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Cappucci U, Proietti M, Casale AM, Schiavo S, Chiavarini S, Accardo S, Manzo S, Piacentini L. Assessing genotoxic effects of plastic leachates in Drosophila melanogaster. CHEMOSPHERE 2024:142440. [PMID: 38821133 DOI: 10.1016/j.chemosphere.2024.142440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
Plastic polymers were largely added with chemical substances to be utilized in the items and product manufacturing. The leachability of these substances is a matter of concern given the wide amount of plastic waste, particularly in terrestrial environments, where soil represents a sink for these novel contaminants and a possible pathway of human health risk. In this study, we integrated genetic, molecular, and behavioral approaches to comparatively evaluate toxicological effects of plastic leachates, virgin and oxodegradable polypropylene (PP) and polyethylene (PE), in Drosophila melanogaster, a novel in vivo model organism for environmental monitoring studies and (eco)toxicological research. The results of this study revealed that while conventional toxicological endpoints such as developmental times and longevity remain largely unaffected, exposure to plastic leachates induces chromosomal abnormalities and transposable element (TE) activation in neural tissues. The combined effects of DNA damage and TE mobilization contribute to genome instability and increase the likelihood of LOH events, thus potentiating tumor growth and metastatic behavior of RasV12 clones. Collectively, these findings indicate that plastic leachates exert genotoxic effects in Drosophila thus highlighting potential risks associated with leachate-related plastic pollution and their implications for ecosystems and human health.
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Affiliation(s)
- Ugo Cappucci
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Mirena Proietti
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Assunta Maria Casale
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Simona Schiavo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Salvatore Chiavarini
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Sara Accardo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Sonia Manzo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy.
| | - Lucia Piacentini
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy.
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Selvaraju D, Wierzbicki F, Kofler R. Experimentally evolving Drosophila erecta populations may fail to establish an effective piRNA-based host defense against invading P-elements. Genome Res 2024; 34:410-425. [PMID: 38490738 PMCID: PMC11067887 DOI: 10.1101/gr.278706.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/07/2024] [Indexed: 03/17/2024]
Abstract
To prevent the spread of transposable elements (TEs), hosts have developed sophisticated defense mechanisms. In mammals and invertebrates, a major defense mechanism operates through PIWI-interacting RNAs (piRNAs). To investigate the establishment of the host defense, we introduced the P-element, one of the most widely studied eukaryotic transposons, into naive lines of Drosophila erecta We monitored the invasion in three replicates for more than 50 generations by sequencing the genomic DNA (using short and long reads), the small RNAs, and the transcriptome at regular intervals. A piRNA-based host defense was rapidly established in two replicates (R1, R4) but not in a third (R2), in which P-element copy numbers kept increasing for over 50 generations. We found that the ping-pong cycle could not be activated in R2, although the ping-pong cycle is fully functional against other TEs. Furthermore, R2 had both insertions in piRNA clusters and siRNAs, suggesting that neither of them is sufficient to trigger the host defense. Our work shows that control of an invading TE requires activation of the ping-pong cycle and that this activation is a stochastic event that may fail in some populations, leading to a proliferation of TEs that ultimately threaten the integrity of the host genome.
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Affiliation(s)
- Divya Selvaraju
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria
| | - Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria;
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3
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Almeida MV, Blumer M, Yuan CU, Sierra P, Price JL, Quah FX, Friman A, Dallaire A, Vernaz G, Putman ALK, Smith AM, Joyce DA, Butter F, Haase AD, Durbin R, Santos ME, Miska EA. Dynamic co-evolution of transposable elements and the piRNA pathway in African cichlid fishes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587621. [PMID: 38617250 PMCID: PMC11014572 DOI: 10.1101/2024.04.01.587621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.
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Affiliation(s)
- Miguel Vasconcelos Almeida
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Moritz Blumer
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- These authors contributed equally
| | - Chengwei Ulrika Yuan
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- These authors contributed equally
| | - Pío Sierra
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jonathan L. Price
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Fu Xiang Quah
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Aleksandr Friman
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Biophysics Graduate Program, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742, USA
| | - Alexandra Dallaire
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Comparative Fungal Biology, Royal Botanic Gardens Kew, Jodrell Laboratory, Richmond TW9 3DS, UK
| | - Grégoire Vernaz
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Present address: Zoological Institute, Department of Environmental Sciences, University of Basel, Vesalgasse 1, Basel, 4051, Switzerland
| | - Audrey L. K. Putman
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Alan M. Smith
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Domino A. Joyce
- School of Natural Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Falk Butter
- Institute of Molecular Biology (IMB), Quantitative Proteomics, Ackermannweg 4, Mainz, 55128, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Südufer, Greifswald, 17493, Germany
| | - Astrid D. Haase
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - M. Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Eric A. Miska
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
- Wellcome/CRUK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
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Garcia S, Kovarik A, Maiwald S, Mann L, Schmidt N, Pascual-Díaz JP, Vitales D, Weber B, Heitkam T. The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics. Mol Biol Evol 2024; 41:msae025. [PMID: 38306580 PMCID: PMC10946416 DOI: 10.1093/molbev/msae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Sophie Maiwald
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | | | - Daniel Vitales
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica–Unitat Associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Beatrice Weber
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Austria
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5
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Chen LG, Lan T, Zhang S, Zhao M, Luo G, Gao Y, Zhang Y, Du Q, Lu H, Li B, Jiao B, Hu Z, Ma Y, Zhao Q, Wang Y, Qian W, Dai J, Jiao Y. A designer synthetic chromosome fragment functions in moss. NATURE PLANTS 2024; 10:228-239. [PMID: 38278952 DOI: 10.1038/s41477-023-01595-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/22/2023] [Indexed: 01/28/2024]
Abstract
Rapid advances in DNA synthesis techniques have enabled the assembly and engineering of viral and microbial genomes, presenting new opportunities for synthetic genomics in multicellular eukaryotic organisms. These organisms, characterized by larger genomes, abundant transposons and extensive epigenetic regulation, pose unique challenges. Here we report the in vivo assembly of chromosomal fragments in the moss Physcomitrium patens, producing phenotypically virtually wild-type lines in which one-third of the coding region of a chromosomal arm is replaced by redesigned, chemically synthesized fragments. By eliminating 55.8% of a 155 kb endogenous chromosomal region, we substantially simplified the genome without discernible phenotypic effects, implying that many transposable elements may minimally impact growth. We also introduced other sequence modifications, such as PCRTag incorporation, gene locus swapping and stop codon substitution. Despite these substantial changes, the complex epigenetic landscape was normally established, albeit with some three-dimensional conformation alterations. The synthesis of a partial multicellular eukaryotic chromosome arm lays the foundation for the synthetic moss genome project (SynMoss) and paves the way for genome synthesis in multicellular organisms.
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Affiliation(s)
- Lian-Ge Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Tianlong Lan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Shuo Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mengkai Zhao
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Guangyu Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yi Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuliang Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qingwei Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Houze Lu
- School of Earth and Space Sciences, Peking University, Beijing, China
| | - Bimeng Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Bingke Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhangli Hu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yingxin Ma
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qiao Zhao
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
| | - Junbiao Dai
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, China.
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6
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Scarpa A, Kofler R. The impact of paramutations on the invasion dynamics of transposable elements. Genetics 2023; 225:iyad181. [PMID: 37819004 PMCID: PMC10697812 DOI: 10.1093/genetics/iyad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
According to the prevailing view, the trap model, the activity of invading transposable elements (TEs) is greatly reduced when a TE copy jumps into a piRNA cluster, which triggers the emergence of piRNAs that silence the TE. One crucial component in the host defence are paramutations. Mediated by maternally deposited piRNAs, paramutations convert TE insertions into piRNA producing loci, thereby transforming selfish TEs into agents of the host defence. Despite this significant effect, the impact of paramutations on the dynamics of TE invasions remains unknown. To address this issue, we performed extensive forward simulations of TE invasions with piRNA clusters and paramutations. We found that paramutations significantly affect TE dynamics, by accelerating the silencing of TE invasions, reducing the number of insertions accumulating during the invasions and mitigating the fitness cost of TEs. We also demonstrate that piRNA production induced by paramutations, an epigenetically inherited trait, may be positively selected. Finally, we show that paramutations may account for three important open problems with the trap model. Firstly, paramutated TE insertions may compensate for the insufficient number of insertions in piRNA clusters observed in previous studies. Secondly, paramutations may explain the discrepancy between the observed and the expected abundance of different TE families in Drosophila melanogaster. Thirdly, piRNA clusters may be crucial to trigger the host defence, but paramutations render the clusters dispensable once the defence has been established. This could account for the lack of TE activation when three major piRNA clusters were deleted in a previous study.
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Affiliation(s)
- Almorò Scarpa
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien 1210, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, Wien 1210, Austria
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7
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Wierzbicki F, Kofler R. The composition of piRNA clusters in Drosophila melanogaster deviates from expectations under the trap model. BMC Biol 2023; 21:224. [PMID: 37858221 PMCID: PMC10588112 DOI: 10.1186/s12915-023-01727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND It is widely assumed that the invasion of a transposable element (TE) in mammals and invertebrates is stopped when a copy of the TE jumps into a piRNA cluster (i.e., the trap model). However, recent works, which for example showed that deletion of three major piRNA clusters has no effect on TE activity, cast doubt on the trap model. RESULTS Here, we test the trap model from a population genetics perspective. Our simulations show that the composition of regions that act as transposon traps (i.e., potentially piRNA clusters) ought to deviate from regions that have no effect on TE activity. We investigated TEs in five Drosophila melanogaster strains using three complementary approaches to test whether the composition of piRNA clusters matches these expectations. We found that the abundance of TE families inside and outside of piRNA clusters is highly correlated, although this is not expected under the trap model. Furthermore, the distribution of the number of TE insertions in piRNA clusters is also much broader than expected. CONCLUSIONS We found that the observed composition of piRNA clusters is not in agreement with expectations under the simple trap model. Dispersed piRNA producing TE insertions and temporal as well as spatial heterogeneity of piRNA clusters may account for these deviations.
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Affiliation(s)
- Filip Wierzbicki
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.
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8
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Baril T, Pym A, Bass C, Hayward A. Transposon accumulation at xenobiotic gene family loci in aphids. Genome Res 2023; 33:1718-1733. [PMID: 37852781 PMCID: PMC10691553 DOI: 10.1101/gr.277820.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/29/2023] [Indexed: 10/20/2023]
Abstract
The evolution of resistance is a major challenge for the sustainable control of pests and pathogens. Thus, a deeper understanding of the evolutionary and genomic mechanisms underpinning resistance evolution is required to safeguard health and food production. Several studies have implicated transposable elements (TEs) in xenobiotic-resistance evolution in insects. However, analyses are generally restricted to one insect species and/or one or a few xenobiotic gene families (XGFs). We examine evidence for TE accumulation at XGFs by performing a comparative genomic analysis across 20 aphid genomes, considering major subsets of XGFs involved in metabolic resistance to insecticides: cytochrome P450s, glutathione S-transferases, esterases, UDP-glucuronosyltransferases, and ABC transporters. We find that TEs are significantly enriched at XGFs compared with other genes. XGFs show similar levels of TE enrichment to those of housekeeping genes. But unlike housekeeping genes, XGFs are not constitutively expressed in germline cells, supporting the selective enrichment of TEs at XGFs rather than enrichment owing to chromatin availability. Hotspots of extreme TE enrichment occur around certain XGFs. We find, in aphids of agricultural importance, particular enrichment of TEs around cytochrome P450 genes with known functions in the detoxification of synthetic insecticides. Our results provide evidence supporting a general role for TEs as a source of genomic variation at host XGFs and highlight the existence of considerable variability in TE content across XGFs and host species. These findings show the need for detailed functional verification analyses to clarify the significance of individual TE insertions and elucidate underlying mechanisms at TE-XGF hotspots.
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Affiliation(s)
- Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Adam Pym
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
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9
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Pulido M, Casacuberta JM. Transposable element evolution in plant genome ecosystems. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102418. [PMID: 37459733 DOI: 10.1016/j.pbi.2023.102418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/22/2023] [Accepted: 06/20/2023] [Indexed: 09/18/2023]
Abstract
The relationship of transposable elements (TEs) with their host genomes has usually been seen as an arms race between TEs and their host genomes. Consequently, TEs are supposed to amplify by bursts of transposition, when the TE escapes host surveillance, followed by long periods of TE quiescence and efficient host control. Recent data obtained from an increasing number of assembled plant genomes and resequencing population datasets show that TE dynamics is more complex and varies among TE families and their host genomes. This variation ranges from large genomes that accommodate large TE populations to genomes that are very active in TE elimination, and from inconspicuous elements with very low activity to elements with high transposition and elimination rates. The dynamics of each TE family results from a long history of interaction with the host in a genome populated by many other TE families, very much like an evolving ecosystem.
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Affiliation(s)
- Marc Pulido
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
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10
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Zhao P, Peng C, Fang L, Wang Z, Liu GE. Taming transposable elements in livestock and poultry: a review of their roles and applications. Genet Sel Evol 2023; 55:50. [PMID: 37479995 PMCID: PMC10362595 DOI: 10.1186/s12711-023-00821-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/30/2023] [Indexed: 07/23/2023] Open
Abstract
Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.
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Affiliation(s)
- Pengju Zhao
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Chen Peng
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Zhengguang Wang
- Hainan Institute of Zhejiang University, Hainan Sanya, 572000, China.
- College of Animal Sciences, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA.
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11
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Castanera R, Morales-Díaz N, Gupta S, Purugganan M, Casacuberta JM. Transposons are important contributors to gene expression variability under selection in rice populations. eLife 2023; 12:RP86324. [PMID: 37467142 PMCID: PMC10393045 DOI: 10.7554/elife.86324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
Transposable elements (TEs) are an important source of genome variability. Here, we analyze their contribution to gene expression variability in rice by performing a TE insertion polymorphism expression quantitative trait locus mapping using expression data from 208 varieties from the Oryza sativa ssp. indica and O. sativa ssp. japonica subspecies. Our data show that TE insertions are associated with changes of expression of many genes known to be targets of rice domestication and breeding. An important fraction of these insertions were already present in the rice wild ancestors, and have been differentially selected in indica and japonica rice populations. Taken together, our results show that small changes of expression in signal transduction genes induced by TE insertions accompany the domestication and adaptation of rice populations.
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Affiliation(s)
- Raúl Castanera
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Noemia Morales-Díaz
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - Sonal Gupta
- Center for Genomics and Systems Biology, New York University, New York, United States
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University, New York, United States
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Josep M Casacuberta
- Centre for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
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12
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Galbraith JD, Hayward A. The influence of transposable elements on animal colouration. Trends Genet 2023:S0168-9525(23)00091-4. [PMID: 37183153 DOI: 10.1016/j.tig.2023.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/16/2023]
Abstract
Transposable elements (TEs) are mobile genetic sequences present within host genomes. TEs can contribute to the evolution of host traits, since transposition is mutagenic and TEs often contain host regulatory and protein coding sequences. We review cases where TEs influence animal colouration, reporting major patterns and outstanding questions. TE-induced colouration phenotypes typically arise via introduction of novel regulatory sequences and splice sites, affecting pigment cell development or pigment synthesis. We discuss if particular TE types may be more frequently involved in the evolution of colour variation in animals, given that examples involving long terminal repeat (LTR) elements appear to dominate. Currently, examples of TE-induced colouration phenotypes in animals mainly concern model and domesticated insect and mammal species. However, several influential recent examples, coupled with increases in genome sequencing, suggest cases reported from wild species will increase considerably.
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Affiliation(s)
- James D Galbraith
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK.
| | - Alexander Hayward
- Faculty of Environment, Science and Economy, University of Exeter, Cornwall TR10 9FE, UK.
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13
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Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KAM, Moreno-Santillán DD, Crookshanks C, Roberts J, Garcia C, Johnson MG, Densmore LD, Stevens RD, Rosen J, Storer JM, Hubley R, Smit AFA, Dávalos LM, Karlsson EK, Lindblad-Toh K, Ray DA. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science 2023; 380:eabn1430. [PMID: 37104570 PMCID: PMC11103246 DOI: 10.1126/science.abn1430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 10/28/2022] [Indexed: 04/29/2023]
Abstract
We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.
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Affiliation(s)
- Austin B. Osmanski
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Nicole S. Paulat
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Jenny Korstian
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Jenna R. Grimshaw
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Michaela Halsey
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | | | | | | | - Jacquelyn Roberts
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Carlos Garcia
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Matthew G. Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | | | - Richard D. Stevens
- Department of Natural Resources Management and Natural Science Research Laboratory, Museum of Texas Tech University, Lubbock, TX, USA
| | | | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | - Liliana M. Dávalos
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, NY, USA
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, NY, USA
| | - Elinor K. Karlsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA, USA
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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14
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Mueller RL, Cressler CE, Schwartz RS, Chong RA, Butler M. Metamorphosis Imposes Variable Constraints on Genome Expansion through Effects on Development. Integr Org Biol 2023; 5:obad015. [PMID: 37143961 PMCID: PMC10153748 DOI: 10.1093/iob/obad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 02/25/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023] Open
Abstract
Genome size varies ∼100,000-fold across eukaryotes and has long been hypothesized to be influenced by metamorphosis in animals. Transposable element accumulation has been identified as a major driver of increase, but the nature of constraints limiting the size of genomes has remained unclear, even as traits such as cell size and rate of development co-vary strongly with genome size. Salamanders, which possess diverse metamorphic and non-metamorphic life histories, join the lungfish in having the largest vertebrate genomes-3 to 40 times that of humans-as well as the largest range of variation in genome size. We tested 13 biologically-inspired hypotheses exploring how the form of metamorphosis imposes varying constraints on genome expansion in a broadly representative phylogeny containing 118 species of salamanders. We show that metamorphosis during which animals undergo the most extensive and synchronous remodeling imposes the most severe constraint against genome expansion, with the severity of constraint decreasing with reduced extent and synchronicity of remodeling. More generally, our work demonstrates the potential for broader interpretation of phylogenetic comparative analysis in exploring the balance of multiple evolutionary pressures shaping phenotypic evolution.
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Affiliation(s)
| | - C E Cressler
- School of Biological Sciences, University of Nebraska Lincoln, Lincoln, NE 68588, USA
| | - R S Schwartz
- Department of Biological Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - R A Chong
- School of Life Sciences, University of Hawai'i, Honolulu, HI 96822, USA
| | - M Butler
- School of Life Sciences, University of Hawai'i, Honolulu, HI 96822, USA
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15
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Wang J, Yuan L, Tang J, Liu J, Sun C, Itgen MW, Chen G, Sessions SK, Zhang G, Mueller RL. Transposable element and host silencing activity in gigantic genomes. Front Cell Dev Biol 2023; 11:1124374. [PMID: 36910142 PMCID: PMC9998948 DOI: 10.3389/fcell.2023.1124374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing via two pathways-the piRNA pathway and KRAB-ZFP transcriptional repression-in the male and female gonads of Ranodon sibiricus, a salamander species with a ∼21 Gb genome. We quantify 1) genomic TE diversity, 2) TE expression, and 3) small RNA expression and find a significant relationship between the expression of piRNAs and TEs they target for silencing in both ovaries and testes. We also quantified TE silencing pathway gene expression in R. sibiricus and 14 other vertebrates with genome sizes ranging from 1 to 130 Gb and find no association between pathway expression and genome size. Taken together, our results reveal that the gigantic R. sibiricus genome includes at least 19 putatively active TE superfamilies, all of which are targeted by the piRNA pathway in proportion to their expression levels, suggesting comprehensive piRNA-mediated silencing. Testes have higher TE expression than ovaries, suggesting that they may contribute more to the species' high genomic TE load. We posit that apparently conflicting interpretations of TE silencing and genomic gigantism in the literature, as well as the absence of a correlation between TE silencing pathway gene expression and genome size, can be reconciled by considering whether the TE community or the host is currently "on the attack" in the arms race dynamic.
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Affiliation(s)
- Jie Wang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Liang Yuan
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Jiaxing Tang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China
| | - Jiongyu Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Cheng Sun
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Michael W Itgen
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Guiying Chen
- College of Life Sciences, Sichuan Normal University, Chengdu, China
| | | | - Guangpu Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,College of Life Sciences, Sichuan Normal University, Chengdu, China
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16
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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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17
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Cong Y, Ye X, Mei Y, He K, Li F. Transposons and Non-coding Regions Drive the Intrafamily Differences of Genome Size in Insects. iScience 2022; 25:104873. [PMID: 36039293 PMCID: PMC9418806 DOI: 10.1016/j.isci.2022.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/24/2022] [Accepted: 07/29/2022] [Indexed: 11/02/2022] Open
Abstract
Genome size (GS) can vary considerably between phylogenetically close species, but the landscape of GS changes in insects remain largely unclear. To better understand the specific evolutionary factors that determine GS in insects, we examined flow cytometry-based published GS data from 1,326 insect species, spanning 700 genera, 155 families, and 21 orders. Model fitting showed that GS generally followed an Ornstein–Uhlenbeck adaptive evolutionary model in Insecta overall. Ancestral reconstruction indicated a likely GS of 1,069 Mb, suggesting that most insect clades appeared to undergo massive genome expansions or contractions. Quantification of genomic components in 56 species from nine families in four insect orders revealed that the proliferation of transposable elements contributed to high variation in GS between close species, such as within Coleoptera. This study sheds lights on the pattern of GS variation in insects and provides a better understanding of insect GS evolution. The most comprehensive variation pattern of insects genome size (GS) to date GS evolution of the Insecta was reflected by the adaptive Ornstein–Uhlenbeck model Ancestral state of insect GS was estimated to be ∼1 Gb Intrafamily GS variations were driven by recent transpositions and non-coding regions
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18
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Gu X, Su Y, Wang T. 转座元件对植物基因组进化、表观遗传和适应性的作用. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Do Ty3/Gypsy Transposable Elements Play Preferential Roles in Sex Chromosome Differentiation? Life (Basel) 2022; 12:life12040522. [PMID: 35455013 PMCID: PMC9025612 DOI: 10.3390/life12040522] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/13/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) comprise a substantial portion of eukaryotic genomes. They have the unique ability to integrate into new locations and serve as the main source of genomic novelties by mediating chromosomal rearrangements and regulating portions of functional genes. Recent studies have revealed that TEs are abundant in sex chromosomes. In this review, we propose evolutionary relationships between specific TEs, such as Ty3/Gypsy, and sex chromosomes in different lineages based on the hypothesis that these elements contributed to sex chromosome differentiation processes. We highlight how TEs can drive the dynamics of sex-determining regions via suppression recombination under a selective force to affect the organization and structural evolution of sex chromosomes. The abundance of TEs in the sex-determining regions originates from TE-poor genomic regions, suggesting a link between TE accumulation and the emergence of the sex-determining regions. TEs are generally considered to be a hallmark of chromosome degeneration. Finally, we outline recent approaches to identify TEs and study their sex-related roles and effects in the differentiation and evolution of sex chromosomes.
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20
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Almeida MV, Vernaz G, Putman AL, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet 2022; 38:529-553. [DOI: 10.1016/j.tig.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022]
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21
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Timmons CM, Shazib SUA, Katz LA. Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution. J Eukaryot Microbiol 2022; 69:e12891. [PMID: 35100457 DOI: 10.1111/jeu.12891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/20/2022] [Accepted: 01/22/2022] [Indexed: 11/27/2022]
Abstract
Mobile genetic elements (MGEs) are transient genetic material that can move either within a single organism's genome or between individuals or species. While historically considered 'junk' DNA (i.e. deleterious or at best neutral), more recent studies reveal the adaptive advantages MGEs provide in lineages across the tree of life. Ciliates, a group of single-celled microbial eukaryotes characterized by nuclear dimorphism, exemplify how epigenetic influences from MGEs shape genome architecture and patterns of molecular evolution. Ciliate nuclear dimorphism may have evolved as a response to transposon invasion and ciliates have since co-opted transposons to carry out programmed DNA deletion. Another example of the effect of MGEs is in providing mechanisms for lateral gene transfer from bacteria, which introduces genetic diversity and, in several cases, drives ecological specialization in ciliates. As a third example, the integration of viral DNA, likely through transduction, provides new genetic material and can change the way host cells defend themselves against other viral pathogens. We argue that the acquisition of MGEs through non-Mendelian patterns of inheritance, coupled with their effects on ciliate genome architecture and expression and persistence throughout evolutionary history, exemplify how the transmission of mobile elements should be considered a mechanism of transgenerational epigenetic inheritance.
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Affiliation(s)
- Caitlin M Timmons
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Shahed U A Shazib
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
| | - Laura A Katz
- Department of Biological Sciences, Smith College, Northampton, Massachusetts, 01063, USA
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22
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Blasio F, Prieto P, Pradillo M, Naranjo T. Genomic and Meiotic Changes Accompanying Polyploidization. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11010125. [PMID: 35009128 PMCID: PMC8747196 DOI: 10.3390/plants11010125] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 05/04/2023]
Abstract
Hybridization and polyploidy have been considered as significant evolutionary forces in adaptation and speciation, especially among plants. Interspecific gene flow generates novel genetic variants adaptable to different environments, but it is also a gene introgression mechanism in crops to increase their agronomical yield. An estimate of 9% of interspecific hybridization has been reported although the frequency varies among taxa. Homoploid hybrid speciation is rare compared to allopolyploidy. Chromosome doubling after hybridization is the result of cellular defects produced mainly during meiosis. Unreduced gametes, which are formed at an average frequency of 2.52% across species, are the result of altered spindle organization or orientation, disturbed kinetochore functioning, abnormal cytokinesis, or loss of any meiotic division. Meiotic changes and their genetic basis, leading to the cytological diploidization of allopolyploids, are just beginning to be understood especially in wheat. However, the nature and mode of action of homoeologous recombination suppressor genes are poorly understood in other allopolyploids. The merger of two independent genomes causes a deep modification of their architecture, gene expression, and molecular interactions leading to the phenotype. We provide an overview of genomic changes and transcriptomic modifications that particularly occur at the early stages of allopolyploid formation.
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Affiliation(s)
- Francesco Blasio
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4048, 14080 Cordova, Spain;
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Tomás Naranjo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
- Correspondence:
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23
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Dal Grande F, Jamilloux V, Choisne N, Calchera A, Rolshausen G, Petersen M, Schulz M, Nilsson MA, Schmitt I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. BIOLOGY 2021; 11:biology11010024. [PMID: 35053022 PMCID: PMC8773270 DOI: 10.3390/biology11010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)69-7542-1856
| | - Véronique Jamilloux
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Nathalie Choisne
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Gregor Rolshausen
- Senckenberg Center for Wildlife Genetics, Clamecystrasse 12, 63571 Gelnhausen, Germany;
| | - Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany;
| | - Meike Schulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Strasse. 9, 60438 Frankfurt am Main, Germany
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24
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Muller H, Loiseau V, Guillier S, Cordaux R, Gilbert C. Assessing the Impact of a Viral Infection on the Expression of Transposable Elements in the Cabbage Looper Moth (Trichoplusia ni). Genome Biol Evol 2021; 13:evab231. [PMID: 34613390 PMCID: PMC8634313 DOI: 10.1093/gbe/evab231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Most studies of stress-induced transposable element (TE) expression have so far focused on abiotic sources of stress. Here, we analyzed the impact of an infection by the AcMNPV baculovirus on TE expression in a cell line (Tnms42) and midgut tissues of the cabbage looper moth (Trichoplusia ni). We find that a large fraction of TE families (576/636 in Tnms42 cells and 503/612 in midgut) is lowly expressed or not expressed at all [≤ 4 transcripts per million (TPM)] in the uninfected condition (median TPM of 0.37 in Tnms42 and 0.46 in midgut cells). In the infected condition, a total of 62 and 187 TE families were differentially expressed (DE) in midgut and Tnms42 cells, respectively, with more up- (46) than downregulated (16) TE families in the former and as many up- (91) as downregulated (96) TE families in the latter. Expression log2 fold changes of DE TE families varied from -4.95 to 9.11 in Tnms42 cells and from -4.28 to 7.66 in midgut. Large variations in expression profiles of DE TEs were observed depending on the type of cells and on time after infection. Overall, the impact of AcMNPV on TE expression in T. ni is moderate but potentially sufficient to affect TE activity and genome architecture. Interestingly, one host-derived TE integrated into AcMNPV genomes is highly expressed in infected Tnms42 cells. This result shows that virus-borne TEs can be expressed, further suggesting that they may be able to transpose and that viruses may act as vectors of horizontal transfer of TEs in insects.
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Affiliation(s)
- Héloïse Muller
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Vincent Loiseau
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Sandra Guillier
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Universite de Poitiers, CNRS, France
| | - Clément Gilbert
- Universite Paris Saclay, CNRS, IRD, UMR Evolution, Genomes, Comportement et Ecologie, Gif-sur-Yvette, France
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25
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Wang Y, Wang Q, Wu Z, Han GZ. Segregating Complete Tf2 Elements Are Largely Neutral in Fission Yeast. Genome Biol Evol 2021; 13:6430117. [PMID: 34791222 PMCID: PMC8634392 DOI: 10.1093/gbe/evab254] [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] [Accepted: 11/10/2021] [Indexed: 11/14/2022] Open
Abstract
Transposable elements (TEs) comprise a large proportion of the eukaryote genomes. Yet it remains poorly understood how TEs influence the fitness of the hosts carrying them. Here, we empirically test the impact of TEs on the host fitness in the fission yeast Schizosaccharomyces pombe. We find that two families of TEs (Tf1 and Tf2 elements), both of which belong to long terminal repeat retrotransposons, are highly polymorphic among individual S. pombe strains. Only 13 complete Tf2 elements are identified in S. pombe laboratory strain 972. These 13 Tf2 elements integrated into host genomes in very recent time and are segregating within the S. pombe population. Through knocking out each of the 13 Tf2 elements in S. pombe strain 972, we find Tf2 knockout does not affect the host fitness, and Tf2 elements do not alter the expression of nearby genes. Challenged by diverse forms of stress, the Tf2 knockout strains do not exhibit different growth rates from wild-type strain. Together, we conclude that segregating complete Tf2 elements insertions are largely neutral to host fitness in the fission yeast. Our study provides genome-wide empirical support for the selfish nature of TEs in fission yeast.
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Affiliation(s)
- Yan Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qin Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhiwei Wu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guan-Zhu Han
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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26
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Riba A, Fumagalli MR, Caselle M, Osella M. A Model-Driven Quantitative Analysis of Retrotransposon Distributions in the Human Genome. Genome Biol Evol 2021; 12:2045-2059. [PMID: 32986810 PMCID: PMC7750997 DOI: 10.1093/gbe/evaa201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2020] [Indexed: 12/21/2022] Open
Abstract
Retrotransposons, DNA sequences capable of creating copies of themselves, compose about half of the human genome and played a central role in the evolution of mammals. Their current position in the host genome is the result of the retrotranscription process and of the following host genome evolution. We apply a model from statistical physics to show that the genomic distribution of the two most populated classes of retrotransposons in human deviates from random placement, and that this deviation increases with time. The time dependence suggests a major role of the host genome dynamics in shaping the current retrotransposon distributions. Focusing on a neutral scenario, we show that a simple model based on random placement followed by genome expansion and sequence duplications can reproduce the empirical retrotransposon distributions, even though more complex and possibly selective mechanisms can have contributed. Besides the inherent interest in understanding the origin of current retrotransposon distributions, this work sets a general analytical framework to analyze quantitatively the effects of genome evolutionary dynamics on the distribution of genomic elements.
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Affiliation(s)
| | - Maria Rita Fumagalli
- Institute of Biophysics - CNR, National Research Council, Genova, Italy.,Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milano, Italy
| | - Michele Caselle
- Department of Physics and INFN, University of Torino, Torino, Italy
| | - Matteo Osella
- Department of Physics and INFN, University of Torino, Torino, Italy
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27
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Drouin M, Hénault M, Hallin J, Landry CR. Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:729264. [PMID: 37744137 PMCID: PMC10512236 DOI: 10.3389/ffunb.2021.729264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 09/26/2023]
Abstract
Transposable element (TE) insertions are a source of structural variation and can cause genetic instability and gene expression changes. A host can limit the spread of TEs with various repression mechanisms. Many examples of plant and animal interspecific hybrids show disrupted TE repression leading to TE propagation. Recent studies in yeast did not find any increase in transposition rate in hybrids. However, this does not rule out the possibility that the transcriptional or translational activity of TEs increases following hybridization because of a disruption of the host TE control mechanisms. Thus, whether total expression of a TE family is higher in hybrids than in their parental species remains to be examined. We leveraged publically available RNA-seq and ribosomal profiling data on yeast artificial hybrids of the Saccharomyces genus and performed differential expression analysis of their LTR retrotransposons (Ty elements). Our analyses of total mRNA levels show that Ty elements are generally not differentially expressed in hybrids, even when the hybrids are exposed to a low temperature stress condition. Overall, only 2/26 Ty families show significantly higher expression in the S. cerevisiae × S. uvarum hybrids while there are 3/26 showing significantly lower expression in the S. cerevisiae x S. paradoxus hybrids. Our analysis of ribosome profiling data of S. cerevisiae × S. paradoxus hybrids shows similar translation efficiency of Ty in both parents and hybrids, except for Ty1_cer showing higher translation efficiency. Overall, our results do not support the hypothesis that hybridization could act as a systematic trigger of TE expression in yeast and suggest that the impact of hybridization on TE activity is strain and TE specific.
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Affiliation(s)
- Marika Drouin
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- PROTEO - Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
| | - Mathieu Hénault
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- PROTEO - Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
| | - Johan Hallin
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- PROTEO - Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
| | - Christian R. Landry
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
- PROTEO - Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, Québec, QC, Canada
- Centre de Recherche en Données Massives de l'Université Laval, Université Laval, Québec, QC, Canada
- Département de Biologie, Université Laval, Québec, QC, Canada
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28
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Patil AB, Vijay N. Repetitive genomic regions and the inference of demographic history. Heredity (Edinb) 2021; 127:151-166. [PMID: 34002046 PMCID: PMC8322061 DOI: 10.1038/s41437-021-00443-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 02/03/2023] Open
Abstract
Inference of demographic histories using whole-genome datasets has provided insights into diversification, adaptation, hybridization, and plant-pathogen interactions, and stimulated debate on the impact of anthropogenic interventions and past climate on species demography. However, the impact of repetitive genomic regions on these inferences has mostly been ignored by masking of repeats. We use the Populus trichocarpa genome (Pop_tri_v3) to show that masking of repeat regions leads to lower estimates of effective population size (Ne) in the distant past in contrast to an increase in Ne estimates in recent times. However, in human datasets, masking of repeats resulted in lower estimates of Ne at all time points. We demonstrate that repeats affect demographic inferences using diverse methods like PSMC, MSMC, SMC++, and the Stairway plot. Our genomic analysis revealed that the biases in Ne estimates were dependent on the repeat class type and its abundance in each atomic interval. Notably, we observed a weak, yet consistently significant negative correlation between the repeat abundance of an atomic interval and the Ne estimates for that interval, which potentially reflects the recombination rate variation within the genome. The rationale for the masking of repeats has been that variants identified within these regions are erroneous. We find that polymorphisms in some repeat classes occur in callable regions and reflect reliable coalescence histories (e.g., LTR Gypsy, LTR Copia). The current demography inference methods do not handle repeats explicitly, and hence the effect of individual repeat classes needs careful consideration in comparative analysis. Deciphering the repeat demographic histories might provide a clear understanding of the processes involved in repeat accumulation.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India.
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29
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Stritt C, Thieme M, Roulin AC. Rare transposable elements challenge the prevailing view of transposition dynamics in plants. AMERICAN JOURNAL OF BOTANY 2021; 108:1310-1314. [PMID: 34415576 PMCID: PMC9290919 DOI: 10.1002/ajb2.1709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 06/01/2023]
Affiliation(s)
- Christoph Stritt
- Institute for Plant and Microbial BiologyUniversity of ZurichZollikerstrasse, 107, 8008ZurichSwitzerland
| | - Michael Thieme
- Institute for Plant and Microbial BiologyUniversity of ZurichZollikerstrasse, 107, 8008ZurichSwitzerland
| | - Anne C. Roulin
- Institute for Plant and Microbial BiologyUniversity of ZurichZollikerstrasse, 107, 8008ZurichSwitzerland
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30
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Shen D, Gao B, Miskey C, Chen C, Sang Y, Zong W, Wang S, Wang Y, Wang X, Ivics Z, Song C. Multiple Invasions of Visitor, a DD41D Family of Tc1/mariner Transposons, throughout the Evolution of Vertebrates. Genome Biol Evol 2021; 12:1060-1073. [PMID: 32602886 DOI: 10.1093/gbe/evaa135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
Although the DD41D (named as Visitor, VS) family of Tc1/mariner transposons was discovered in Arthropods and Mollusca, the evolution profile of this family is still largely unknown. We found that VS is widespread in the animal kingdom, including 140 species of 18 orders in invertebrates and 30 species of 12 orders in vertebrates, and one land plant species. Our data revealed multiple horizontal transfer events in both invertebrates and vertebrates and invasion into multiple lineages of mammals, including Chiroptera (seven species), Dasyuromorphia/Marsupialia (one species), Didelphimorphia/Marsupialia (one species), Diprotodontia/Marsupialia (two species), and Primates (one species). Phylogenetic analysis revealed a close relationship of VSs to DD37D/maT and DD34D/mariner and confirmed that VSs with the DD40D signature identified previously are not a distinct family but originated from DD41D/VS. Age analysis revealed that the most recent invasion of VSs was found in ray-finned fishes and a toad, followed by relatively young invasions in bats and marsupials, whereas VSs in mammals, jawless fishes, and lizards were mainly represented by ancient copies, suggesting old age. Phylogenetic analyses and comparison of pairwise distances between VSs and recombination-activating gene 1 (RAG1) support horizontal transfer events of VSs in vertebrates. The intact VSs from bats were nonfunctional as determined by the transposition activity assay. Some vertebrate lineages and species were identified as the hot hosts of Tc1/mariner transposons. Overall, our study presents the evolution profile of VSs and suggests that VSs play roles in diversifying and shaping the genomes of diverse animal lineages.
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Affiliation(s)
- Dan Shen
- College of Animal Science & Technology, Yangzhou University, China.,Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Bo Gao
- College of Animal Science & Technology, Yangzhou University, China
| | - Csaba Miskey
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, China
| | - Yatong Sang
- College of Animal Science & Technology, Yangzhou University, China
| | - Wencheng Zong
- College of Animal Science & Technology, Yangzhou University, China
| | - Saisai Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Yali Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, China
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, China
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31
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Lorrain C, Feurtey A, Möller M, Haueisen J, Stukenbrock E. Dynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses. G3-GENES GENOMES GENETICS 2021; 11:6173990. [PMID: 33724368 PMCID: PMC8759822 DOI: 10.1093/g3journal/jkab068] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/19/2021] [Indexed: 01/29/2023]
Abstract
Transposable elements (TEs) impact genome plasticity, architecture, and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defense mechanisms that can counter-balance TE expansion and spread. Closely related species can harbor drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here, we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and repeat-induced point mutation signatures in 26 genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The 26 genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation, and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.
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Affiliation(s)
- Cécile Lorrain
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany.,Université de Lorraine/INRAE, UMR 1136 Interactions Arbres/Microorganismes, INRAE Centre Grand Est-Nancy, Champenoux 54280, France
| | - Alice Feurtey
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Mareike Möller
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Janine Haueisen
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
| | - Eva Stukenbrock
- Environmental Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany.,Environmental Genomics, Christian-Albrechts University of Kiel, Kiel 24118, Germany
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32
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Ohtani H, Iwasaki YW. Rewiring of chromatin state and gene expression by transposable elements. Dev Growth Differ 2021; 63:262-273. [DOI: 10.1111/dgd.12735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 01/18/2023]
Affiliation(s)
- Hitoshi Ohtani
- Laboratory of Genome and Epigenome Dynamics Department of Animal Sciences Graduate School of Bioagricultural Sciences Nagoya University Nagoya Japan
| | - Yuka W. Iwasaki
- Department of Molecular Biology Keio University School of Medicine Tokyo Japan
- Japan Science and Technology Agency (JST) Precursory Research for Embryonic Science and Technology (PRESTO) Saitama Japan
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33
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RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays. PLoS Genet 2021; 17:e1009326. [PMID: 34125827 PMCID: PMC8224964 DOI: 10.1371/journal.pgen.1009326] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/24/2021] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
In large complex plant genomes, RNA-directed DNA methylation (RdDM) ensures that epigenetic silencing is maintained at the boundary between genes and flanking transposable elements. In maize, RdDM is dependent on Mediator of Paramutation1 (Mop1), a gene encoding a putative RNA dependent RNA polymerase. Here we show that although RdDM is essential for the maintenance of DNA methylation of a silenced MuDR transposon in maize, a loss of that methylation does not result in a restoration of activity. Instead, heritable maintenance of silencing is maintained by histone modifications. At one terminal inverted repeat (TIR) of this element, heritable silencing is mediated via histone H3 lysine 9 dimethylation (H3K9me2), and histone H3 lysine 27 dimethylation (H3K27me2), even in the absence of DNA methylation. At the second TIR, heritable silencing is mediated by histone H3 lysine 27 trimethylation (H3K27me3), a mark normally associated with somatically inherited gene silencing. We find that a brief exposure of high temperature in a mop1 mutant rapidly reverses both of these modifications in conjunction with a loss of transcriptional silencing. These reversals are heritable, even in mop1 wild-type progeny in which methylation is restored at both TIRs. These observations suggest that DNA methylation is neither necessary to maintain silencing, nor is it sufficient to initiate silencing once has been reversed. However, given that heritable reactivation only occurs in a mop1 mutant background, these observations suggest that DNA methylation is required to buffer the effects of environmental stress on transposable elements. Most plant genomes are mostly transposable elements (TEs), most of which are held in check by modifications of both DNA and histones. The bulk of silenced TEs are associated with methylated DNA and histone H3 lysine 9 dimethylation (H3K9me2). In contrast, epigenetically silenced genes are often associated with histone lysine 27 trimethylation (H3K27me3). Although stress can affect each of these modifications, plants are generally competent to rapidly reset them following that stress. Here we demonstrate that although DNA methylation is not required to maintain silencing of the MuDR element, it is essential for preventing heat-induced, stable and heritable changes in both H3K9me2 and H3K27me3 at this element, and for concomitant changes in transcriptional activity. These finding suggest that RdDM acts to buffer the effects of heat on silenced transposable elements, and that a loss of DNA methylation under conditions of stress can have profound and long-lasting effects on epigenetic silencing in maize.
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34
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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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35
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Miller WB, Enguita FJ, Leitão AL. Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution. Cells 2021; 10:1125. [PMID: 34066959 PMCID: PMC8148535 DOI: 10.3390/cells10051125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 12/16/2022] Open
Abstract
Neo-Darwinism presumes that biological variation is a product of random genetic replication errors and natural selection. Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving. CBE upholds that the cornerstone of biology is the intelligent measuring cell. Since all biological information that is available to cells is ambiguous, multicellularity arises from the cellular requirement to maximize the validity of available environmental information. This is best accomplished through collective measurement purposed towards maintaining and optimizing individual cellular states of homeorhesis as dynamic flux that sustains cellular equipoise. The collective action of the multicellular measurement and assessment of information and its collaborative communication is natural cellular engineering. Its yield is linked cellular ecologies and mutualized niche constructions that comprise biofilms and holobionts. In this context, biological variation is the product of collective differential assessment of ambiguous environmental cues by networking intelligent cells. Such concerted action is enabled by non-random natural genomic editing in response to epigenetic impacts and environmental stresses. Random genetic activity can be either constrained or deployed as a 'harnessing of stochasticity'. Therefore, genes are cellular tools. Selection filters cellular solutions to environmental stresses to assure continuous cellular-organismal-environmental complementarity. Since all multicellular eukaryotes are holobionts as vast assemblages of participants of each of the three cellular domains (Prokaryota, Archaea, Eukaryota) and the virome, multicellular variation is necessarily a product of co-engineering among them.
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Affiliation(s)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal;
| | - Ana Lúcia Leitão
- MEtRICs, Department of Sciences and Technology of Biomass, NOVA School of Science and Technology, FCT NOVA, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal;
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36
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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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37
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Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species. Genes (Basel) 2021; 12:genes12020175. [PMID: 33513919 PMCID: PMC7911463 DOI: 10.3390/genes12020175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/19/2022] Open
Abstract
Pericentromeric heterochromatin in Drosophila generally consists of repetitive DNA, forming the environment associated with gene silencing. Despite the expanding knowledge of the impact of transposable elements (TEs) on the host genome, little is known about the evolution of pericentromeric heterochromatin, its structural composition, and age. During the evolution of the Drosophilidae, hundreds of genes have become embedded within pericentromeric regions yet retained activity. We investigated a pericentromeric heterochromatin fragment found in D. virilis and related species, describing the evolution of genes in this region and the age of TE invasion. Regardless of the heterochromatic environment, the amino acid composition of the genes is under purifying selection. However, the selective pressure affects parts of genes in varying degrees, resulting in expansion of gene introns due to TEs invasion. According to the divergence of TEs, the pericentromeric heterochromatin of the species of virilis group began to form more than 20 million years ago by invasions of retroelements, miniature inverted repeat transposable elements (MITEs), and Helitrons. Importantly, invasions into the heterochromatin continue to occur by TEs that fall under the scope of piRNA silencing. Thus, the pericentromeric heterochromatin, in spite of its ability to induce silencing, has the means for being dynamic, incorporating the regions of active transcription.
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38
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Mulholland CB, Nishiyama A, Ryan J, Nakamura R, Yiğit M, Glück IM, Trummer C, Qin W, Bartoschek MD, Traube FR, Parsa E, Ugur E, Modic M, Acharya A, Stolz P, Ziegenhain C, Wierer M, Enard W, Carell T, Lamb DC, Takeda H, Nakanishi M, Bultmann S, Leonhardt H. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals. Nat Commun 2020; 11:5972. [PMID: 33235224 PMCID: PMC7686362 DOI: 10.1038/s41467-020-19603-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.
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Affiliation(s)
- Christopher B Mulholland
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Joel Ryan
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Merve Yiğit
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Ivo M Glück
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Carina Trummer
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Weihua Qin
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael D Bartoschek
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Franziska R Traube
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Miha Modic
- The Francis Crick Institute and UCL Queen Square Institute of Neurology, London, UK
| | - Aishwarya Acharya
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Paul Stolz
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Christoph Ziegenhain
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Wolfgang Enard
- Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Thomas Carell
- Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Don C Lamb
- Physical Chemistry, Department of Chemistry, Center for Nanoscience, Nanosystems Initiative Munich and Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
| | - Heinrich Leonhardt
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), Human Biology and BioImaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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39
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Greenhalgh R, Dermauw W, Glas JJ, Rombauts S, Wybouw N, Thomas J, Alba JM, Pritham EJ, Legarrea S, Feyereisen R, Van de Peer Y, Van Leeuwen T, Clark RM, Kant MR. Genome streamlining in a minute herbivore that manipulates its host plant. eLife 2020; 9:56689. [PMID: 33095158 PMCID: PMC7738191 DOI: 10.7554/elife.56689] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.
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Affiliation(s)
- Robert Greenhalgh
- School of Biological Sciences, University of Utah, Salt Lake City, United States
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Joris J Glas
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Nicky Wybouw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Juan M Alba
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Saioa Legarrea
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Richard M Clark
- School of Biological Sciences, University of Utah, Salt Lake City, United States.,Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, United States
| | - Merijn R Kant
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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40
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Bourgeois Y, Ruggiero RP, Hariyani I, Boissinot S. Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidences and simulations. PLoS Genet 2020; 16:e1009082. [PMID: 33017388 PMCID: PMC7561263 DOI: 10.1371/journal.pgen.1009082] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 10/15/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
The interactions between transposable elements (TEs) and their hosts constitute one of the most profound co-evolutionary processes found in nature. The population dynamics of TEs depends on factors specific to each TE families, such as the rate of transposition and insertional preference, the demographic history of the host and the genomic landscape. How these factors interact has yet to be investigated holistically. Here we are addressing this question in the green anole (Anolis carolinensis) whose genome contains an extraordinary diversity of TEs (including non-LTR retrotransposons, SINEs, LTR-retrotransposons and DNA transposons). We observed a positive correlation between recombination rate and frequency of TEs and densities for LINEs, SINEs and DNA transposons. For these elements, there was a clear impact of demography on TE frequency and abundance, with a loss of polymorphic elements and skewed frequency spectra in recently expanded populations. On the other hand, some LTR-retrotransposons displayed patterns consistent with a very recent phase of intense amplification. To determine how demography, genomic features and intrinsic properties of TEs interact we ran simulations using SLiM3. We determined that i) short TE insertions are not strongly counter-selected, but long ones are, ii) neutral demographic processes, linked selection and preferential insertion may explain positive correlations between average TE frequency and recombination, iii) TE insertions are unlikely to have been massively recruited in recent adaptation. We demonstrate that deterministic and stochastic processes have different effects on categories of TEs and that a combination of empirical analyses and simulations can disentangle these mechanisms.
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Affiliation(s)
- Yann Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, United Kingdom
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
- * E-mail: (YB); (SB)
| | - Robert P. Ruggiero
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
- Department of Biology, Southeast Missouri State University, Cape Girardeau, MO, United States of America
| | - Imtiyaz Hariyani
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island Campus, Abu Dhabi, United Arab Emirates
- * E-mail: (YB); (SB)
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41
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Blommaert J. Genome size evolution: towards new model systems for old questions. Proc Biol Sci 2020; 287:20201441. [PMID: 32842932 PMCID: PMC7482279 DOI: 10.1098/rspb.2020.1441] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
Genome size (GS) variation is a fundamental biological characteristic; however, its evolutionary causes and consequences are the topic of ongoing debate. Whether GS is a neutral trait or one subject to selective pressures, and how strong these selective pressures are, may remain open questions. Fundamentally, the genomic sequences responsible for this variation directly impact the potential evolutionary outcomes and, equally, are the targets of different evolutionary pressures. For example, duplications and deletions of genic regions (large or small) can have immediate and drastic phenotypic effects, while an expansion or contraction of non-coding DNA is less likely to cause catastrophic phenotypic effects. However, in the long term, the accumulation or deletion of ncDNA is likely to have larger effects. Modern sequencing technologies are allowing for the dissection of these proximate causes, but a combination of these new technologies with more traditional evolutionary experiments and approaches could revolutionize this debate and potentially resolve many of these arguments. Here, I discuss an ambitious way forward for GS research, putting it in context of historical debates, theories and sometimes contradictory evidence, and highlighting the promise of combining new sequencing technologies and analytical developments with more traditional experimental evolution approaches.
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Affiliation(s)
- Julie Blommaert
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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42
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Nieto Feliner G, Casacuberta J, Wendel JF. Genomics of Evolutionary Novelty in Hybrids and Polyploids. Front Genet 2020; 11:792. [PMID: 32849797 PMCID: PMC7399645 DOI: 10.3389/fgene.2020.00792] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.
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Affiliation(s)
- Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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43
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Kofler R. piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions. Genome Biol Evol 2020; 12:736-749. [PMID: 32219390 PMCID: PMC7259680 DOI: 10.1093/gbe/evaa064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 12/21/2022] Open
Abstract
piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. Moreover, larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high, and TE insertions are recessive. If piRNA clusters are too small, the load of deleterious TE insertions that accumulate during a TE invasion may drive populations extinct before an effective piRNA-based defense against the TE can be established. Our findings are solely based on three well-supported assumptions: 1) TEs multiply within genomes, 2) TEs are mostly deleterious, and 3) piRNA clusters act as transposon traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, the piRNA clusters of some species meet our observed minimum size requirements, whereas the clusters of other species do not. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, which is possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.
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Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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44
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Naciri Y, Linder HP. The genetics of evolutionary radiations. Biol Rev Camb Philos Soc 2020; 95:1055-1072. [PMID: 32233014 DOI: 10.1111/brv.12598] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
With the realization that much of the biological diversity on Earth has been generated by discrete evolutionary radiations, there has been a rapid increase in research into the biotic (key innovations) and abiotic (key environments) circumstances in which such radiations took place. Here we focus on the potential importance of population genetic structure and trait genetic architecture in explaining radiations. We propose a verbal model describing the stages of an evolutionary radiation: first invading a suitable adaptive zone and expanding both spatially and ecologically through this zone; secondly, diverging genetically into numerous distinct populations; and, finally, speciating. There are numerous examples of the first stage; the difficulty, however, is explaining how genetic diversification can take place from the establishment of a, presumably, genetically depauperate population in a new adaptive zone. We explore the potential roles of epigenetics and transposable elements (TEs), of neutral process such as genetic drift in combination with trait genetic architecture, of gene flow limitation through isolation by distance (IBD), isolation by ecology and isolation by colonization, the possible role of intra-specific competition, and that of admixture and hybridization in increasing the genetic diversity of the founding populations. We show that many of the predictions of this model are corroborated. Most radiations occur in complex adaptive zones, which facilitate the establishment of many small populations exposed to genetic drift and divergent selection. We also show that many radiations (especially those resulting from long-distance dispersal) were established by polyploid lineages, and that many radiating lineages have small genome sizes. However, there are several other predictions which are not (yet) possible to test: that epigenetics has played a role in radiations, that radiations occur more frequently in clades with small gene flow distances, or that the ancestors of radiations had large fundamental niches. At least some of these may be testable in the future as more genome and epigenome data become available. The implication of this model is that many radiations may be hard polytomies because the genetic divergence leading to speciation happens within a very short time, and that the divergence history may be further obscured by hybridization. Furthermore, it suggests that only lineages with the appropriate genetic architecture will be able to radiate, and that such a radiation will happen in a meta-population environment. Understanding the genetic architecture of a lineage may be an essential part of accounting for why some lineages radiate, and some do not.
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Affiliation(s)
- Yamama Naciri
- Plant Systematics and Biodiversity Laboratory, Department of Botany and Plant biology of the University of Geneva, 1 Chemin de l'Impératrice, CH-1292, Chambésy, Geneva, Switzerland
| | - H Peter Linder
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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45
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Abstract
Since Barbara McClintock’s groundbreaking discovery of mobile DNA sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, genome evolution, and human health. Transposable elements are a major constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is profound, as over 100 human heritable diseases have been attributed to transposon insertions. Transposition can be highly mutagenic, perturbing genome integrity and gene expression in a wide range of organisms. This mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the generation of defined mutant libraries. More recently, barcoding applications and methods for RNA-directed transposition are being used towards new phenotypic screens and studies relevant for gene therapy. Thus, transposable elements are significant in affecting biology both
in vivo and in the laboratory, and this review will survey advances in understanding the biological role of transposons and relevant laboratory applications of these powerful molecular tools.
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Affiliation(s)
- Anuj Kumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.,Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
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46
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Abstract
In mammals and invertebrates, the proliferation of an invading transposable element (TE) is thought to be stopped by an insertion into a piRNA cluster. Here, we explore the dynamics of TE invasions under this trap model using computer simulations. We found that piRNA clusters confer a substantial benefit, effectively preventing extinction of host populations from a proliferation of deleterious TEs. TE invasions consist of three distinct phases: first, the TE amplifies within the population, next TE proliferation is stopped by segregating cluster insertions, and finally the TE is inactivated by fixation of a cluster insertion. Suppression by segregating cluster insertions is unstable and bursts of TE activity may yet occur. The transposition rate and the population size mostly influence the length of the phases but not the amount of TEs accumulating during an invasion. Solely, the size of piRNA clusters was identified as a major factor influencing TE abundance. We found that a single nonrecombining cluster is more efficient in stopping invasions than clusters distributed over several chromosomes. Recombination among cluster sites makes it necessary that each diploid carries, on the average, four cluster insertions to stop an invasion. Surprisingly, negative selection in a model with piRNA clusters can lead to a novel equilibrium state, where TE copy numbers remain stable despite only some individuals in a population carrying a cluster insertion. In Drosophila melanogaster, the trap model accounts for the abundance of TEs produced in the germline but fails to predict the abundance of TEs produced in the soma.
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Affiliation(s)
- Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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47
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Lu H, Cui X, Zhao Y, Magwanga RO, Li P, Cai X, Zhou Z, Wang X, Liu Y, Xu Y, Hou Y, Peng R, Wang K, Liu F. Identification of a genome-specific repetitive element in the Gossypium D genome. PeerJ 2020; 8:e8344. [PMID: 31915591 PMCID: PMC6944119 DOI: 10.7717/peerj.8344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/04/2019] [Indexed: 01/15/2023] Open
Abstract
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.
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Affiliation(s)
- Hejun Lu
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Namur, Belgium.,Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xinglei Cui
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yanyan Zhao
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Richard Odongo Magwanga
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.,School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo-Kenya, Bondo, Kenya
| | - Pengcheng Li
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xiaoyan Cai
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Zhongli Zhou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xingxing Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yanchao Xu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuqing Hou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China.,Tarium University, Alar, Xinjiang, China
| | - Fang Liu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
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Lu H, Cui X, Zhao Y, Magwanga RO, Li P, Cai X, Zhou Z, Wang X, Liu Y, Xu Y, Hou Y, Peng R, Wang K, Liu F. Identification of a genome-specific repetitive element in the Gossypium D genome. PeerJ 2020; 8:e8344. [PMID: 31915591 DOI: 10.7287/peerj.preprints.27806v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/04/2019] [Indexed: 05/23/2023] Open
Abstract
The activity of genome-specific repetitive sequences is the main cause of genome variation between Gossypium A and D genomes. Through comparative analysis of the two genomes, we retrieved a repetitive element termed ICRd motif, which appears frequently in the diploid Gossypium raimondii (D5) genome but rarely in the diploid Gossypium arboreum (A2) genome. We further explored the existence of the ICRd motif in chromosomes of G. raimondii, G. arboreum, and two tetraploid (AADD) cotton species, Gossypium hirsutum and Gossypium barbadense, by fluorescence in situ hybridization (FISH), and observed that the ICRd motif exists in the D5 and D-subgenomes but not in the A2 and A-subgenomes. The ICRd motif comprises two components, a variable tandem repeat (TR) region and a conservative sequence (CS). The two constituents each have hundreds of repeats that evenly distribute across 13 chromosomes of the D5genome. The ICRd motif (and its repeats) was revealed as the common conservative region harbored by ancient Long Terminal Repeat Retrotransposons. Identification and investigation of the ICRd motif promotes the study of A and D genome differences, facilitates research on Gossypium genome evolution, and provides assistance to subgenome identification and genome assembling.
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Affiliation(s)
- Hejun Lu
- Gembloux Agro-Bio Tech, University of Liège, Gembloux, Namur, Belgium
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xinglei Cui
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yanyan Zhao
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Richard Odongo Magwanga
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Bondo-Kenya, Bondo, Kenya
| | - Pengcheng Li
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xiaoyan Cai
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Zhongli Zhou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Xingxing Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yanchao Xu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Yuqing Hou
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- Tarium University, Alar, Xinjiang, China
| | - Fang Liu
- Research Base of Tarium University, State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
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Pimpinelli S, Piacentini L. Environmental change and the evolution of genomes: Transposable elements as translators of phenotypic plasticity into genotypic variability. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13497] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sergio Pimpinelli
- Istituto Pasteur Italia Fondazione Cenci‐Bolognetti and Department of Biology and Biotechnology ‘C. Darwin’ Sapienza University of Rome Rome Italy
| | - Lucia Piacentini
- Istituto Pasteur Italia Fondazione Cenci‐Bolognetti and Department of Biology and Biotechnology ‘C. Darwin’ Sapienza University of Rome Rome Italy
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50
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Wideman JG, Novick A, Muñoz-Gómez SA, Doolittle WF. Neutral evolution of cellular phenotypes. Curr Opin Genet Dev 2019; 58-59:87-94. [PMID: 31574422 DOI: 10.1016/j.gde.2019.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/29/2022]
Abstract
Eukaryotes exhibit a great diversity of cellular and subcellular morphologies, but their basic underlying architecture is fairly constant. All have a nucleus, Golgi, cytoskeleton, plasma membrane, vesicles, ribosomes, and all known lineages but one have mitochondrion-related organelles. Moreover, most eukaryotes undergo processes such as mitosis, meiosis, DNA recombination, and often perform feats such as phagocytosis, and amoeboid and flagellar movement. With all of these commonalities, it is obvious that eukaryotes evolved from a common ancestor, but it is not obvious how eukaryotes came to have their diverse structural phenotypes. Are these phenotypes adaptations to particular niches, their evolution dominated by positive natural selection? Or is eukaryotic cellular diversity substantially the product of neutral evolutionary processes, with adaptation either illusory or a secondary consequence? In this paper, we outline how a hierarchical view of phenotype can be used to articulate a neutral theory of phenotypic evolution, involving processes such as gene loss, gene replacement by homologues or analogues, gene duplication followed by subfunctionalization, and constructive neutral evolution. We suggest that neutral iterations of these processes followed by entrenchment of their products can explain much of the diversity of cellular, developmental, and biochemical phenotypes of unicellular eukaryotes and should be explored in addition to adaptive explanations.
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Affiliation(s)
- Jeremy G Wideman
- Centre for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85287, USA; Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Aaron Novick
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Philosophy, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada; Department of Philosophy, Purdue University, West Lafayette, IN, 47907, USA
| | - Sergio A Muñoz-Gómez
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - W Ford Doolittle
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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