Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects
Abstract Background Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolutio...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-01-01
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| Series: | BMC Evolutionary Biology |
| Online Access: | http://link.springer.com/article/10.1186/s12862-018-1324-9 |
| _version_ | 1818695395873652736 |
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| author | Malte Petersen David Armisén Richard A. Gibbs Lars Hering Abderrahman Khila Georg Mayer Stephen Richards Oliver Niehuis Bernhard Misof |
| author_facet | Malte Petersen David Armisén Richard A. Gibbs Lars Hering Abderrahman Khila Georg Mayer Stephen Richards Oliver Niehuis Bernhard Misof |
| author_sort | Malte Petersen |
| collection | DOAJ |
| description | Abstract Background Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. Results Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6% in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58% in the malaria mosquito (Diptera) and the migratory locust (Orthoptera), and a possible relationship between the content and diversity of TEs and the genome size. Conclusion While most insect orders exhibit a characteristic TE composition, we also observed intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera. Our findings shed light on common patterns and reveal lineage-specific differences in content and evolution of TEs in insects. We anticipate our study to provide the basis for future comparative research on the insect TE repertoire. |
| first_indexed | 2024-12-17T13:44:48Z |
| format | Article |
| id | doaj.art-71eddfd3758b494dbf86442da4a9a225 |
| institution | Directory Open Access Journal |
| issn | 1471-2148 |
| language | English |
| last_indexed | 2024-12-17T13:44:48Z |
| publishDate | 2019-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Evolutionary Biology |
| spelling | doaj.art-71eddfd3758b494dbf86442da4a9a2252022-12-21T21:46:10ZengBMCBMC Evolutionary Biology1471-21482019-01-0119111510.1186/s12862-018-1324-9Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insectsMalte Petersen0David Armisén1Richard A. Gibbs2Lars Hering3Abderrahman Khila4Georg Mayer5Stephen Richards6Oliver Niehuis7Bernhard Misof8University of BonnUniversité de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of MedicineDepartment of Zoology, Institute of Biology, University of KasselUniversité de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1Department of Zoology, Institute of Biology, University of KasselHuman Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of MedicineDepartment of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of FreiburgZoological Research Museum Alexander Koenig, Center for Molecular Biodiversity ResearchAbstract Background Transposable elements (TEs) are a major component of metazoan genomes and are associated with a variety of mechanisms that shape genome architecture and evolution. Despite the ever-growing number of insect genomes sequenced to date, our understanding of the diversity and evolution of insect TEs remains poor. Results Here, we present a standardized characterization and an order-level comparison of arthropod TE repertoires, encompassing 62 insect and 11 outgroup species. The insect TE repertoire contains TEs of almost every class previously described, and in some cases even TEs previously reported only from vertebrates and plants. Additionally, we identified a large fraction of unclassifiable TEs. We found high variation in TE content, ranging from less than 6% in the antarctic midge (Diptera), the honey bee and the turnip sawfly (Hymenoptera) to more than 58% in the malaria mosquito (Diptera) and the migratory locust (Orthoptera), and a possible relationship between the content and diversity of TEs and the genome size. Conclusion While most insect orders exhibit a characteristic TE composition, we also observed intraordinal differences, e.g., in Diptera, Hymenoptera, and Hemiptera. Our findings shed light on common patterns and reveal lineage-specific differences in content and evolution of TEs in insects. We anticipate our study to provide the basis for future comparative research on the insect TE repertoire.http://link.springer.com/article/10.1186/s12862-018-1324-9 |
| spellingShingle | Malte Petersen David Armisén Richard A. Gibbs Lars Hering Abderrahman Khila Georg Mayer Stephen Richards Oliver Niehuis Bernhard Misof Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects BMC Evolutionary Biology |
| title | Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects |
| title_full | Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects |
| title_fullStr | Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects |
| title_full_unstemmed | Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects |
| title_short | Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects |
| title_sort | diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects |
| url | http://link.springer.com/article/10.1186/s12862-018-1324-9 |
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