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Zhang C, Wang L, Dou L, Yue B, Xing J, Li J. Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species. Genes (Basel) 2023; 14:1244. [PMID: 37372423 DOI: 10.3390/genes14061244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/04/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Noctuidae is known to have high species diversity, although the genomic diversity of Noctuidae species has yet to be studied extensively. Investigation of transposable elements (TEs) in this family can improve our understanding of the genomic diversity of Noctuidae. In this study, we annotated and characterized genome-wide TEs in ten noctuid species belonging to seven genera. With multiple annotation pipelines, we constructed a consensus sequence library containing 1038-2826 TE consensus. The genome content of TEs showed high variation in the ten Noctuidae genomes, ranging from 11.3% to 45.0%. The relatedness analysis indicated that the TE content, especially the content of LINEs and DNA transposons, is positively correlated with the genome size (r = 0.86, p-value = 0.001). We identified SINE/B2 as a lineage-specific subfamily in Trichoplusia ni, a species-specific expansion of the LTR/Gypsy subfamily in Spodoptera exigua, and a recent expansion of SINE/5S subfamily in Busseola fusca. We further revealed that of the four TE classes, only LINEs showed phylogenetic signals with high confidence. We also examined how the expansion of TEs contributed to the evolution of noctuid genomes. Moreover, we identified 56 horizontal transfer TE (HTT) events among the ten noctuid species and at least three HTT events between the nine Noctuidae species and 11 non-noctuid arthropods. One of the HTT events of a Gypsy transposon might have caused the recent expansion of the Gypsy subfamily in the S. exigua genome. By determining the TE content, dynamics, and HTT events in the Noctuidae genomes, our study emphasized that TE activities and HTT events substantially impacted the Noctuidae genome evolution.
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Affiliation(s)
- Chunhui Zhang
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Lei Wang
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Liang Dou
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jing Li
- Key Laboratory of Bio-Resources and Eco-Environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610065, China
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2
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Grandchamp A, Kühl L, Lebherz M, Brüggemann K, Parsch J, Bornberg-Bauer E. Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster. Genome Res 2023; 33:872-890. [PMID: 37442576 PMCID: PMC10519401 DOI: 10.1101/gr.277482.122] [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: 11/15/2022] [Accepted: 06/06/2023] [Indexed: 07/15/2023]
Abstract
Novel genes are essential for evolutionary innovations and differ substantially even between closely related species. Recently, multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related sister genomes. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating genomes. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors of de novo genes that emerged within a single species. We sequenced and assembled genomes with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few neORFs shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of ORFs, for example, by forming new start and stop codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in neORFs emergence. Furthermore, transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate, are rapidly purged, but surviving neORFs spread neutrally through populations and within genomes.
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Affiliation(s)
- Anna Grandchamp
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
| | - Lucas Kühl
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Marie Lebherz
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Kathrin Brüggemann
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, 82152 Munich, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
- Max Planck Institute for Biology Tübingen, Department of Protein Evolution, 72076 Tübingen, Germany
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3
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Zakharenko LP, Petrovskii DV, Bykov RA. The P-Element Has Not Significant Effect on the Drosophila simulans Viability. Mol Biol 2023. [DOI: 10.1134/s0026893323020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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4
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Abstract
The detection and quantification of transposable elements (TE) are notoriously challenging despite their relevance in evolutionary genomics and molecular ecology. The main hurdle is caused by the dependence of numerous tools on genome assemblies, whose level of completion directly affects the comparability of the results across species or populations. dnaPipeTE, whose use is demonstrated here, tackles this issue by directly performing TE detection, classification, and quantification from unassembled short reads. This chapter details all the required steps to perform a comparative analysis of the TE content between two related species, starting from the installation of a recently containerized version of the program to the post-processing of the outputs.
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Affiliation(s)
- Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
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5
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Drown MK, DeLiberto AN, Flack N, Doyle M, Westover AG, Proefrock JC, Heilshorn S, D’Alessandro E, Crawford DL, Faulk C, Oleksiak MF. Sequencing Bait: Nuclear and Mitogenome Assembly of an Abundant Coastal Tropical and Subtropical Fish, Atherinomorus stipes. Genome Biol Evol 2022; 14:6648392. [PMID: 35866575 PMCID: PMC9348626 DOI: 10.1093/gbe/evac111] [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: 07/13/2022] [Indexed: 02/01/2023] Open
Abstract
Genetic data from nonmodel species can inform ecology and physiology, giving insight into a species' distribution and abundance as well as their responses to changing environments, all of which are important for species conservation and management. Moreover, reduced sequencing costs and improved long-read sequencing technology allows researchers to readily generate genomic resources for nonmodel species. Here, we apply Oxford Nanopore long-read sequencing and low-coverage (∼1x) whole genome short-read sequencing technology (Illumina) to assemble a genome and examine population genetics of an abundant tropical and subtropical fish, the hardhead silverside (Atherinomorus stipes). These fish are found in shallow coastal waters and are frequently included in ecological models because they serve as abundant prey for commercially and ecologically important species. Despite their importance in sub-tropical and tropical ecosystems, little is known about their population connectivity and genetic diversity. Our A. stipes genome assembly is about 1.2 Gb with comparable repetitive element content (∼47%), number of protein duplication events, and DNA methylation patterns to other teleost fish species. Among five sampled populations spanning 43 km of South Florida and the Florida Keys, we find little population structure suggesting high population connectivity.
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Affiliation(s)
| | | | - Nicole Flack
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minnesota, USA
| | - Meghan Doyle
- The Rosenstiel School, University of Miami, Florida, USA
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Sicat JPA, Visendi P, Sewe SO, Bouvaine S, Seal SE. Characterization of transposable elements within the Bemisia tabaci species complex. Mob DNA 2022; 13:12. [PMID: 35440097 PMCID: PMC9017028 DOI: 10.1186/s13100-022-00270-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background Whiteflies are agricultural pests that cause negative impacts globally to crop yields resulting at times in severe economic losses and food insecurity. The Bemisia tabaci whitefly species complex is the most damaging in terms of its broad crop host range and its ability to serve as vector for over 400 plant viruses. Genomes of whiteflies belonging to this species complex have provided valuable genomic data; however, transposable elements (TEs) within these genomes remain unexplored. This study provides the first accurate characterization of TE content within the B. tabaci species complex. Results This study identified that an average of 40.61% of the genomes of three whitefly species (MEAM1, MEDQ, and SSA-ECA) consists of TEs. The majority of the TEs identified were DNA transposons (22.85% average) while SINEs (0.14% average) were the least represented. This study also compared the TE content of the three whitefly genomes with three other hemipteran genomes and found significantly more DNA transposons and less LINEs in the whitefly genomes. A total of 63 TE superfamilies were identified to be present across the three whitefly species (39 DNA transposons, six LTR, 16 LINE, and two SINE). The sequences of the identified TEs were clustered which generated 5766 TE clusters. A total of 2707 clusters were identified as uniquely found within the whitefly genomes while none of the generated clusters were from both whitefly and non-whitefly TE sequences. This study is the first to characterize TEs found within different B. tabaci species and has created a standardized annotation workflow that could be used to analyze future whitefly genomes. Conclusion This study is the first to characterize the landscape of TEs within the B. tabaci whitefly species complex. The characterization of these elements within the three whitefly genomes shows that TEs occupy significant portions of B. tabaci genomes, with DNA transposons representing the vast majority. This study also identified TE superfamilies and clusters of TE sequences of potential interest, providing essential information, and a framework for future TE studies within this species complex. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00270-6.
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Affiliation(s)
- Juan Paolo A Sicat
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK.
| | - Paul Visendi
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Steven O Sewe
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Gillingham, Chatham, ME4 4TB, UK
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7
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Gilbert C, Belliardo C. The diversity of endogenous viral elements in insects. CURRENT OPINION IN INSECT SCIENCE 2022; 49:48-55. [PMID: 34839030 DOI: 10.1016/j.cois.2021.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 11/02/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
We provide an overview of the currently known diversity of viral sequences integrated into insect genomes. Such endogenous viral elements (EVE) have so far been annotated in at least eight insect orders and can be assigned to at least three families of large double-stranded (ds) DNA viruses, at least 22 families of RNA viruses, and three families of single-stranded DNA viruses. The study of these EVE has already produced important insights into insect-virus interactions, including the discovery of a new form of adaptive antiviral immunity. Insect EVE diversity will continue to increase as new insect genomes and exogenous viruses are sequenced, which will continue to make paleovirology a vibrant research field in this group of animals in the years to come.
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Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, Gif-sur-Yvette, 91198, France.
| | - Carole Belliardo
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, 06903, France; MYCOPHYTO, 540 Avenue de la Plaine, Mougins, 06250, France
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8
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Kataoka K, Togawa Y, Sanno R, Asahi T, Yura K. Dissecting cricket genomes for the advancement of entomology and entomophagy. Biophys Rev 2022; 14:75-97. [PMID: 35340598 PMCID: PMC8921346 DOI: 10.1007/s12551-021-00924-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/30/2021] [Indexed: 12/13/2022] Open
Abstract
Significant advances in biophysical methods such as next-generation sequencing technologies have now opened the way to conduct evolutionary and applied research based on the genomic information of greatly diverse insects. Crickets belonging to Orthoptera (Insecta: Polyneoptera), one of the most flourishing groups of insects, have contributed to the development of multiple scientific fields including developmental biology and neuroscience and have been attractive targets in evolutionary ecology for their diverse ecological niches. In addition, crickets have recently gained recognition as food and feed. However, the genomic information underlying their biological basis and application research toward breeding is currently underrepresented. In this review, we summarize the progress of genomics of crickets. First, we outline the phylogenetic position of crickets in insects and then introduce recent studies on cricket genomics and transcriptomics in a variety of fields. Furthermore, we present findings from our analysis of polyneopteran genomes, with a particular focus on their large genome sizes, chromosome number, and repetitive sequences. Finally, how the cricket genome can be beneficial to the food industry is discussed. This review is expected to enhance greater recognition of how important the cricket genomes are to the multiple biological fields and how basic research based on cricket genome information can contribute to tackling global food security.
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Affiliation(s)
- Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Yuki Togawa
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Toru Asahi
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
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9
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Affiliation(s)
| | - Francisco J. Ruiz-Ruano
- Department of Organismal Biology – Systematic Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
- School of Biological Sciences, Norwich Research Park University of East Anglia, Norwich, UK
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10
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Vargas-Chavez C, Longo Pendy NM, Nsango SE, Aguilera L, Ayala D, González J. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Res 2021; 32:189-202. [PMID: 34965939 PMCID: PMC8744685 DOI: 10.1101/gr.275761.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/24/2021] [Indexed: 11/28/2022]
Abstract
Anopheles coluzzii is one of the primary vectors of human malaria in sub-Saharan Africa. Recently, it has spread into the main cities of Central Africa threatening vector control programs. The adaptation of An. coluzzii to urban environments partly results from an increased tolerance to organic pollution and insecticides. Some of the molecular mechanisms for ecological adaptation are known, but the role of transposable elements (TEs) in the adaptive processes of this species has not been studied yet. As a first step toward assessing the role of TEs in rapid urban adaptation, we sequenced using long reads six An. coluzzii genomes from natural breeding sites in two major Central Africa cities. We de novo annotated TEs in these genomes and in an additional high-quality An. coluzzii genome, and we identified 64 new TE families. TEs were nonrandomly distributed throughout the genome with significant differences in the number of insertions of several superfamilies across the studied genomes. We identified seven putatively active families with insertions near genes with functions related to vectorial capacity, and several TEs that may provide promoter and transcription factor binding sites to insecticide resistance and immune-related genes. Overall, the analysis of multiple high-quality genomes allowed us to generate the most comprehensive TE annotation in this species to date and identify several TE insertions that could potentially impact both genome architecture and the regulation of functionally relevant genes. These results provide a basis for future studies of the impact of TEs on the biology of An. coluzzii.
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Affiliation(s)
- Carlos Vargas-Chavez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Neil Michel Longo Pendy
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,École Doctorale Régional (EDR) en Infectiologie Tropicale d'Afrique Centrale, BP 876, Franceville, Gabon
| | - Sandrine E Nsango
- Faculté de Médecine et des Sciences Pharmaceutiques, Université de Douala, BP 2701, Douala, Cameroun
| | - Laura Aguilera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Diego Ayala
- Centre Interdisciplinaire de Recherches Médicales de Franceville (CIRMF), BP 769, Franceville, Gabon.,Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle (MIVEGEC), Université Montpellier, CNRS, IRD, 64501 Montpellier, France
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
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Parisot N, Vargas-Chávez C, Goubert C, Baa-Puyoulet P, Balmand S, Beranger L, Blanc C, Bonnamour A, Boulesteix M, Burlet N, Calevro F, Callaerts P, Chancy T, Charles H, Colella S, Da Silva Barbosa A, Dell'Aglio E, Di Genova A, Febvay G, Gabaldón T, Galvão Ferrarini M, Gerber A, Gillet B, Hubley R, Hughes S, Jacquin-Joly E, Maire J, Marcet-Houben M, Masson F, Meslin C, Montagné N, Moya A, Ribeiro de Vasconcelos AT, Richard G, Rosen J, Sagot MF, Smit AFA, Storer JM, Vincent-Monegat C, Vallier A, Vigneron A, Zaidman-Rémy A, Zamoum W, Vieira C, Rebollo R, Latorre A, Heddi A. The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol 2021; 19:241. [PMID: 34749730 PMCID: PMC8576890 DOI: 10.1186/s12915-021-01158-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. RESULTS We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. CONCLUSIONS Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.
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Affiliation(s)
- Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Carlos Vargas-Chávez
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Present Address: Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Clément Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, New York, 14853, USA
- Present Address: Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Séverine Balmand
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Louis Beranger
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Caroline Blanc
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aymeric Bonnamour
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Federica Calevro
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Patrick Callaerts
- Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, KU Leuven, University of Leuven, B-3000, Leuven, Belgium
| | - Théo Chancy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | - Stefano Colella
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - André Da Silva Barbosa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Alex Di Genova
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
- Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gérard Febvay
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Toni Gabaldón
- Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Mechanisms of Disease, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Institut Catalan de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Alexandra Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | | | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Justin Maire
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Florent Masson
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain
| | | | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653, Le Rheu, France
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | | | | | | | - Agnès Vallier
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aurélien Vigneron
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Department of Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128, Mainz, Germany
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Waël Zamoum
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France.
- ERABLE European Team, INRIA, Rhône-Alpes, France.
| | - Rita Rebollo
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
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12
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Huang T, Gu W, Liu E, Shi X, Wang B, Wu W, Dong F, Xu G. Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss). Genomics 2021; 113:3533-3543. [PMID: 34450291 DOI: 10.1016/j.ygeno.2021.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 07/28/2021] [Accepted: 08/22/2021] [Indexed: 01/19/2023]
Abstract
Chromosomal ploidy manipulation is one of the means to create excellent germplasm. Triploid fish could provide an ideal sterile model for searching of a underlying mechanism of abnormality in meiosis. The complete understanding of the coding and noncoding RNAs regulating sterility caused by meiosis abnormality is still not well understood. By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at three different developmental stages between the diploid (XX) and triploid (XXX) female rainbow trout. These stages were gonads before differentiation (65 days post fertilisation, dpf), at the beginning of morphological differences (180 dpf) and showing clear difference between diploids and triploids (600 dpf), respectively. A majority of differentially expressed (DE) RNAs were identified, and 22 DE mRNAs related to oocyte meiosis and homologous recombination were characterized. The predicted miRNA-mRNA/lncRNA networks of 3 developmental stages were constructed based on the target pairs of DE lncRNA-miRNA and DE mRNA-miRNA. According to the networks, meiosis-related gene of ccne1 was targeted by dre-miR-15a-5p_R + 1, and 6 targeted DE lncRNAs were identified. Also, qRT-PCR was performed to validate the credibility of the network. Overall, this study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish. The mRNA, lncRNA and miRNA screened in this study may be helpful to identify the functional elements regulating fertility of rainbow trout, which may provide reference for character improvement in aquaculture.
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Affiliation(s)
- Tianqing Huang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Wei Gu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Enhui Liu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Xiulan Shi
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Bingqian Wang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Wenhua Wu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Fulin Dong
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | - Gefeng Xu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China.
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13
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Mérel V, Gibert P, Buch I, Rada VR, Estoup A, Gautier M, Fablet M, Boulesteix M, Vieira C. The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions. Mol Biol Evol 2021; 38:4252-4267. [PMID: 34021759 PMCID: PMC8476158 DOI: 10.1093/molbev/msab155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we characterized the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo, and found that TEs occupy 47% of the genome and are mostly located in gene poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied variation of TE abundance in genomic data from 16 invasive and six native populations of D. suzukii. We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity θ̂w a proxy of effective population size. We did not find any correlation between TE contents and bioclimatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 2,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g. transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.
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Affiliation(s)
- Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Patricia Gibert
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Inessa Buch
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Valentina Rodriguez Rada
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Arnaud Estoup
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Mathieu Gautier
- CBGP, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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14
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Muller H, Ogereau D, Da Lage JL, Capdevielle C, Pollet N, Fortuna T, Jeannette R, Kaiser L, Gilbert C. Draft nuclear genome and complete mitogenome of the Mediterranean corn borer, Sesamia nonagrioides, a major pest of maize. G3-GENES GENOMES GENETICS 2021; 11:6272226. [PMID: 33963397 PMCID: PMC8495949 DOI: 10.1093/g3journal/jkab155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/24/2021] [Indexed: 12/29/2022]
Abstract
The Mediterranean corn borer (Sesamia nonagrioides, Noctuidae, Lepidoptera) is a major pest of maize in Europe and Africa. Here, we report an assembly of the nuclear and mitochondrial genome of a pool of inbred males and females third-instar larvae, based on short- and long-read sequencing. The complete mitochondrial genome is 15,330 bp and contains all expected 13 and 24 protein-coding and RNA genes, respectively. The nuclear assembly is 1021 Mb, composed of 2553 scaffolds and it has an N50 of 1105 kb. It is more than twice larger than that of all Noctuidae species sequenced to date, mainly due to a higher repeat content. A total of 17,230 protein-coding genes were predicted, including 15,776 with InterPro domains. We provide detailed annotation of genes involved in sex determination (doublesex, insulin-like growth factor 2 mRNA-binding protein, and P-element somatic inhibitor) and of alpha-amylase genes possibly involved in interaction with parasitoid wasps. We found no evidence of recent horizontal transfer of bracovirus genes from parasitoid wasps. These genome assemblies provide a solid molecular basis to study insect genome evolution and to further develop biocontrol strategies against S. nonagrioides.
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Affiliation(s)
- Héloïse Muller
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, 69342 Lyon Cedex 07, France
| | - David Ogereau
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Jean-Luc Da Lage
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Claire Capdevielle
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Nicolas Pollet
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Taiadjana Fortuna
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Rémi Jeannette
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Laure Kaiser
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France
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15
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Abstract
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of genetic tools that allow to uncover mechanistic links between genotype and phenotype. Moreover, given its worldwide distribution in diverse habitats and its moderate genome-size, Drosophila has proven very powerful for population genetics inference and was one of the first eukaryotes whose genome was fully sequenced. In this book chapter, we provide a brief historical overview of research in Drosophila and then focus on recent advances during the genomic era. After describing different types and sources of genomic data, we discuss mechanisms of neutral evolution including the demographic history of Drosophila and the effects of recombination and biased gene conversion. Then, we review recent advances in detecting genome-wide signals of selection, such as soft and hard selective sweeps. We further provide a brief introduction to background selection, selection of noncoding DNA and codon usage and focus on the role of structural variants, such as transposable elements and chromosomal inversions, during the adaptive process. Finally, we discuss how genomic data helps to dissect neutral and adaptive evolutionary mechanisms that shape genetic and phenotypic variation in natural populations along environmental gradients. In summary, this book chapter serves as a starting point to Drosophila population genomics and provides an introduction to the system and an overview to data sources, important population genetic concepts and recent advances in the field.
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16
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Gilbert C, Peccoud J, Cordaux R. Transposable Elements and the Evolution of Insects. ANNUAL REVIEW OF ENTOMOLOGY 2021; 66:355-372. [PMID: 32931312 DOI: 10.1146/annurev-ento-070720-074650] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Insects are major contributors to our understanding of the interaction between transposable elements (TEs) and their hosts, owing to seminal discoveries, as well as to the growing number of sequenced insect genomes and population genomics and functional studies. Insect TE landscapes are highly variable both within and across insect orders, although phylogenetic relatedness appears to correlate with similarity in insect TE content. This correlation is unlikely to be solely due to inheritance of TEs from shared ancestors and may partly reflect preferential horizontal transfer of TEs between closely related species. The influence of insect traits on TE landscapes, however, remains unclear. Recent findings indicate that, in addition to being involved in insect adaptations and aging, TEs are seemingly at the cornerstone of insect antiviral immunity. Thus, TEs are emerging as essential insect symbionts that may have deleterious or beneficial consequences on their hosts, depending on context.
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Affiliation(s)
- Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198 Gif-sur-Yvette, France;
| | - Jean Peccoud
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France
| | - Richard Cordaux
- Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, Unité Mixte de Recherche 7267 Centre National de la Recherche Scientifique, Université de Poitiers, 86073 Poitiers CEDEX 9, France
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17
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Palazzo AF, Koonin EV. Functional Long Non-coding RNAs Evolve from Junk Transcripts. Cell 2020; 183:1151-1161. [PMID: 33068526 DOI: 10.1016/j.cell.2020.09.047] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/20/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022]
Abstract
Transcriptome studies reveal pervasive transcription of complex genomes, such as those of mammals. Despite popular arguments for functionality of most, if not all, of these transcripts, genome-wide analysis of selective constraints indicates that most of the produced RNA are junk. However, junk is not garbage. On the contrary, junk transcripts provide the raw material for the evolution of diverse long non-coding (lnc) RNAs by non-adaptive mechanisms, such as constructive neutral evolution. The generation of many novel functional entities, such as lncRNAs, that fuels organismal complexity does not seem to be driven by strong positive selection. Rather, the weak selection regime that dominates the evolution of most multicellular eukaryotes provides ample material for functional innovation with relatively little adaptation involved.
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Affiliation(s)
- Alexander F Palazzo
- Department of Biochemistry, University of Toronto, Toronto, ON M5G 1M1, Canada.
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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18
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Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing. Sci Rep 2020; 10:11227. [PMID: 32641717 PMCID: PMC7343843 DOI: 10.1038/s41598-020-67373-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/02/2020] [Indexed: 12/31/2022] Open
Abstract
Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies already exist for this species but contain pervasive assembly errors and are highly fragmented, which limits their values. Our purpose here was to improve the assembly of the D. suzukii genome and to annotate it in a way that facilitates comparisons with D. melanogaster. For this, we generated PacBio long-read sequencing data and assembled a novel, high-quality D. suzukii genome assembly. It is one of the largest Drosophila genomes, notably because of the expansion of its repeatome. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome. As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our assembly and annotation constitute a high-quality genomic resource that can be used for both high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii.
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19
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Mérel V, Boulesteix M, Fablet M, Vieira C. Transposable elements in Drosophila. Mob DNA 2020; 11:23. [PMID: 32636946 PMCID: PMC7334843 DOI: 10.1186/s13100-020-00213-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/25/2022] Open
Abstract
Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.
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Affiliation(s)
- Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
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20
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Impact of transposable elements on genome size variation between two closely related crustacean species. Anal Biochem 2020; 600:113770. [DOI: 10.1016/j.ab.2020.113770] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/13/2020] [Accepted: 05/05/2020] [Indexed: 12/19/2022]
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21
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Hjelmen CE, Holmes VR, Burrus CG, Piron E, Mynes M, Garrett MA, Blackmon H, Johnston JS. Thoracic underreplication in Drosophila species estimates a minimum genome size and the dynamics of added DNA. Evolution 2020; 74:1423-1436. [PMID: 32438451 DOI: 10.1111/evo.14022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/05/2020] [Accepted: 05/17/2020] [Indexed: 12/11/2022]
Abstract
Many cells in the thorax of Drosophila were found to stall during replication, a phenomenon known as underreplication. Unlike underreplication in nuclei of salivary and follicle cells, this stall occurs with less than one complete round of replication. This stall point allows precise estimations of early-replicating euchromatin and late-replicating heterochromatin regions, providing a powerful tool to investigate the dynamics of structural change across the genome. We measure underreplication in 132 species across the Drosophila genus and leverage these data to propose a model for estimating the rate at which additional DNA is accumulated as heterochromatin and euchromatin and also predict the minimum genome size for Drosophila. According to comparative phylogenetic approaches, the rates of change of heterochromatin differ strikingly between Drosophila subgenera. Although these subgenera differ in karyotype, there were no differences by chromosome number, suggesting other structural changes may influence accumulation of heterochromatin. Measurements were taken for both sexes, allowing the visualization of genome size and heterochromatin changes for the hypothetical path of XY sex chromosome differentiation. Additionally, the model presented here estimates a minimum genome size in Sophophora remarkably close to the smallest insect genome measured to date, in a species over 200 million years diverged from Drosophila.
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Affiliation(s)
- Carl E Hjelmen
- Department of Biology, Texas A&M University, College Station, Texas.,Department of Entomology, Texas A&M University, College Station, Texas
| | | | - Crystal G Burrus
- Department of Biology, Texas A&M University, College Station, Texas
| | - Elizabeth Piron
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Melissa Mynes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Margaret A Garrett
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas
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22
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Bayega A, Djambazian H, Tsoumani KT, Gregoriou ME, Sagri E, Drosopoulou E, Mavragani-Tsipidou P, Giorda K, Tsiamis G, Bourtzis K, Oikonomopoulos S, Dewar K, Church DM, Papanicolaou A, Mathiopoulos KD, Ragoussis J. De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly. BMC Genomics 2020; 21:259. [PMID: 32228451 PMCID: PMC7106766 DOI: 10.1186/s12864-020-6672-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 03/13/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The olive fruit fly, Bactrocera oleae, is the most important pest in the olive fruit agribusiness industry. This is because female flies lay their eggs in the unripe fruits and upon hatching the larvae feed on the fruits thus destroying them. The lack of a high-quality genome and other genomic and transcriptomic data has hindered progress in understanding the fly's biology and proposing alternative control methods to pesticide use. RESULTS Genomic DNA was sequenced from male and female Demokritos strain flies, maintained in the laboratory for over 45 years. We used short-, mate-pair-, and long-read sequencing technologies to generate a combined male-female genome assembly (GenBank accession GCA_001188975.2). Genomic DNA sequencing from male insects using 10x Genomics linked-reads technology followed by mate-pair and long-read scaffolding and gap-closing generated a highly contiguous 489 Mb genome with a scaffold N50 of 4.69 Mb and L50 of 30 scaffolds (GenBank accession GCA_001188975.4). RNA-seq data generated from 12 tissues and/or developmental stages allowed for genome annotation. Short reads from both males and females and the chromosome quotient method enabled identification of Y-chromosome scaffolds which were extensively validated by PCR. CONCLUSIONS The high-quality genome generated represents a critical tool in olive fruit fly research. We provide an extensive RNA-seq data set, and genome annotation, critical towards gaining an insight into the biology of the olive fruit fly. In addition, elucidation of Y-chromosome sequences will advance our understanding of the Y-chromosome's organization, function and evolution and is poised to provide avenues for sterile insect technique approaches.
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Affiliation(s)
- Anthony Bayega
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - Haig Djambazian
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - Konstantina T. Tsoumani
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Maria-Eleni Gregoriou
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Efthimia Sagri
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Eleni Drosopoulou
- Department of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Kristina Giorda
- Integrated DNA Technologies, Inc., 1710 Commercial Park, Coralville, Iowa, 52241 USA
| | - George Tsiamis
- Department of Environmental Engineering, University of Patras, Agrinio, Greece
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Spyridon Oikonomopoulos
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - Ken Dewar
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Canada
| | - Deanna M. Church
- Inscripta, Inc., 5500 Central Avenue #220, Boulder, CO 80301 USA
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753 Australia
| | - Kostas D. Mathiopoulos
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Jiannis Ragoussis
- McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Canada
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23
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Hjelmen CE, Parrott JJ, Srivastav SP, McGuane AS, Ellis LL, Stewart AD, Johnston JS, Tarone AM. Effect of Phenotype Selection on Genome Size Variation in Two Species of Diptera. Genes (Basel) 2020; 11:genes11020218. [PMID: 32093067 PMCID: PMC7074110 DOI: 10.3390/genes11020218] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 02/11/2020] [Accepted: 02/15/2020] [Indexed: 11/16/2022] Open
Abstract
Genome size varies widely across organisms yet has not been found to be related to organismal complexity in eukaryotes. While there is no evidence for a relationship with complexity, there is evidence to suggest that other phenotypic characteristics, such as nucleus size and cell-cycle time, are associated with genome size, body size, and development rate. However, what is unknown is how the selection for divergent phenotypic traits may indirectly affect genome size. Drosophila melanogaster were selected for small and large body size for up to 220 generations, while Cochliomyia macellaria were selected for 32 generations for fast and slow development. Size in D. melanogaster significantly changed in terms of both cell-count and genome size in isolines, but only the cell-count changed in lines which were maintained at larger effective population sizes. Larger genome sizes only occurred in a subset of D. melanogaster isolines originated from flies selected for their large body size. Selection for development time did not change average genome size yet decreased the within-population variation in genome size with increasing generations of selection. This decrease in variation and convergence on a similar mean genome size was not in correspondence with phenotypic variation and suggests stabilizing selection on genome size in laboratory conditions.
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Affiliation(s)
- Carl E. Hjelmen
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- Correspondence: or
| | - Jonathan J. Parrott
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- School of Mathematical and Natural Sciences, Arizona State University, Glendale, AZ 85306, USA
| | - Satyam P. Srivastav
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Alexander S. McGuane
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Harris County Institute of Forensic Sciences, 1861 Old Spanish Trail, Houston, TX 77054, USA
| | - Lisa L. Ellis
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
- Department of Biology, Houston Baptist University, Houston, TX 77074, USA
| | | | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
| | - Aaron M. Tarone
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA; (J.J.P.); (S.P.S.); (A.S.M.); (L.L.E.); (J.S.J.); (A.M.T.)
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Hill T, Koseva BS, Unckless RL. The Genome of Drosophila innubila Reveals Lineage-Specific Patterns of Selection in Immune Genes. Mol Biol Evol 2020; 36:1405-1417. [PMID: 30865231 PMCID: PMC6573480 DOI: 10.1093/molbev/msz059] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pathogenic microbes can exert extraordinary evolutionary pressure on their hosts. They can spread rapidly and sicken or even kill their host to promote their own proliferation. Because of this strong selective pressure, immune genes are some of the fastest evolving genes across metazoans, as highlighted in mammals and insects. Drosophila melanogaster serves as a powerful model for studying host/pathogen evolution. While Drosophila melanogaster are frequently exposed to various pathogens, little is known about D. melanogaster's ecology, or if they are representative of other Drosophila species in terms of pathogen pressure. Here, we characterize the genome of Drosophila innubila, a mushroom-feeding species highly diverged from D. melanogaster and investigate the evolution of the immune system. We find substantial differences in the rates of evolution of immune pathways between D. innubila and D. melanogaster. Contrasting what was previously found for D. melanogaster, we find little evidence of rapid evolution of the antiviral RNAi genes and high rates of evolution in the Toll pathway. This suggests that, while immune genes tend to be rapidly evolving in most species, the specific genes that are fastest evolving may depend either on the pathogens faced by the host and/or divergence in the basic architecture of the host's immune system.
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Affiliation(s)
- Tom Hill
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS
| | | | - Robert L Unckless
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS
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25
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Gichuki DK, Ma L, Zhu Z, Du C, Li Q, Hu G, Zhong Z, Li H, Wang Q, Xin H. Genome size, chromosome number determination, and analysis of the repetitive elements in Cissus quadrangularis. PeerJ 2019; 7:e8201. [PMID: 31875149 PMCID: PMC6927348 DOI: 10.7717/peerj.8201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 11/13/2019] [Indexed: 02/03/2023] Open
Abstract
Cissus quadrangularis (Vitaceae) is a perennial climber endemic to Africa and is characterized by succulent angular stems. The plant grows in arid and semi-arid regions of Africa especially in the African savanna. The stem of C. quadrangularis has a wide range of applications in both human and animal medicine, but there is limited cytogenetic information available for this species. In this study, the chromosome number, genome size, and genome composition for C. quadrangularis were determined. Flow cytometry results indicated that the genome size of C. quadrangularis is approximately 2C = 1.410 pg. Fluorescence microscopy combined with DAPI stain showed the chromosome numbers to be 2n = 48. It is likely that C. quadrangularis has a tetraploid genome after considering the basic chromosome numbers in Cissus genus (n = 10, 11, or 12). A combination of low-throughput genome sequencing and bioinformatics analysis allowed identification and quantification of repetitive elements that make up about 52% of the C. quadrangularis genome, which was dominated by LTR-retrotransposons. Two LTR superfamilies were identified as Copia and Gypsy, with 24% and 15% of the annotated clusters, respectively. The comparison of repeat elements for C. quadrangularis, Vitis vinifera, and four other selected members in the Cissus genus revealed a high diversity in the repetitive element components, which could suggest recent amplification events in the Cissus genus. Our data provides a platform for further studies on the phylogeny and karyotype evolution in this genus and in the family Vitaceae.
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Affiliation(s)
- Duncan Kiragu Gichuki
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, Peoples Republic of China
| | - Lu Ma
- Shenzhen Tobeacon Technology Co. Ltd., Shenzhen, Peoples Republic of China
| | - Zhenfei Zhu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, Peoples Republic of China
| | - Chang Du
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Qingyun Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Guangwan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Zhixiang Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Honglin Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Qingfeng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Haiping Xin
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
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26
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Hjelmen CE, Blackmon H, Holmes VR, Burrus CG, Johnston JS. Genome Size Evolution Differs Between Drosophila Subgenera with Striking Differences in Male and Female Genome Size in Sophophora. G3 (BETHESDA, MD.) 2019; 9:3167-3179. [PMID: 31358560 PMCID: PMC6778784 DOI: 10.1534/g3.119.400560] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/26/2019] [Indexed: 11/29/2022]
Abstract
Genome size varies across the tree of life, with no clear correlation to organismal complexity or coding sequence, but with differences in non-coding regions. Phylogenetic methods have recently been incorporated to further disentangle this enigma, yet most of these studies have focused on widely diverged species. Few have compared patterns of genome size change in closely related species with known structural differences in the genome. As a consequence, the relationship between genome size and differences in chromosome number or inter-sexual differences attributed to XY systems are largely unstudied. We hypothesize that structural differences associated with chromosome number and X-Y chromosome differentiation, should result in differing rates and patterns of genome size change. In this study, we utilize the subgenera within the Drosophila to ask if patterns and rates of genome size change differ between closely related species with differences in chromosome numbers and states of the XY system. Genome sizes for males and females of 152 species are used to answer these questions (with 92 newly added or updated estimates). While we find no relationship between chromosome number and genome size or chromosome number and inter-sexual differences in genome size, we find evidence for differing patterns of genome size change between the subgenera, and increasing rates of change throughout time. Estimated shifts in rates of change in sex differences in genome size occur more often in Sophophora and correspond to known neo-sex events.
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Affiliation(s)
- Carl E Hjelmen
- Department of Biology and
- Department of Entomology, Texas A&M University, College Station, TX 77843
| | - Heath Blackmon
- Department of Entomology, Texas A&M University, College Station, TX 77843
| | | | - Crystal G Burrus
- Department of Entomology, Texas A&M University, College Station, TX 77843
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27
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Chak STC, Rubenstein DR. TERAD: Extraction of transposable element composition from RADseq data. Mol Ecol Resour 2019; 19:1681-1688. [PMID: 31479576 DOI: 10.1111/1755-0998.13080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 12/31/2022]
Abstract
Transposable elements (TEs) - selfish DNA sequences that can move within the genome - comprise a large proportion of the genomes of many organisms. Although low-coverage whole-genome sequencing can be used to survey TE composition, it is noneconomical for species with large quantities of DNA. Here, we utilize restriction-site associated DNA sequencing (RADSeq) as an alternative method to survey TE composition. First, we demonstrate in silico that double digest restriction-site associated DNA sequencing (ddRADseq) markers contain the same TE compositions as whole genome assemblies across arthropods. Next, we show empirically using eight Synalpheus snapping shrimp species with large genomes that TE compositions from ddRADseq and low-coverage whole-genome sequencing are comparable within and across species. Finally, we develop a new bioinformatic pipeline, TERAD, to extract TE compositions from RADseq data. Our study expands the utility of RADseq to study the repeatome, making comparative studies of genome structure for species with large genomes more tractable and affordable.
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Affiliation(s)
- Solomon T C Chak
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Dustin R Rubenstein
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
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28
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He Y, Tian S, Tian P. Fundamental asymmetry of insertions and deletions in genomes size evolution. J Theor Biol 2019; 482:109983. [PMID: 31445016 DOI: 10.1016/j.jtbi.2019.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 08/18/2019] [Accepted: 08/21/2019] [Indexed: 12/01/2022]
Abstract
The origin of large genomes that underlies the long standing "C-value enigma" is only partially explained by selfish DNA. We investigated insertions and deletions (indels) of nucleotides and discussed their relevance in size evolution of random biological sequences (RBS) and genomes. By developing a probabilistic model of RBS based on size evolution of expandable sites in a thought perfect genome, it was found that insertion bias engenders exponential increase of average RBS sizes. When combined with existing large segments of genome that are not subject to selection pressure (e.g. selfish DNA), such insertion bias results in explosive expansion of genomes, and therefore helps explain the "C value enigma" besides selfish DNA. Such increase of RBS size is caused by the fundamental asymmetry of indels, with insertions result in more available sites and deletions result in less deletable nucleotides. In qualitative agreement with the size distribution of known genomes, tails of RBS size distributions exhibit exponential decay with probabilities of larger RBS segments being smaller. Unsurprisingly, a slight deletion bias (higher deletions probabilities) results in a slow decrease of average RBS size and may lead to their eventual vanishing. Contrary to intuition, strictly balanced insertion and deletion results in linearly increasing instead of completely fixed RBS size. Nonetheless, such slow linear increase of average RBS sizes with time are small in magnitude and are consequently not influential on genome size evolution, and certainly not a major contributor for the "C-value enigma". Our model suggested that insertion bias of nucleotides may provide complementary explanation for large genomes besides selfish DNA. The fundamental indel asymmetry is applicable for all forms of genomic insertions and deletions. Long-lasting exponential increase of genome size present energy and material requirement that is impossible to sustain. We therefore concluded that if there were explosively accelerating expansion caused by significant effective insertion bias for any survival species, it must have occurred sporadically. Our model also provided an explanation for the observed proportional evolution of genome size.
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Affiliation(s)
- Yang He
- School of Life Sciences, Jilin University Changchun, 2699 Qianjin Street, China 130012
| | - Suyan Tian
- Division of Clinical Epidemiology, First Hospital of The Jilin University, 71 Xinmin Street, Changchun, China, 130021.
| | - Pu Tian
- School of Life Sciences and MOE Key laboratory of Molecular Enzymology and Engineering, Jilin University 2699 Qianjin Street, Changchun, China 130012.
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29
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Fonseca PM, Moura RD, Wallau GL, Loreto ELS. The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies. Chromosome Res 2019; 27:203-219. [DOI: 10.1007/s10577-019-09609-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/19/2019] [Accepted: 04/22/2019] [Indexed: 02/06/2023]
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30
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Wu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes (Basel) 2019; 10:genes10050338. [PMID: 31064091 PMCID: PMC6562904 DOI: 10.3390/genes10050338] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/09/2019] [Accepted: 04/26/2019] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous in arthropods. However, analyses of large-scale and long-term coevolution between TEs and host genomes remain scarce in arthropods. Here, we choose 14 representative Arthropoda species from eight orders spanning more than 500 million years of evolution. By developing an unbiased TE annotation pipeline, we obtained 87 to 2266 TE reference sequences in a species, which is a considerable improvement compared to the reference TEs previously annotated in Repbase. We find that TE loads are diversified among species and were previously underestimated. The highly species- and time-specific expansions and contractions, and intraspecific sequence diversification are the leading driver of long terminal repeat (LTR) dynamics in Lepidoptera. Terminal inverted repeats (TIRs) proliferated substantially in five species with large genomes. A phylogenetic comparison reveals that the loads of multiple TE subfamilies are positively correlated with genome sizes. We also identified a few horizontally transferred TE candidates across nine species. In addition, we set up the Arthropod Transposable Elements database (ArTEdb) to provide TE references and annotations. Collectively, our results provide high-quality TE references and uncover that TE loads and expansion histories vary greatly among arthropods, which implies that TEs are an important driving force shaping the evolution of genomes through gain and loss.
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Affiliation(s)
- Changcheng Wu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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31
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Lerat E, Casacuberta J, Chaparro C, Vieira C. On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses. Genes (Basel) 2019; 10:genes10040258. [PMID: 30935103 PMCID: PMC6523952 DOI: 10.3390/genes10040258] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so.
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Affiliation(s)
- Emmanuelle Lerat
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Cristian Chaparro
- CNRS, IHPE UMR 5244, University of Perpignan Via Domitia, IFREMER, University Montpellier, F-66860 Perpignan, France.
| | - Cristina Vieira
- CNRS, Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, UMR 5558, F-69622 Villeurbanne, France.
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32
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Hjelmen CE, Garrett MA, Holmes VR, Mynes M, Piron E, Johnston JS. Genome Size Evolution within and between the Sexes. J Hered 2019; 110:219-228. [PMID: 30476187 DOI: 10.1093/jhered/esy063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 11/21/2018] [Indexed: 02/02/2023] Open
Abstract
Genome sizes are known to vary between closely related species, but the patterns behind this variation have yet to be fully understood. Although this variation has been evaluated between species and within sexes, unknown is the extent to which this variation is driven by differentiation in sex chromosomes. To address this longstanding question, we examine the mode and tempo of genome size evolution for a total of 87 species of Drosophilidae, estimating and updating male genome size values for 44 of these species. We compare the evolution of genome size within each sex to the evolution of the differences between the sexes. Utilizing comparative phylogenetic methods, we find that male and female genome size evolution is largely a neutral process, reflective of phylogenetic relatedness between species, which supports the newly proposed accordion model for genome size change. When similarly analyzed, the difference between the sexes due to heteromorphic sex chromosomes is a dynamic process; the male-female genome size difference increases with time with or without known neo-Y events or complete loss of the Y. Observed instances of rapid change match theoretical expectations and known neo-Y and Y loss events in individual species.
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Affiliation(s)
- Carl E Hjelmen
- Department of Entomology, Texas A&M University, College Station, TX
| | - Margaret A Garrett
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
| | - V Renee Holmes
- Department of Entomology, Texas A&M University, College Station, TX
| | - Melissa Mynes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
| | - Elizabeth Piron
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX
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33
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Diesel JF, Ortiz MF, Marinotti O, Vasconcelos ATR, Loreto ELS. A re-annotation of the Anopheles darlingi mobilome. Genet Mol Biol 2019; 42:125-131. [PMID: 30672977 PMCID: PMC6428116 DOI: 10.1590/1678-4685-gmb-2017-0300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 04/19/2018] [Indexed: 12/02/2022] Open
Abstract
The mobilome, portion of the genome composed of transposable elements (TEs), of
Anopheles darlingi was described together with the genome
of this species. Here, this mobilome was revised using similarity and de
novo search approaches. A total of 5.6% of the A.
darlingi genome is derived of TEs. Class I gypsy
and copia were the most abundant superfamilies, corresponding
to 22.36% of the mobilome. Non-LTR elements of the R1 and
Jockey superfamilies account for 11% of the TEs. Among
Class II TEs, the mariner superfamily is the most abundant
(16.01%). Approximately 87% of the A. darlingi mobilome consist
of short, truncated and/or degenerated copies of TEs. Only three
retrotransposons, two belonging to gypsy and one to
copia superfamilies, are putatively active elements. Only
one Class II element, belonging to the mariner superfamily, is
putatively active, having 12 copies in the genome. The TE landscape of
A. darlingi is formed primarily by degenerated elements
and, therefore, somewhat stable. Future applications of TE-based vectors for
genetic transformation of A. darlingi should take into
consideration mariner and piggyBac
transposons, because full length and putatively active copies of these elements
are present in its genome.
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Affiliation(s)
- Jose Francisco Diesel
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
| | - Mauro F Ortiz
- Programa de Pós-Graduação de Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Osvaldo Marinotti
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, USA
| | - Ana Tereza R Vasconcelos
- Laboratório de Bioinformática do Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brazil
| | - Elgion L S Loreto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, RS, Brazil
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34
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Li SF, Guo YJ, Li JR, Zhang DX, Wang BX, Li N, Deng CL, Gao WJ. The landscape of transposable elements and satellite DNAs in the genome of a dioecious plant spinach ( Spinacia oleracea L.). Mob DNA 2019; 10:3. [PMID: 30675191 PMCID: PMC6337768 DOI: 10.1186/s13100-019-0147-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/07/2019] [Indexed: 11/10/2022] Open
Abstract
Background Repetitive sequences, including transposable elements (TEs) and satellite DNAs, occupy a considerable portion of plant genomes. Analysis of the repeat fraction benefits the understanding of genome structure and evolution. Spinach (Spinacia oleracea L.), an important vegetable crop, is also a model dioecious plant species for studying sex determination and sex chromosome evolution. However, the repetitive sequences of the spinach genome have not been fully investigated. Results We extensively analyzed the repetitive components of draft spinach genome, especially TEs and satellites, by different strategies. A total of 16,002 full-length TEs were identified. Among the most abundant long terminal repeat (LTR) retrotransposons (REs), Copia elements were overrepresented compared with Gypsy ones. Angela was the most dominating Copia lineage; Ogre/Tat was the most abundant Gypsy lineage. The mean insertion age of LTR-REs was 1.42 million years; approximately 83.7% of these elements were retrotransposed during the last two million years. RepeatMasker totally masked about 64.05% of the spinach genome, with LTR-REs, non-LTR-REs, and DNA transposons occupying 49.2, 2.4, and 5.6%, respectively. Fluorescence in situ hybridization (FISH) analysis showed that most LTR-REs dispersed all over the chromosomes, by contrast, elements of CRM lineage were distributed at the centromeric region of all chromosomes. In addition, Ogre/Tat lineage mainly accumulated on sex chromosomes, and satellites Spsat2 and Spsat3 were exclusively located at the telomeric region of the short arm of sex chromosomes. Conclusions We reliably annotated the TE fraction of the draft genome of spinach. FISH analysis indicates that Ogre/Tat lineage and the sex chromosome-specific satellites DNAs might participate in sex chromosome formation and evolution. Based on FISH signals of microsatellites, together with 45S rDNA, a fine karyotype of spinach was established. This study improves our knowledge of repetitive sequence organization in spinach genome and aids in accurate spinach karyotype construction. Electronic supplementary material The online version of this article (10.1186/s13100-019-0147-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shu-Fen Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Yu-Jiao Guo
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jia-Rong Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Dong-Xu Zhang
- 2College of Life Science, Shanxi Datong University, Datong, 037009 China
| | - Bing-Xiao Wang
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ning Li
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- 1College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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35
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Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, Richards S, Niehuis O, Misof B. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol 2019; 19:11. [PMID: 30626321 PMCID: PMC6327564 DOI: 10.1186/s12862-018-1324-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022] Open
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.
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Affiliation(s)
- Malte Petersen
- University of Bonn, Bonn, Germany
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
- Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt, 60325 Germany
| | - David Armisén
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Lars Hering
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Abderrahman Khila
- Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d’Italie, Lyon, 69364 France
| | - Georg Mayer
- Department of Zoology, Institute of Biology, University of Kassel, Heinrich-Plett-Str. 40, Kassel, 34132 Germany
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, 77030 TX USA
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, Freiburg (Brsg.), 79104 Germany
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Center for Molecular Biodiversity Research, Adenauerallee 160, Bonn, 53113 Germany
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Marburger S, Alexandrou MA, Taggart JB, Creer S, Carvalho G, Oliveira C, Taylor MI. Whole genome duplication and transposable element proliferation drive genome expansion in Corydoradinae catfishes. Proc Biol Sci 2019; 285:rspb.2017.2732. [PMID: 29445022 PMCID: PMC5829208 DOI: 10.1098/rspb.2017.2732] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/25/2018] [Indexed: 01/12/2023] Open
Abstract
Genome size varies significantly across eukaryotic taxa and the largest changes are typically driven by macro-mutations such as whole genome duplications (WGDs) and proliferation of repetitive elements. These two processes may affect the evolutionary potential of lineages by increasing genetic variation and changing gene expression. Here, we elucidate the evolutionary history and mechanisms underpinning genome size variation in a species-rich group of Neotropical catfishes (Corydoradinae) with extreme variation in genome size—0.6 to 4.4 pg per haploid cell. First, genome size was quantified in 65 species and mapped onto a novel fossil-calibrated phylogeny. Two evolutionary shifts in genome size were identified across the tree—the first between 43 and 49 Ma (95% highest posterior density (HPD) 36.2–68.1 Ma) and the second at approximately 19 Ma (95% HPD 15.3–30.14 Ma). Second, restriction-site-associated DNA (RAD) sequencing was used to identify potential WGD events and quantify transposable element (TE) abundance in different lineages. Evidence of two lineage-scale WGDs was identified across the phylogeny, the first event occurring between 54 and 66 Ma (95% HPD 42.56–99.5 Ma) and the second at 20–30 Ma (95% HPD 15.3–45 Ma) based on haplotype numbers per contig and between 35 and 44 Ma (95% HPD 30.29–64.51 Ma) and 20–30 Ma (95% HPD 15.3–45 Ma) based on SNP read ratios. TE abundance increased considerably in parallel with genome size, with a single TE-family (TC1-IS630-Pogo) showing several increases across the Corydoradinae, with the most recent at 20–30 Ma (95% HPD 15.3–45 Ma) and an older event at 35–44 Ma (95% HPD 30.29–64.51 Ma). We identified signals congruent with two WGD duplication events, as well as an increase in TE abundance across different lineages, making the Corydoradinae an excellent model system to study the effects of WGD and TEs on genome and organismal evolution.
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Affiliation(s)
- Sarah Marburger
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Markos A Alexandrou
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK.,Wildlands Conservation Science, LLC PO Box 1846, Lompoc, CA 93438, USA
| | - John B Taggart
- Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, Gwynedd LL57 2UW, UK
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências/UNESP, Rua Professor Doutor Antonio Celso Wagner Zanin, s/n°18618-689 Botucatu, São Paulo, Brazil
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Guio L, González J. New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans. Methods Mol Biol 2019; 1910:505-530. [PMID: 31278675 DOI: 10.1007/978-1-4939-9074-0_16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Understanding the abundance, diversity, and distribution of TEs in genomes is crucial to understand genome structure, function, and evolution. Advances in whole-genome sequencing techniques, as well as in bioinformatics tools, have increased our ability to detect and analyze the transposable element content in genomes. In addition to reference genomes, we now have access to population datasets in which multiple individuals within a species are sequenced. In this chapter, we highlight the recent advances in the study of TE population dynamics focusing on fruit flies and humans, which represent two extremes in terms of TE abundance, diversity, and activity. We review the most recent methodological approaches applied to the study of TE dynamics as well as the new knowledge on host factors involved in the regulation of TE activity. In addition to transposition rates, we also focus on TE deletion rates and on the selective forces that affect the dynamics of TEs in genomes.
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Affiliation(s)
- Lain Guio
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Josefa González
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
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38
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Simão MC, Haudry A, Granzotto A, de Setta N, Carareto CMA. Helena and BS: Two Travellers between the Genera Drosophila and Zaprionus. Genome Biol Evol 2018; 10:2671-2685. [PMID: 30165545 PMCID: PMC6179348 DOI: 10.1093/gbe/evy184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2018] [Indexed: 12/20/2022] Open
Abstract
The frequency of horizontal transfers of transposable elements (HTTs) varies among the types of elements according to the transposition mode and the geographical and temporal overlap of the species involved in the transfer. The drosophilid species of the genus Zaprionus and those of the melanogaster, obscura, repleta, and virilis groups of the genus Drosophila investigated in this study shared space and time at some point in their evolutionary history. This is particularly true of the subgenus Zaprionus and the melanogaster subgroup, which overlapped both geographically and temporally in Tropical Africa during their period of origin and diversification. Here, we tested the hypothesis that this overlap may have facilitated the transfer of retrotransposons without long terminal repeats (non-LTRs) between these species. We estimated the HTT frequency of the non-LTRs BS and Helena at the genome-wide scale by using a phylogenetic framework and a vertical and horizontal inheritance consistence analysis (VHICA). An excessively low synonymous divergence among distantly related species and incongruities between the transposable element and species phylogenies allowed us to propose at least four relatively recent HTT events of Helena and BS involving ancestors of the subgroup melanogaster and ancestors of the subgenus Zaprionus during their concomitant diversification in Tropical Africa, along with older possible events between species of the subgenera Drosophila and Sophophora. This study provides the first evidence for HTT of non-LTRs retrotransposons between Drosophila and Zaprionus, including an in-depth reconstruction of the time frame and geography of these events.
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Affiliation(s)
- Maryanna C Simão
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
| | - Annabelle Haudry
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Adriana Granzotto
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
| | - Nathalia de Setta
- Universidade Federal do ABC (UFABC), Centro de Ciências Naturais e Humanas (CCNH), São Bernardo do Campo, SP, Brazil
| | - Claudia M A Carareto
- Universidade Estadual Paulista (Unesp), Instituto de Biociências Letras e Ciências Exatas (Ibilce), Câmpus São José do Rio Preto, SP, Brazil
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da Silva AF, Dezordi FZ, Loreto ELS, Wallau GL. Drosophila parasitoid wasps bears a distinct DNA transposon profile. Mob DNA 2018; 9:23. [PMID: 30002736 PMCID: PMC6035795 DOI: 10.1186/s13100-018-0127-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/19/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The majority of Eukaryotic genomes are composed of a small portion of stable (non-mobile) genes and a large fraction of parasitic mobile elements such as transposable elements and endogenous viruses: the Mobilome. Such important component of many genomes are normally underscored in genomic analysis and detailed characterized mobilomes only exists for model species. In this study, we used a combination of de novo and homology approaches to characterize the Mobilome of two non-model parasitoid wasp species. RESULTS The different methodologies employed for TE characterization recovered TEs with different features as TE consensus number and size. Moreover, some TEs were detected only by one or few methodologies. RepeatExplorer and dnaPipeTE estimated a low TE content of 5.86 and 4.57% for Braconidae wasp and 5.22% and 7.42% for L. boulardi species, respectively. Both mobilomes are composed by a miscellaneous of ancient and recent elements. Braconidae wasps presented a large diversity of Maverick/Polintons Class II TEs while other TE superfamilies were more equally diverse in both species. Phylogenetic analysis of reconstructed elements showed that vertical transfer is the main mode of transmission. CONCLUSION Different methodologies should be used complementarity in order to achieve better mobilome characterization. Both wasps genomes have one of the lower mobilome estimates among all Hymenoptera genomes studied so far and presented a higher proportion of Class II than Class I TEs. The large majority of superfamilies analyzed phylogenetically showed that the elements are being inherited by vertical transfer. Overall, we achieved a deep characterization of the mobilome in two non-model parasitoid wasps improving our understanding of their evolution.
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Affiliation(s)
- Alexandre Freitas da Silva
- Pós Graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães (IAM), Recife, Pernambuco Brazil
| | - Filipe Zimmer Dezordi
- Pós Graduação em Biociências e Biotecnologia em Saúde, Instituto Aggeu Magalhães (IAM), Recife, Pernambuco Brazil
| | - Elgion Lucio Silva Loreto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Santa Maria, Santa Maria, Rio Grande do Sul Brazil
| | - Gabriel Luz Wallau
- Departamento de Entomologia, Instituto Aggeu Magalhães (IAM), Fundação Oswaldo Cruz (FIOCRUZ/PE), Recife, Pernambuco Brazil
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40
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Hill T, Betancourt AJ. Extensive exchange of transposable elements in the Drosophila pseudoobscura group. Mob DNA 2018; 9:20. [PMID: 29946370 PMCID: PMC6006672 DOI: 10.1186/s13100-018-0123-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/01/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND As species diverge, so does their transposable element (TE) content. Within a genome, TE families may eventually become dormant due to host-silencing mechanisms, natural selection and the accumulation of inactive copies. The transmission of active copies from a TE families, both vertically and horizontally between species, can allow TEs to escape inactivation if it occurs often enough, as it may allow TEs to temporarily escape silencing in a new host. Thus, the contribution of horizontal exchange to TE persistence has been of increasing interest. RESULTS Here, we annotated TEs in five species with sequenced genomes from the D. pseudoobscura species group, and curated a set of TE families found in these species. We found that, compared to host genes, many TE families showed lower neutral divergence between species, consistent with recent transmission of TEs between species. Despite these transfers, there are differences in the TE content between species in the group. CONCLUSIONS The TE content is highly dynamic in the D. pseudoobscura species group, frequently transferring between species, keeping TEs active. This result highlights how frequently transposable elements are transmitted between sympatric species and, despite these transfers, how rapidly species TE content can diverge.
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Affiliation(s)
- Tom Hill
- The Department of Molecular Biosciences, University of Kansas, 4055 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS 66045 USA
| | - Andrea J. Betancourt
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
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Chromosome Evolution in Connection with Repetitive Sequences and Epigenetics in Plants. Genes (Basel) 2017; 8:genes8100290. [PMID: 29064432 PMCID: PMC5664140 DOI: 10.3390/genes8100290] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 01/18/2023] Open
Abstract
Chromosome evolution is a fundamental aspect of evolutionary biology. The evolution of chromosome size, structure and shape, number, and the change in DNA composition suggest the high plasticity of nuclear genomes at the chromosomal level. Repetitive DNA sequences, which represent a conspicuous fraction of every eukaryotic genome, particularly in plants, are found to be tightly linked with plant chromosome evolution. Different classes of repetitive sequences have distinct distribution patterns on the chromosomes. Mounting evidence shows that repetitive sequences may play multiple generative roles in shaping the chromosome karyotypes in plants. Furthermore, recent development in our understanding of the repetitive sequences and plant chromosome evolution has elucidated the involvement of a spectrum of epigenetic modification. In this review, we focused on the recent evidence relating to the distribution pattern of repetitive sequences in plant chromosomes and highlighted their potential relevance to chromosome evolution in plants. We also discussed the possible connections between evolution and epigenetic alterations in chromosome structure and repatterning, such as heterochromatin formation, centromere function, and epigenetic-associated transposable element inactivation.
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42
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Talla V, Suh A, Kalsoom F, Dincă V, Vila R, Friberg M, Wiklund C, Backström N. Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies. Genome Biol Evol 2017; 9:2491-2505. [PMID: 28981642 PMCID: PMC5737376 DOI: 10.1093/gbe/evx163] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2016] [Indexed: 12/14/2022] Open
Abstract
Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths.
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Affiliation(s)
- Venkat Talla
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Alexander Suh
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Faheema Kalsoom
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Vlad Dincă
- Animal Biodiversity and Evolution Program, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Roger Vila
- Animal Biodiversity and Evolution Program, Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
| | - Magne Friberg
- Department of Plant Ecology and Evolution, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
| | - Christer Wiklund
- Division of Ecology, Department of Zoology, Stockholm University, Sweden
| | - Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Sweden
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Ritchie H, Jamieson AJ, Piertney SB. Genome size variation in deep-sea amphipods. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170862. [PMID: 28989783 PMCID: PMC5627123 DOI: 10.1098/rsos.170862] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/16/2017] [Indexed: 06/07/2023]
Abstract
Genome size varies considerably across taxa, and extensive research effort has gone into understanding whether variation can be explained by differences in key ecological and life-history traits among species. The extreme environmental conditions that characterize the deep sea have been hypothesized to promote large genome sizes in eukaryotes. Here we test this supposition by examining genome sizes among 13 species of deep-sea amphipods from the Mariana, Kermadec and New Hebrides trenches. Genome sizes were estimated using flow cytometry and found to vary nine-fold, ranging from 4.06 pg (4.04 Gb) in Paralicella caperesca to 34.79 pg (34.02 Gb) in Alicella gigantea. Phylogenetic independent contrast analysis identified a relationship between genome size and maximum body size, though this was largely driven by those species that display size gigantism. There was a distinct shift in the genome size trait diversification rate in the supergiant amphipod A. gigantea relative to the rest of the group. The variation in genome size observed is striking and argues against genome size being driven by a common evolutionary history, ecological niche and life-history strategy in deep-sea amphipods.
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Affiliation(s)
- H. Ritchie
- Institute of Biological and Environmental Sciences, University of Aberdeen, Zoology Building, Aberdeen AB24 2TZ, UK
| | - A. J. Jamieson
- Oceanlab, University of Aberdeen, Newburgh, Aberdeenshire AB41 6AA, UK
| | - S. B. Piertney
- Institute of Biological and Environmental Sciences, University of Aberdeen, Zoology Building, Aberdeen AB24 2TZ, UK
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Leung W, Shaffer CD, Chen EJ, Quisenberry TJ, Ko K, Braverman JM, Giarla TC, Mortimer NT, Reed LK, Smith ST, Robic S, McCartha SR, Perry DR, Prescod LM, Sheppard ZA, Saville KJ, McClish A, Morlock EA, Sochor VR, Stanton B, Veysey-White IC, Revie D, Jimenez LA, Palomino JJ, Patao MD, Patao SM, Himelblau ET, Campbell JD, Hertz AL, McEvilly MF, Wagner AR, Youngblom J, Bedi B, Bettincourt J, Duso E, Her M, Hilton W, House S, Karimi M, Kumimoto K, Lee R, Lopez D, Odisho G, Prasad R, Robbins HL, Sandhu T, Selfridge T, Tsukashima K, Yosif H, Kokan NP, Britt L, Zoellner A, Spana EP, Chlebina BT, Chong I, Friedman H, Mammo DA, Ng CL, Nikam VS, Schwartz NU, Xu TQ, Burg MG, Batten SM, Corbeill LM, Enoch E, Ensign JJ, Franks ME, Haiker B, Ingles JA, Kirkland LD, Lorenz-Guertin JM, Matthews J, Mittig CM, Monsma N, Olson KJ, Perez-Aragon G, Ramic A, Ramirez JR, Scheiber C, Schneider PA, Schultz DE, Simon M, Spencer E, Wernette AC, Wykle ME, Zavala-Arellano E, McDonald MJ, Ostby K, Wendland P, DiAngelo JR, Ceasrine AM, Cox AH, Docherty JEB, Gingras RM, Grieb SM, Pavia MJ, Personius CL, Polak GL, Beach DL, Cerritos HL, Horansky EA, Sharif KA, Moran R, Parrish S, Bickford K, Bland J, Broussard J, Campbell K, Deibel KE, Forka R, Lemke MC, Nelson MB, O'Keeffe C, Ramey SM, Schmidt L, Villegas P, Jones CJ, Christ SL, Mamari S, Rinaldi AS, Stity G, Hark AT, Scheuerman M, Silver Key SC, McRae BD, Haberman AS, Asinof S, Carrington H, Drumm K, Embry T, McGuire R, Miller-Foreman D, Rosen S, Safa N, Schultz D, Segal M, Shevin Y, Svoronos P, Vuong T, Skuse G, Paetkau DW, Bridgman RK, Brown CM, Carroll AR, Gifford FM, Gillespie JB, Herman SE, Holtcamp KL, Host MA, Hussey G, Kramer DM, Lawrence JQ, Martin MM, Niemiec EN, O'Reilly AP, Pahl OA, Quintana G, Rettie EAS, Richardson TL, Rodriguez AE, Rodriguez MO, Schiraldi L, Smith JJ, Sugrue KF, Suriano LJ, Takach KE, Vasquez AM, Velez X, Villafuerte EJ, Vives LT, Zellmer VR, Hauke J, Hauser CR, Barker K, Cannon L, Parsamian P, Parsons S, Wichman Z, Bazinet CW, Johnson DE, Bangura A, Black JA, Chevee V, Einsteen SA, Hilton SK, Kollmer M, Nadendla R, Stamm J, Fafara-Thompson AE, Gygi AM, Ogawa EE, Van Camp M, Kocsisova Z, Leatherman JL, Modahl CM, Rubin MR, Apiz-Saab SS, Arias-Mejias SM, Carrion-Ortiz CF, Claudio-Vazquez PN, Espada-Green DM, Feliciano-Camacho M, Gonzalez-Bonilla KM, Taboas-Arroyo M, Vargas-Franco D, Montañez-Gonzalez R, Perez-Otero J, Rivera-Burgos M, Rivera-Rosario FJ, Eisler HL, Alexander J, Begley SK, Gabbard D, Allen RJ, Aung WY, Barshop WD, Boozalis A, Chu VP, Davis JS, Duggal RN, Franklin R, Gavinski K, Gebreyesus H, Gong HZ, Greenstein RA, Guo AD, Hanson C, Homa KE, Hsu SC, Huang Y, Huo L, Jacobs S, Jia S, Jung KL, Wai-Chee Kong S, Kroll MR, Lee BM, Lee PF, Levine KM, Li AS, Liu C, Liu MM, Lousararian AP, Lowery PB, Mallya AP, Marcus JE, Ng PC, Nguyen HP, Patel R, Precht H, Rastogi S, Sarezky JM, Schefkind A, Schultz MB, Shen D, Skorupa T, Spies NC, Stancu G, Vivian Tsang HM, Turski AL, Venkat R, Waldman LE, Wang K, Wang T, Wei JW, Wu DY, Xiong DD, Yu J, Zhou K, McNeil GP, Fernandez RW, Menzies PG, Gu T, Buhler J, Mardis ER, Elgin SCR. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element. G3 (BETHESDA, MD.) 2017; 7:2439-2460. [PMID: 28667019 PMCID: PMC5555453 DOI: 10.1534/g3.117.040907] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 04/03/2017] [Indexed: 11/24/2022]
Abstract
The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster, but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes (e.g., larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae Compared to D. melanogaster, the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains.
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Affiliation(s)
- Wilson Leung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | - Elizabeth J Chen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | - Kevin Ko
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - John M Braverman
- Department of Biology, Saint Joseph's University, Philadelphia, PA 19131
| | | | - Nathan T Mortimer
- School of Biological Sciences, Illinois State University, Normal, IL 61790
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35401
| | - Sheryl T Smith
- Department of Biology, Arcadia University, Glenside, PA 19038
| | - Srebrenka Robic
- Department of Biology, Agnes Scott College, Decatur, GA 30030
| | | | | | | | | | - Ken J Saville
- Department of Biology, Albion College, Albion, MI 49224
| | | | | | | | | | | | - Dennis Revie
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Luis A Jimenez
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Jennifer J Palomino
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Melissa D Patao
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Shane M Patao
- Department of Biology, California Lutheran University, Thousand Oaks, CA 91360
| | - Edward T Himelblau
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Jaclyn D Campbell
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Alexandra L Hertz
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Maddison F McEvilly
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - Allison R Wagner
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93405
| | - James Youngblom
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Baljit Bedi
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Jeffery Bettincourt
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Erin Duso
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Maiye Her
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - William Hilton
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Samantha House
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Masud Karimi
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Kevin Kumimoto
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Rebekah Lee
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Darryl Lopez
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - George Odisho
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Ricky Prasad
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Holly Lyn Robbins
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Tanveer Sandhu
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
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- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Kara Tsukashima
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Hani Yosif
- Department of Biology, California State University, Stanislaus, Turlock, CA 95382
| | - Nighat P Kokan
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Latia Britt
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Alycia Zoellner
- Department of Natural Sciences, Cardinal Stritch University, Milwaukee, WI 53217
| | - Eric P Spana
- Department of Biology, Duke University, Durham, NC 27708
| | - Ben T Chlebina
- Department of Biology, Duke University, Durham, NC 27708
| | - Insun Chong
- Department of Biology, Duke University, Durham, NC 27708
| | | | - Danny A Mammo
- Department of Biology, Duke University, Durham, NC 27708
| | - Chun L Ng
- Department of Biology, Duke University, Durham, NC 27708
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- Department of Biology, Duke University, Durham, NC 27708
| | - Martin G Burg
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Spencer M Batten
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Lindsay M Corbeill
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Erica Enoch
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Jesse J Ensign
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Mary E Franks
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Breanna Haiker
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
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- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Lyndsay D Kirkland
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
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- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Jordan Matthews
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
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- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Nicholaus Monsma
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Katherine J Olson
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Guillermo Perez-Aragon
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
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- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
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- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Christopher Scheiber
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Patrick A Schneider
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Devon E Schultz
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Matthew Simon
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Eric Spencer
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Adam C Wernette
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Maxine E Wykle
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Elizabeth Zavala-Arellano
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Mitchell J McDonald
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Kristine Ostby
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | - Peter Wendland
- Departments of Biomedical Sciences and Cell and Molecular Biology, Grand Valley State University, Allendale, MI 49401
| | | | | | - Amanda H Cox
- Department of Biology, Hofstra University, Hempstead, NY 11549
| | | | | | | | - Michael J Pavia
- Department of Biology, Hofstra University, Hempstead, NY 11549
| | | | | | - Dale L Beach
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | - Heaven L Cerritos
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | - Edward A Horansky
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909
| | - Karim A Sharif
- Department of Biology, Massasoit Community College, Brockton, MA 02302
| | - Ryan Moran
- Department of Biology, Massasoit Community College, Brockton, MA 02302
| | - Susan Parrish
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - Jennifer Bland
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - Kerry Campbell
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - Richard Forka
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Monika C Lemke
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Marlee B Nelson
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - S Mariel Ramey
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Luke Schmidt
- Department of Biology, McDaniel College, Westminster, MD 21157
| | - Paola Villegas
- Department of Biology, McDaniel College, Westminster, MD 21157
| | | | - Stephanie L Christ
- Department of Biological Sciences, Moravian College, Bethlehem, PA 18018
| | - Sami Mamari
- Department of Biological Sciences, Moravian College, Bethlehem, PA 18018
| | - Adam S Rinaldi
- Department of Biological Sciences, Moravian College, Bethlehem, PA 18018
| | - Ghazal Stity
- Department of Biological Sciences, Moravian College, Bethlehem, PA 18018
| | - Amy T Hark
- Department of Biology, Muhlenberg College, Allentown, PA 18104
| | - Mark Scheuerman
- Department of Biology, Muhlenberg College, Allentown, PA 18104
| | - S Catherine Silver Key
- Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC 27707
| | - Briana D McRae
- Department of Biological & Biomedical Sciences, North Carolina Central University, Durham, NC 27707
| | | | - Sam Asinof
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | | | - Kelly Drumm
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Terrance Embry
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | | | | | - Stella Rosen
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Nadia Safa
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Darrin Schultz
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Matt Segal
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Yakov Shevin
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | | | - Tam Vuong
- Department of Biology, Oberlin College, Oberlin, OH 44074
| | - Gary Skuse
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY 14623
| | - Don W Paetkau
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | | | - Alicia R Carroll
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | | | - Susan E Herman
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Misha A Host
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Gabrielle Hussey
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Joan Q Lawrence
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Ellen N Niemiec
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Olivia A Pahl
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | | | | | | | - Mona O Rodriguez
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Laura Schiraldi
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Joanna J Smith
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | - Kelsey F Sugrue
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Kaitlyn E Takach
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Ximena Velez
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Laura T Vives
- Department of Biology, Saint Mary's College, Notre Dame, IN 46556
| | | | - Jeanette Hauke
- Department of Biology, Simmons College, Boston, MA 02115
| | - Charles R Hauser
- Bioinformatics Program, St. Edward's University, Austin, TX 78704
| | - Karolyn Barker
- Bioinformatics Program, St. Edward's University, Austin, TX 78704
| | - Laurie Cannon
- Bioinformatics Program, St. Edward's University, Austin, TX 78704
| | | | - Samantha Parsons
- Bioinformatics Program, St. Edward's University, Austin, TX 78704
| | | | | | - Diana E Johnson
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Abubakarr Bangura
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Jordan A Black
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Victoria Chevee
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Sarah A Einsteen
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Sarah K Hilton
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Max Kollmer
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Rahul Nadendla
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Joyce Stamm
- Department of Biology, University of Evansville, Evansville, IN 47722
| | | | - Amber M Gygi
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Emmy E Ogawa
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Matt Van Camp
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Zuzana Kocsisova
- Department of Biology, University of Evansville, Evansville, IN 47722
| | - Judith L Leatherman
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639
| | - Cassie M Modahl
- Department of Biological Sciences, University of Northern Colorado, Greeley, CO 80639
| | - Michael R Rubin
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | - Susana S Apiz-Saab
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | | | | | | | | | | | | | | | - Joseph Perez-Otero
- Department of Biology, University of Puerto Rico at Cayey, Cayey, PR 00736
| | | | | | - Heather L Eisler
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | - Jackie Alexander
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | - Samatha K Begley
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | - Deana Gabbard
- Department of Biology, University of the Cumberlands, Williamsburg, KY 40769
| | - Robert J Allen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Wint Yan Aung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - William D Barshop
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Amanda Boozalis
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Vanessa P Chu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jeremy S Davis
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Ryan N Duggal
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Robert Franklin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Katherine Gavinski
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Heran Gebreyesus
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Henry Z Gong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Rachel A Greenstein
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Averill D Guo
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Casey Hanson
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kaitlin E Homa
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Simon C Hsu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Yi Huang
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Lucy Huo
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Sarah Jacobs
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Sasha Jia
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kyle L Jung
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Sarah Wai-Chee Kong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Matthew R Kroll
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Brandon M Lee
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Paul F Lee
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kevin M Levine
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Amy S Li
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Chengyu Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Max Mian Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Adam P Lousararian
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Peter B Lowery
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Allyson P Mallya
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Joseph E Marcus
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Patrick C Ng
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Hien P Nguyen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Ruchik Patel
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Hashini Precht
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Suchita Rastogi
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jonathan M Sarezky
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Adam Schefkind
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Michael B Schultz
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Delia Shen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Tara Skorupa
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Nicholas C Spies
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Gabriel Stancu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | - Alice L Turski
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Rohit Venkat
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Leah E Waldman
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kaidi Wang
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Tracy Wang
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jeffrey W Wei
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Dennis Y Wu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - David D Xiong
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jack Yu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Karen Zhou
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Gerard P McNeil
- Department of Biology, York College / CUNY, Jamaica, NY 11451
| | | | | | - Tingting Gu
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Jeremy Buhler
- Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Elaine R Mardis
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63108
| | - Sarah C R Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
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Lower SS, Johnston JS, Stanger-Hall KF, Hjelmen CE, Hanrahan SJ, Korunes K, Hall D. Genome Size in North American Fireflies: Substantial Variation Likely Driven by Neutral Processes. Genome Biol Evol 2017; 9:1499-1512. [PMID: 28541478 PMCID: PMC5499882 DOI: 10.1093/gbe/evx097] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic genomes show tremendous size variation across taxa. Proximate explanations for genome size variation include differences in ploidy and amounts of noncoding DNA, especially repetitive DNA. Ultimate explanations include selection on physiological correlates of genome size such as cell size, which in turn influence body size, resulting in the often-observed correlation between body size and genome size. In this study, we examined body size and repetitive DNA elements in relationship to the evolution of genome size in North American representatives of a single beetle family, the Lampyridae (fireflies). The 23 species considered represent an excellent study system because of the greater than 5-fold range of genome sizes, documented here using flow cytometry, and the 3-fold range in body size, measured using pronotum width. We also identified common genomic repetitive elements using low-coverage sequencing. We found a positive relationship between genome size and repetitive DNA, particularly retrotransposons. Both genome size and these elements were evolving as expected given phylogenetic relatedness. We also tested whether genome size varied with body size and found no relationship. Together, our results suggest that genome size is evolving neutrally in fireflies.
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Affiliation(s)
| | | | | | | | | | | | - David Hall
- Department of Genetics, University of Georgia
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Bargues N, Lerat E. Evolutionary history of LTR-retrotransposons among 20 Drosophila species. Mob DNA 2017; 8:7. [PMID: 28465726 PMCID: PMC5408442 DOI: 10.1186/s13100-017-0090-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 04/21/2017] [Indexed: 12/26/2022] Open
Abstract
Background The presence of transposable elements (TEs) in genomes is known to explain in part the variations of genome sizes among eukaryotes. Even among closely related species, the variation of TE amount may be striking, as for example between the two sibling species, Drosophila melanogaster and D. simulans. However, not much is known concerning the TE content and dynamics among other Drosophila species. The sequencing of several Drosophila genomes, covering the two subgenus Sophophora and Drosophila, revealed a large variation of the repeat content among these species but no much information is known concerning their precise TE content. The identification of some consensus sequences of TEs from the various sequenced Drosophila species allowed to get an idea concerning their variety in term of diversity of superfamilies but the used classification remains very elusive and ambiguous. Results We choose to focus on LTR-retrotransposons because they represent the most widely represented class of TEs in the Drosophila genomes. In this work, we describe for the first time the phylogenetic relationship of each LTR-retrotransposon family described in 20 Drosophila species, compute their proportion in their respective genomes and identify several new cases of horizontal transfers. Conclusion All these results allow us to have a clearer view on the evolutionary history of LTR retrotransposons among Drosophila that seems to be mainly driven by vertical transmissions although the implications of horizontal transfers, losses and intra-specific diversification are clearly also at play. Electronic supplementary material The online version of this article (doi:10.1186/s13100-017-0090-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicolas Bargues
- CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
| | - Emmanuelle Lerat
- CNRS, UMR 5558, Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Claude Bernard Lyon 1, F-69622 Villeurbanne, France
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47
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Hjelmen CE, Johnston JS. The mode and tempo of genome size evolution in the subgenus Sophophora. PLoS One 2017; 12:e0173505. [PMID: 28267812 PMCID: PMC5340367 DOI: 10.1371/journal.pone.0173505] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/21/2017] [Indexed: 01/05/2023] Open
Abstract
Genome size varies widely across organisms, with no apparent tie to organismal complexity. While genome size is inherited, there is no established evolutionary model for this trait. Hypotheses have been postulated for the observed variation in genome sizes across species, most notably the effective population size hypothesis, the mutational equilibrium hypothesis, and the adaptive hypothesis. While much data has been collected on genome size, the above hypotheses have largely ignored impacts from phylogenetic relationships. In order to test these competing hypotheses, genome sizes of 87 Sophophora species were analyzed in a comparative phylogenetic approach using Pagel’s parameters of evolution, Blomberg’s K, Abouheif’s Cmean and Moran’s I. In addition to testing the mode and rate of genome size evolution in Sophophora species, the effect of number of taxa on detection of phylogenetic signal was analyzed for each of these comparative phylogenetic methods. Sophophora genome size was found to be dependent on the phylogeny, indicating that evolutionary time was important for predicting the variation among species. Genome size was found to evolve gradually on branches of the tree, with a rapid burst of change early in the phylogeny. These results suggest that Sophophora genome size has experienced gradual changes, which support the largely theoretical mutational equilibrium hypothesis. While some methods (Abouheif’s Cmean and Moran’s I) were found to be affected by increasing taxa numbers, more commonly used methods (λ and Blomberg’s K) were found to have increasing reliability with increasing taxa number, with significantly more support with fifteen or more taxa. Our results suggest that these comparative phylogenetic methods, with adequate taxon sampling, can be a powerful way to uncover the enigma that is genome size variation through incorporation of phylogenetic relationships.
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Affiliation(s)
- Carl E. Hjelmen
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| | - J. Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, Texas, United States of America
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Cicconardi F, Di Marino D, Olimpieri PP, Arthofer W, Schlick-Steiner BC, Steiner FM. Chemosensory adaptations of the mountain fly Drosophila nigrosparsa (Insecta: Diptera) through genomics' and structural biology's lenses. Sci Rep 2017; 7:43770. [PMID: 28256589 PMCID: PMC5335605 DOI: 10.1038/srep43770] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/30/2017] [Indexed: 01/14/2023] Open
Abstract
Chemoreception is essential for survival. Some chemicals signal the presence of nutrients or toxins, others the proximity of mating partners, competitors, or predators. Chemical signal transduction has therefore been studied in multiple organisms. In Drosophila species, a number of odorant receptor genes and various other types of chemoreceptors were found. Three main gene families encode for membrane receptors and one for globular proteins that shuttle compounds with different degrees of affinity and specificity towards receptors. By sequencing the genome of Drosophila nigrosparsa, a habitat specialist restricted to montane/alpine environment, and combining genomics and structural biology techniques, we characterised odorant, gustatory, ionotropic receptors and odorant binding proteins, annotating 189 loci and modelling the protein structure of two ionotropic receptors and one odorant binding protein. We hypothesise that the D. nigrosparsa genome experienced gene loss and various evolutionary pressures (diversifying positive selection, relaxation, and pseudogenisation), as well as structural modification in the geometry and electrostatic potential of the two ionotropic receptor binding sites. We discuss possible trajectories in chemosensory adaptation processes, possibly enhancing compound affinity and mediating the evolution of more specialized food, and a fine-tuned mechanism of adaptation.
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MESH Headings
- Adaptation, Physiological/genetics
- Animals
- Drosophila/genetics
- Drosophila Proteins/classification
- Drosophila Proteins/genetics
- Genomic Library
- Genomics/methods
- Models, Molecular
- Multigene Family/genetics
- Phylogeny
- Protein Conformation
- Receptors, Cell Surface/classification
- Receptors, Cell Surface/genetics
- Receptors, Ionotropic Glutamate/chemistry
- Receptors, Ionotropic Glutamate/classification
- Receptors, Ionotropic Glutamate/genetics
- Receptors, Odorant/chemistry
- Receptors, Odorant/classification
- Receptors, Odorant/genetics
- Sequence Analysis, DNA/methods
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Affiliation(s)
- Francesco Cicconardi
- Institute of Ecology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | - Daniele Di Marino
- Department of Informatics, Institute of Computational Science, University of Italian Switzerland, Lugano, Switzerland
| | | | - Wolfgang Arthofer
- Institute of Ecology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
| | | | - Florian M. Steiner
- Institute of Ecology, University of Innsbruck, Technikerstr. 25, 6020 Innsbruck, Austria
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