences of TEs’ epigenetic effects, and propose possible influences of such effects on the evolution of both hosts and TEs themselves. These unique evolutionary consequences indicate that TEs’ epigenetic effect is not only a crucial component of TE biology but could also be a significant contributor to genome function and evolution.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York State, United States of America
| | - Yuh Chwen G. Lee
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
- * E-mail:
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33
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Mérel V, Boulesteix M, Fablet M, Vieira C. Transposable elements in Drosophila. Mob DNA 2020; 11:23. [PMID: 32636946 PMCID: PMC7334843 DOI: 10.1186/s13100-020-00213-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/25/2022] Open
Abstract
Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.
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Affiliation(s)
- Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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34
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Wang B, Liang X, Gleason ML, Hsiang T, Zhang R, Sun G. A chromosome-scale assembly of the smallest Dothideomycete genome reveals a unique genome compaction mechanism in filamentous fungi. BMC Genomics 2020; 21:321. [PMID: 32326892 PMCID: PMC7181583 DOI: 10.1186/s12864-020-6732-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/14/2020] [Indexed: 11/19/2022] Open
Abstract
Background The wide variation in the size of fungal genomes is well known, but the reasons for this size variation are less certain. Here, we present a chromosome-scale assembly of ectophytic Peltaster fructicola, a surface-dwelling extremophile, based on long-read DNA sequencing technology, to assess possible mechanisms associated with genome compaction. Results At 18.99 million bases (Mb), P. fructicola possesses one of the smallest known genomes sequence among filamentous fungi. The genome is highly compact relative to other fungi, with substantial reductions in repeat content, ribosomal DNA copies, tRNA gene quantity, and intron sizes, as well as intergenic lengths and the size of gene families. Transposons take up just 0.05% of the entire genome, and no full-length transposon was found. We concluded that reduced genome sizes in filamentous fungi such as P. fructicola, Taphrina deformans and Pneumocystis jirovecii occurred through reduction in ribosomal DNA copy number and reduced intron sizes. These dual mechanisms contrast with genome reduction in the yeast fungus Saccharomyces cerevisiae, whose small and compact genome is associated solely with intron loss. Conclusions Our results reveal a unique genomic compaction architecture of filamentous fungi inhabiting plant surfaces, and broaden the understanding of the mechanisms associated with compaction of fungal genomes.
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Affiliation(s)
- Bo Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.,MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiaofei Liang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Rong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Guangyu Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
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35
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Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin. PLoS Genet 2020; 16:e1008673. [PMID: 32203508 PMCID: PMC7147806 DOI: 10.1371/journal.pgen.1008673] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/10/2020] [Accepted: 02/14/2020] [Indexed: 01/02/2023] Open
Abstract
Membraneless pericentromeric heterochromatin (PCH) domains play vital roles in chromosome dynamics and genome stability. However, our current understanding of 3D genome organization does not include PCH domains because of technical challenges associated with repetitive sequences enriched in PCH genomic regions. We investigated the 3D architecture of Drosophila melanogaster PCH domains and their spatial associations with the euchromatic genome by developing a novel analysis method that incorporates genome-wide Hi-C reads originating from PCH DNA. Combined with cytogenetic analysis, we reveal a hierarchical organization of the PCH domains into distinct “territories.” Strikingly, H3K9me2-enriched regions embedded in the euchromatic genome show prevalent 3D interactions with the PCH domain. These spatial contacts require H3K9me2 enrichment, are likely mediated by liquid-liquid phase separation, and may influence organismal fitness. Our findings have important implications for how PCH architecture influences the function and evolution of both repetitive heterochromatin and the gene-rich euchromatin. The three dimensional (3D) organization of genomes in cell nuclei can influence a wide variety of genome functions. However, most of our understanding of this critical architecture has been limited to the gene-rich euchromatin, and largely ignores the gene-poor and repeat-rich pericentromeric heterochromatin, or PCH. PCH comprises a large part of most eukaryotic genomes, forms 3D membraneless PCH domains in nuclei, and plays a vital role in chromosome dynamics and genome stability. In this study, we developed a new method that overcomes the technical challenges imposed by the highly repetitive PCH DNA, and generated a comprehensive picture of its 3D organization. Combined with image analyses, we reveal a hierarchical organization of the PCH domains. Surprisingly, we showed that distant euchromatic regions enriched for repressive epigenetic marks also dynamically interact with the main PCH domains. These 3D interactions are likely mediated by liquid-liquid phase separation (similar to how oil and vinegar separate in salad dressing) and the resulting liquid-like fusion events, and can influence the fitness of individuals. Our discoveries have strong implications for how seemingly “junk” DNA could impact functions in the gene-rich euchromatin.
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36
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Ellison CE, Cao W. Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster. Nucleic Acids Res 2020; 48:290-303. [PMID: 31754714 PMCID: PMC6943127 DOI: 10.1093/nar/gkz1080] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 01/29/2023] Open
Abstract
Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which has provided important insight into the population dynamics of TEs. However, such approaches are not able to identify insertions of uncharacterized TEs, nor can they assemble the full sequence of inserted elements. Here, we use nanopore sequencing and Hi-C scaffolding to produce de novo genome assemblies for two wild strains of Drosophila melanogaster from the Drosophila Genetic Reference Panel (DGRP). Ovarian piRNA populations and Illumina split-read TE insertion profiles have been previously produced for both strains. We find that nanopore sequencing with Hi-C scaffolding produces highly contiguous, chromosome-length scaffolds, and we identify hundreds of TE insertions that were missed by Illumina-based methods, including a novel micropia-like element that has recently invaded the DGRP population. We also find hundreds of piRNA-producing loci that are specific to each strain. Some of these loci are created by strain-specific TE insertions, while others appear to be epigenetically controlled. Our results suggest that Illumina approaches reveal only a portion of the repetitive sequence landscape of eukaryotic genomes and that population-level resequencing using long reads is likely to provide novel insight into the evolutionary dynamics of repetitive elements.
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Affiliation(s)
- Christopher E Ellison
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Weihuan Cao
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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37
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Uzunović J, Josephs EB, Stinchcombe JR, Wright SI. Transposable Elements Are Important Contributors to Standing Variation in Gene Expression in Capsella Grandiflora. Mol Biol Evol 2020; 36:1734-1745. [PMID: 31028401 DOI: 10.1093/molbev/msz098] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) make up a significant portion of eukaryotic genomes and are important drivers of genome evolution. However, the extent to which TEs affect gene expression variation on a genome-wide scale in comparison with other types of variants is still unclear. We characterized TE insertion polymorphisms and their association with gene expression in 124 whole-genome sequences from a single population of Capsella grandiflora, and contrasted this with the effects of single nucleotide polymorphisms (SNPs). Population frequency of insertions was negatively correlated with distance to genes, as well as density of conserved noncoding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare SNPs contribute equally to up- and down-regulation, but have a weaker individual effect than TEs. An expression quantitative trait loci (eQTL) analysis shows that a greater proportion of common TEs are eQTLs as opposed to common SNPs, and a third of the genes with TE eQTLs do not have SNP eQTLs. In contrast with rare TE insertions, common insertions are more likely to increase expression, consistent with recent models of cis-regulatory evolution favoring enhancer alleles. Taken together, these results imply that TEs are a significant contributor to gene expression variation and are individually more likely than rare SNPs to cause extreme changes in gene expression.
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Affiliation(s)
- Jasmina Uzunović
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Koffler Scientific Reserve, University of Toronto, Toronto, Ontario, Canada
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
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38
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Luo S, Zhang H, Duan Y, Yao X, Clark AG, Lu J. The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster. BMC Evol Biol 2020; 20:14. [PMID: 31992188 PMCID: PMC6988346 DOI: 10.1186/s12862-020-1580-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 01/13/2020] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The piwi-interacting RNAs (piRNAs) are small non-coding RNAs that specifically repress transposable elements (TEs) in the germline of Drosophila. Despite our expanding understanding of TE:piRNA interaction, whether there is an evolutionary arms race between TEs and piRNAs was unclear. RESULTS Here, we studied the population genomics of TEs and piRNAs in the worldwide strains of D. melanogaster. By conducting a correlation analysis between TE contents and the abundance of piRNAs from ovaries of representative strains of D. melanogaster, we find positive correlations between TEs and piRNAs in six TE families. Our simulations further highlight that TE activities and the strength of purifying selection against TEs are important factors shaping the interactions between TEs and piRNAs. Our studies also suggest that the de novo generation of piRNAs is an important mechanism to repress the newly invaded TEs. CONCLUSIONS Our results revealed the existence of an evolutionary arms race between the copy numbers of TEs and the abundance of antisense piRNAs at the population level. Although the interactions between TEs and piRNAs are complex and many factors should be considered to impact their interaction dynamics, our results suggest the emergence, repression specificity and strength of piRNAs on TEs should be considered in studying the landscapes of TE insertions in Drosophila. These results deepen our understanding of the interactions between piRNAs and TEs, and also provide novel insights into the nature of genomic conflicts of other forms.
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Affiliation(s)
- Shiqi Luo
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- College of Plant Protection, Beijing Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing, 100193, China
| | - Hong Zhang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Xinmin Yao
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, College of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
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39
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Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. Nat Commun 2019; 10:4872. [PMID: 31653862 PMCID: PMC6814777 DOI: 10.1038/s41467-019-12884-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 09/25/2019] [Indexed: 12/11/2022] Open
Abstract
It has been hypothesized that individually-rare hidden structural variants (SVs) could account for a significant fraction of variation in complex traits. Here we identified more than 20,000 euchromatic SVs from 14 Drosophila melanogaster genome assemblies, of which ~40% are invisible to high specificity short-read genotyping approaches. SVs are common, with 31.5% of diploid individuals harboring a SV in genes larger than 5kb, and 24% harboring multiple SVs in genes larger than 10kb. SV minor allele frequencies are rarer than amino acid polymorphisms, suggesting that SVs are more deleterious. We show that a number of functionally important genes harbor previously hidden structural variants likely to affect complex phenotypes. Furthermore, SVs are overrepresented in candidate genes associated with quantitative trait loci mapped using the Drosophila Synthetic Population Resource. We conclude that SVs are ubiquitous, frequently constitute a heterogeneous allelic series, and can act as rare alleles of large effect.
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40
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Stewart NB, Rogers RL. Chromosomal rearrangements as a source of new gene formation in Drosophila yakuba. PLoS Genet 2019; 15:e1008314. [PMID: 31545792 PMCID: PMC6776367 DOI: 10.1371/journal.pgen.1008314] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 10/03/2019] [Accepted: 07/17/2019] [Indexed: 11/19/2022] Open
Abstract
The origins of new genes are among the most fundamental questions in evolutionary biology. Our understanding of the ways that new genetic material appears and how that genetic material shapes population variation remains incomplete. De novo genes and duplicate genes are a key source of new genetic material on which selection acts. To better understand the origins of these new gene sequences, we explored the ways that structural variation might alter expression patterns and form novel transcripts. We provide evidence that chromosomal rearrangements are a source of novel genetic variation that facilitates the formation of de novo exons in Drosophila. We identify 51 cases of de novo exon formation created by chromosomal rearrangements in 14 strains of D. yakuba. These new genes inherit transcription start signals and open reading frames when the 5' end of existing genes are combined with previously untranscribed regions. Such new genes would appear with novel peptide sequences, without the necessity for secondary transitions from non-coding RNA to protein. This mechanism of new peptide formations contrasts with canonical theory of de novo gene progression requiring non-coding intermediaries that must acquire new mutations prior to loss via pseudogenization. Hence, these mutations offer a means to de novo gene creation and protein sequence formation in a single mutational step, answering a long standing open question concerning new gene formation. We further identify gene expression changes to 134 existing genes, indicating that these mutations can alter gene regulation. Population variability for chromosomal rearrangements is considerable, with 2368 rearrangements observed across 14 inbred lines. More rearrangements were identified on the X chromosome than any of the autosomes, suggesting the X is more susceptible to chromosome alterations. Together, these results suggest that chromosomal rearrangements are a source of variation in populations that is likely to be important to explain genetic and therefore phenotypic diversity.
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Affiliation(s)
- Nicholas B. Stewart
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- Department of Biological Sciences, Ft Hays State University, Ft Hays, Kansas, United States of America
| | - Rebekah L. Rogers
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, North Carolina, United States of America
- * E-mail:
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41
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Abstract
Among the multitude of papers published yearly in scientific journals, precious few publications may be worth looking back in half a century to appreciate the significance of the discoveries that would later become common knowledge and get a chance to shape a field or several adjacent fields. Here, Kimura's fundamental concept of neutral mutation-random drift, which was published 50 years ago, is re-examined in light of its pervasive influence on comparative genomics and, more specifically, on the contribution of transposable elements to eukaryotic genome evolution.
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Affiliation(s)
- Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA
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42
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Merenciano M, Iacometti C, González J. A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster. Mob DNA 2019; 10:10. [PMID: 30911338 PMCID: PMC6415491 DOI: 10.1186/s13100-019-0152-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/28/2019] [Indexed: 01/19/2023] Open
Abstract
Transposable elements (TEs) are not randomly distributed in the genome. A genome-wide analysis of the D. melanogaster genome found that differences in TE density across 50 kb genomic regions was due both to transposition and duplication. At smaller genomic scales, promoter regions of hsp genes and the promoter region of CG18446 have been shown to accumulate TE insertions. In this work, we have further analyzed the promoter region of CG18446. We screened 218 strains collected in 15 natural populations, and we found that the CG18446 promoter region contains 20 independent roo insertions. Based on phylogenetic analysis, we suggest that the presence of multiple roo insertions in this region is likely to be the result of several bursts of transposition. Moreover, we found that the roo insertional cluster in the CG18446 promoter region is unique: no other promoter region in the genome contains a similar number of roo insertions. We found that, similar to hsp gene promoters, chromatin accessibility could be one of the factors explaining the recurrent insertions of roo elements in CG18446 promoter region.
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Affiliation(s)
- Miriam Merenciano
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain
| | - Camillo Iacometti
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain.,2Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Josefa González
- 1Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Passeig Maritim de la Barceloneta 37,49, 08003 Barcelona, Spain
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43
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Lerat E, Goubert C, Guirao‐Rico S, Merenciano M, Dufour A, Vieira C, González J. Population-specific dynamics and selection patterns of transposable element insertions in European natural populations. Mol Ecol 2019; 28:1506-1522. [PMID: 30506554 PMCID: PMC6849870 DOI: 10.1111/mec.14963] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/30/2018] [Accepted: 11/05/2018] [Indexed: 01/02/2023]
Abstract
Transposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome-wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations. Taking advantage of the European Drosophila population genomics consortium (DrosEU) sequencing data set, we have identified and measured the dynamics of TEs in a large sample of European Drosophila melanogaster natural populations. We showed that the mobilome landscape is population-specific and highly diverse depending on the TE family. In contrast with previous studies based on SNP variants, no geographical structure was observed for TE abundance or TE divergence in European populations. We further identified de novo individual insertions using two available programs and, as expected, most of the insertions were present at low frequencies. Nevertheless, we identified a subset of TEs present at high frequencies and located in genomic regions with a high recombination rate. These TEs are candidates for being the target of positive selection, although neutral processes should be discarded before reaching any conclusion on the type of selection acting on them. Finally, parallel patterns of association between the frequency of TE insertions and several geographical and temporal variables were found between European and North American populations, suggesting that TEs can be potentially implicated in the adaptation of populations across continents.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Clément Goubert
- Molecular Biology and GeneticsCornell UniversityIthacaNew York
| | - Sara Guirao‐Rico
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Anne‐Béatrice Dufour
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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44
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Choi JY, Purugganan MD. Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice. Mol Biol Evol 2019; 35:365-382. [PMID: 29126199 PMCID: PMC5850837 DOI: 10.1093/molbev/msx284] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on five factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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45
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Adrion JR, Begun DJ, Hahn MW. Patterns of transposable element variation and clinality in
Drosophila. Mol Ecol 2019; 28:1523-1536. [DOI: 10.1111/mec.14961] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/14/2018] [Accepted: 11/15/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Jeffrey R. Adrion
- Department of Biology University of Oregon Eugene Oregon
- Department of Biology Indiana University Bloomington Indiana
| | - David J. Begun
- Department of Evolution and Ecology University of California Davis, Davis California
| | - Matthew W. Hahn
- Department of Biology Indiana University Bloomington Indiana
- Department of Computer Science Indiana University Bloomington Indiana
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46
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Guio L, González J. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans. Methods Mol Biol 2019; 1910:505-530. [PMID: 31278675 DOI: 10.1007/978-1-4939-9074-0_16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.
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Affiliation(s)
- Lain Guio
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
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47
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Kelleher ES, Jaweria J, Akoma U, Ortega L, Tang W. QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline. PLoS Biol 2018; 16:e2006040. [PMID: 30376574 PMCID: PMC6207299 DOI: 10.1371/journal.pbio.2006040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/26/2018] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) are obligate genetic parasites that propagate in host genomes by replicating in germline nuclei, thereby ensuring transmission to offspring. This selfish replication not only produces deleterious mutations—in extreme cases, TE mobilization induces genotoxic stress that prohibits the production of viable gametes. Host genomes could reduce these fitness effects in two ways: resistance and tolerance. Resistance to TE propagation is enacted by germline-specific small-RNA-mediated silencing pathways, such as the Piwi-interacting RNA (piRNA) pathway, and is studied extensively. However, it remains entirely unknown whether host genomes may also evolve tolerance by desensitizing gametogenesis to the harmful effects of TEs. In part, the absence of research on tolerance reflects a lack of opportunity, as small-RNA-mediated silencing evolves rapidly after a new TE invades, thereby masking existing variation in tolerance. We have exploited the recent historical invasion of the Drosophila melanogaster genome by P-element DNA transposons in order to study tolerance of TE activity. In the absence of piRNA-mediated silencing, the genotoxic stress imposed by P-elements disrupts oogenesis and, in extreme cases, leads to atrophied ovaries that completely lack germline cells. By performing quantitative trait locus (QTL) mapping on a panel of recombinant inbred lines (RILs) that lack piRNA-mediated silencing of P-elements, we uncovered multiple QTL that are associated with differences in tolerance of oogenesis to P-element transposition. We localized the most significant QTL to a small 230-kb euchromatic region, with the logarithm of the odds (LOD) peak occurring in the bruno locus, which codes for a critical and well-studied developmental regulator of oogenesis. Genetic, cytological, and expression analyses suggest that bruno dosage modulates germline stem cell (GSC) loss in the presence of P-element activity. Our observations reveal segregating variation in TE tolerance for the first time, and implicate gametogenic regulators as a source of tolerant variants in natural populations. Transposable elements (TEs), or “jumping genes,” are mobile fragments of selfish DNA that leave deleterious mutations and DNA damage in their wake as they spread through host genomes. Their harmful effects are known to select for resistance by the host, in which the propagation of TEs is regulated and reduced. Here, we study for the first time whether host cells might also exhibit tolerance to TEs, by reducing their harmful effects without directly controlling their movement. By taking advantage of a panel of wild-type Drosophila melanogaster that lack resistance to P-element DNA transposons, we identified a small region of the genome that influences tolerance of P-element activity. We further demonstrate that a gene within that region, bruno, strongly influences the negative effects of P-element mobilization on the fly. When bruno dosage is reduced, the fertility of females carrying mobile P-elements is enhanced. The bruno locus encodes a protein with no known role in TE regulation but multiple well-characterized functions in oogenesis. We propose that bruno function reduces tolerance of the developing oocyte to DNA damage that is caused by P-elements.
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Affiliation(s)
- Erin S. Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- * E-mail:
| | - Jaweria Jaweria
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Uchechukwu Akoma
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lily Ortega
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Wenpei Tang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
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48
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Manee MM, Jackson J, Bergman CM. Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila. Genome Biol Evol 2018; 10:1533-1545. [PMID: 29850787 PMCID: PMC6007792 DOI: 10.1093/gbe/evy104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2018] [Indexed: 12/15/2022] Open
Abstract
Highly conserved noncoding elements (CNEs) constitute a significant proportion of the genomes of multicellular eukaryotes. The function of most CNEs remains elusive, but growing evidence indicates they are under some form of purifying selection. Noncoding regions in many species also harbor large numbers of transposable element (TE) insertions, which are typically lineage specific and depleted in exons because of their deleterious effects on gene function or expression. However, it is currently unknown whether the landscape of TE insertions in noncoding regions is random or influenced by purifying selection on CNEs. Here, we combine comparative and population genomic data in Drosophila melanogaster to show that the abundance of TE insertions in intronic and intergenic CNEs is reduced relative to random expectation, supporting the idea that selective constraints on CNEs eliminate a proportion of TE insertions in noncoding regions. However, we find no evidence for differences in the allele frequency spectra for polymorphic TE insertions in CNEs versus those in unconstrained spacer regions, suggesting that the distribution of fitness effects acting on observable TE insertions is similar across different functional compartments in noncoding DNA. Our results provide evidence that selective constraints on CNEs contribute to shaping the landscape of TE insertion in eukaryotic genomes, and provide further evidence that CNEs are indeed functionally constrained and not simply mutational cold spots.
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Affiliation(s)
- Manee M Manee
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.,National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.,Center of Excellence for Genomics (CEG), King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - John Jackson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.,Department of Genetics, University of Georgia, Athens, GA.,Institute of Bioinformatics, University of Georgia, Athens, GA
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49
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Stritt C, Gordon SP, Wicker T, Vogel JP, Roulin AC. Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon. Genome Biol Evol 2018; 10:304-318. [PMID: 29281015 PMCID: PMC5786231 DOI: 10.1093/gbe/evx276] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2017] [Indexed: 01/05/2023] Open
Abstract
Transposable element (TE) activity has emerged as a major cause of variation in genome size and structure among species. To what extent TEs contribute to genetic variation and divergence within species, however, is much less clear, mainly because population genomic data have so far only been available for the classical model organisms. In this study, we use the annual Mediterranean grass Brachypodium distachyon to investigate TE dynamics in natural populations. Using whole-genome sequencing data for 53 natural accessions, we identified more than 5,400 TE polymorphisms across the studied genomes. We found, first, that while population bottlenecks and expansions have shaped genetic diversity in B. distachyon, these events did not lead to lineage-specific activations of TE families, as observed in other species. Instead, the same families have been active across the species range and TE activity is homogeneous across populations, indicating the presence of conserved regulatory mechanisms. Second, almost half of the TE insertion polymorphisms are accession-specific, most likely because of recent activity in expanding populations and the action of purifying selection. And finally, although TE insertion polymorphisms are underrepresented in and around genes, more than 1,000 of them occur in genic regions and could thus contribute to functional divergence. Our study shows that while TEs in B. distachyon are “well-behaved” compared with TEs in other species with larger genomes, they are an abundant source of lineage-specific genetic variation and may play an important role in population divergence and adaptation.
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Affiliation(s)
- Christoph Stritt
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - Sean P Gordon
- DOE Joint Genome Institute, Walnut Creek, California
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, California
| | - Anne C Roulin
- Institute for Plant and Microbial Biology, University of Zurich, Switzerland
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50
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Jiang X, Tang H, Mohammed Ismail W, Lynch M. A Maximum-Likelihood Approach to Estimating the Insertion Frequencies of Transposable Elements from Population Sequencing Data. Mol Biol Evol 2018; 35:2560-2571. [PMID: 30099533 PMCID: PMC6188571 DOI: 10.1093/molbev/msy152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Transposable elements (TEs) contribute to a large fraction of the expansion of many eukaryotic genomes due to the capability of TEs duplicating themselves through transposition. A first step to understanding the roles of TEs in a eukaryotic genome is to characterize the population-wide variation of TE insertions in the species. Here, we present a maximum-likelihood (ML) method for estimating allele frequencies and detecting selection on TE insertions in a diploid population, based on the genotypes at TE insertion sites detected in multiple individuals sampled from the population using paired-end (PE) sequencing reads. Tests of the method on simulated data show that it can accurately estimate the allele frequencies of TE insertions even when the PE sequencing is conducted at a relatively low coverage (=5X). The method can also detect TE insertions under strong selection, and the detection ability increases with sample size in a population, although a substantial fraction of actual TE insertions under selection may be undetected. Application of the ML method to genomic sequencing data collected from a natural Daphnia pulex population shows that, on the one hand, most (>90%) TE insertions present in the reference D. pulex genome are either fixed or nearly fixed (with allele frequencies >0.95); on the other hand, among the nonreference TE insertions (i.e., those detected in some individuals in the population but absent from the reference genome), the majority (>70%) are still at low frequencies (<0.1). Finally, we detected a substantial fraction (∼9%) of nonreference TE insertions under selection.
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Affiliation(s)
- Xiaoqian Jiang
- Department of Biology, Indiana University, Bloomington, IN
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN
| | | | - Michael Lynch
- Center for Mechanisms of Evolution, Arizona State University, Temple, AZ
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