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Filée J, Farhat S, Higuet D, Teysset L, Marie D, Thomas-Bulle C, Hourdez S, Jollivet D, Bonnivard E. Comparative genomic and transcriptomic analyses of transposable elements in polychaetous annelids highlight LTR retrotransposon diversity and evolution. Mob DNA 2021; 12:24. [PMID: 34715903 PMCID: PMC8556966 DOI: 10.1186/s13100-021-00252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/08/2021] [Indexed: 11/24/2022] Open
Abstract
Background With the expansion of high throughput sequencing, we now have access to a larger number of genome-wide studies analyzing the Transposable elements (TEs) composition in a wide variety of organisms. However, genomic analyses often remain too limited in number and diversity of species investigated to study in depth the dynamics and evolutionary success of the different types of TEs among metazoans. Therefore, we chose to investigate the use of transcriptomes to describe the diversity of TEs in phylogenetically related species by conducting the first comparative analysis of TEs in two groups of polychaetes and evaluate the diversity of TEs that might impact genomic evolution as a result of their mobility. Results We present a detailed analysis of TEs distribution in transcriptomes extracted from 15 polychaetes depending on the number of reads used during assembly, and also compare these results with additional TE scans on associated low-coverage genomes. We then characterized the clades defined by 1021 LTR-retrotransposon families identified in 26 species. Clade richness was highly dependent on the considered superfamily. Copia elements appear rare and are equally distributed in only three clades, GalEa, Hydra and CoMol. Among the eight BEL/Pao clades identified in annelids, two small clades within the Sailor lineage are new for science. We characterized 17 Gypsy clades of which only 4 are new; the C-clade largely dominates with a quarter of the families. Finally, all species also expressed for the majority two distinct transcripts encoding PIWI proteins, known to be involved in control of TEs mobilities. Conclusions This study shows that the use of transcriptomes assembled from 40 million reads was sufficient to access to the diversity and proportion of the transposable elements compared to those obtained by low coverage sequencing. Among LTR-retrotransposons Gypsy elements were unequivocally dominant but results suggest that the number of Gypsy clades, although high, may be more limited than previously thought in metazoans. For BEL/Pao elements, the organization of clades within the Sailor lineage appears more difficult to establish clearly. The Copia elements remain rare and result from the evolutionary consistent success of the same three clades. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-021-00252-0.
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Affiliation(s)
- Jonathan Filée
- Laboratoire Evolution, Genomes, Comportement, Ecologie CNRS, Université Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Sarah Farhat
- Marine Animal Disease Laboratory, School of Marine and Atmospheric Sciences, Stony Brook University, 100 Nicolls Road, Stony Brook, NY, 11794-5000, USA
| | - Dominique Higuet
- Institut de Systématique, Evolution, Biodiversité (ISYEB) - Sorbonne Université, Muséum National d'Histoire Naturel, CNRS, EPHE, Université des Antilles, 7 quai Saint Bernard, 75252, Paris Cedex 05, France
| | - Laure Teysset
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Laboratoire Biologie du Développement, UMR7622, "Transgenerational Epigenetics & small RNA Biology", F-75005, Paris, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Camille Thomas-Bulle
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Stephane Hourdez
- UMR8222 LECOB CNRS-Sorbonne Université, Observatoire Océanologique de Banyuls, 1 avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France
| | - Eric Bonnivard
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier, 29688, Roscoff, France.
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Thomas-Bulle C, Piednoël M, Donnart T, Filée J, Jollivet D, Bonnivard É. Mollusc genomes reveal variability in patterns of LTR-retrotransposons dynamics. BMC Genomics 2018; 19:821. [PMID: 30442098 PMCID: PMC6238403 DOI: 10.1186/s12864-018-5200-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/25/2018] [Indexed: 01/06/2023] Open
Abstract
Background The three superfamilies of Long Terminal Repeat (LTR) retrotransposons are a widespread kind of transposable element and a major factor in eukaryotic genome evolution. In metazoans, recent studies suggested that Copia LTR-retrotransposons display specific dynamic compared to the more abundant and diverse Gypsy elements. Indeed, Copia elements show a relative scarcity and the prevalence of only a few clades in specific hosts. Thus, BEL/Pao seems to be the second most abundant superfamily. However, the generality of these assumptions remains to be assessed. Therefore, we carried out the first large-scale comparative genomic analysis of LTR-retrotransposons in molluscs. The aim of this study was to analyse the diversity, copy numbers, genomic proportions and distribution of LTR-retrotransposons in a large host phylum. Results We compare nine genomes of molluscs and further added LTR-retrotransposons sequences detected in databases for 47 additional species. We identified 1709 families, which enabled us to define 31 clades. We show that clade richness was highly dependent on the considered superfamily. We found only three Copia clades, including GalEa and Hydra which appear to be widely distributed and highly dominant as they account for 96% of the characterised Copia elements. Among the seven BEL/Pao clades identified, Sparrow and Surcouf are characterised for the first time. We find no BEL or Pao elements, but the rare clades Dan and Flow are present in molluscs. Finally, we characterised 21 Gypsy clades, only five of which had been previously described, the C-clade being the most abundant one. Even if they are found in the same number of host species, Copia elements are clearly less abundant than BEL/Pao elements in copy number or genomic proportions, while Gypsy elements are always the most abundant ones whatever the parameter considered. Conclusions Our analysis confirms the contrasting dynamics of Copia and Gypsy elements in metazoans and indicates that BEL/Pao represents the second most abundant superfamily, probably reflecting an intermediate dynamic. Altogether, the data obtained in several taxa highly suggest that these patterns can be generalised for most metazoans. Finally, we highlight the importance of using database information in complement of genome analyses when analyzing transposable element diversity. Electronic supplementary material The online version of this article (10.1186/s12864-018-5200-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Camille Thomas-Bulle
- Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France. .,Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier CS90074, 29688, Roscoff, France.
| | - Mathieu Piednoël
- Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France
| | - Tifenn Donnart
- Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France
| | - Jonathan Filée
- Laboratoire Evolution, Génomes, Comportement, Ecologie; CNRS, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144 AD2M, Station Biologique de Roscoff, Place Georges Teissier CS90074, 29688, Roscoff, France
| | - Éric Bonnivard
- Sorbonne Université, Univ Antilles, CNRS, Institut de Biologie Paris Seine (IBPS), Laboratoire Evolution Paris Seine, F-75005, Paris, France
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