DOI 10.1186/s13100-021-00252-0 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.
Transposable elements, LTR-retrotransposons, Polychaetous annelids, Transcriptoms, PIWI proteins
| File | Pages | Size | Access | |
|---|---|---|---|---|
Publisher's official version | 24 | 4 Mo | ||
Additional file 1. Summary of previous data on annelid transposable elements | 2 | 110 Ko | ||
Additional file 2. Standard classification of annelid species studied. | 2 | 174 Ko | ||
Additional file 3. DNA C-values for species of annelids. | - | 11 Ko | ||
Additional file 4. Scatter plot showing the relationship between transcripts, clusters and TE family numbers. The graphs represent the data obtained on all the assembled transcriptomes for the ... | 3 | 336 Ko | ||
Additional file 5. Heat maps of TE types identified in 12 remaining annelids according to the number of reads used for the transcriptome assembly | - | 41 Ko | ||
Additional file 6. Heat maps of TE types identified in the low-coverage genome or in the transcriptome of the six remaining annelids. For each species, proportions of TEs in the genome (G, left ... | 1 | 105 Ko | ||
Additional file 7. Phylogenetic relationships of Integrase sequences of Copia retrotransposons based on Neighbor-Joining analysis of Integrase domain amino acid sequences. The Copia families... | 1 | 425 Ko | ||
Additional file 8. Phylogenetic relationships of Integrase sequences of BEL/Pao retrotransposons based on Neighbor-Joining analysis of Integrase domain amino acid sequences. The BEL/Pao families ... | 1 | 748 Ko | ||
Additional file 9. Phylogenetic relationships among Gypsy clades. This tree is a simplified representation of Figure 9, in which annelid elements from the same clade are represented by compressed... | 1 | 18 Ko | ||
Additional file 10. Distribution of Gypsy clades within annelids. Tanglegram-like representation of connections between Gypsy clades and annelid species within an ordered list of species names ... | 1 | 259 Ko | ||
Additional file 11. Example of long transcripts containing multiple fragments of diverse transposable element origins reminiscent of piRNA cluster structure. Schematic representations of transcripts | - | 2 Mo | ||
Additional file 12. Annelid species localization. | - | 24 Ko | ||
Additional file 13. Source of annelid elements added to the reference database. | - | 13 Ko | ||
Additional file 14. Amino acid sequences of annelid elements added to the reference database. | - | 159 Ko | ||
Additional file 15. Categories of transposable elements used and their correspondence in the referenced databases | - | 15 Ko | ||
Additional file 16. Annelid transcripts that potentially contain a TE fragment | - | 81 Mo |
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