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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 column) or transcriptomes assembled from 40 million reads (T, right column) are shown the same way as in Figure 3. The total number of TE families detected is indicated above each column. Brasp - Branchinotogluma sp.; Lepwil - Lepidonotopodium williamsae; Harful - Harmothoe fuligineum; Harsp - Harmothoe sp.; Pefu - Pettitbonesia furcosetosa; Pgras - P.grasslei. (.xls)

Additional file 1. Summary of previous data on annelid transposable elements (.pdf)

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 15 species of annelids (all), as well as the detail for the transcriptomes obtained for increasing subsamples of reads (Millions). (.pdf)

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 subtrees. All LTR-retrotransposons from a clade found in annelids are depicted in color. The reference Gypsy elements and Gypsy clades previously reported in the GypsyDatabase are in black. Node statistical support (>70%) was obtained through non-parametric bootstrapping using 100 replicates. (.pdf)

Additional file 1: Figure S1. Phylogeny of Alveolata. Proteomes from 89 alveolates genomes and transcriptome assemblies from the MMETSP project ( https://zenodo.org/record/257026/files/ ) were used to create orthologous groups using orthofinder v2.2 with the diamond BLAST similarity search. Single ortholog alignments were pruned using PhyloTreePruner v.1.0 (minimum taxa to keep 44 and support value 0.9) and realigned using mafft v7 and filtered with Gblocks v.0.91b (−b5 = a -p = n). Filtered alignments were concatenated using seqCat.pl and a phylogenetic tree was produced under Maximum Likelihood framework using RAxML v8.2.9 with the PROTGAMMALGF model of sequence evolution and 101 bootstraps. Asterics represent support values of 95 and above. A detailed method can be found in Kayal et al. 2018 BMC Evol. Biol. ( https://doi.org/10.1186/s12862-018-1142-0 ). The full tree can be found at http://mmo.sb-roscoff.fr/jbrowseAmoebophrya/ . Figure S2. SSU rDNA sequence identity (in percentage, relative to A25 and A120 compared to other species). Figure S3. Distribution of k-mer in A25 and A120 genomes. Figure S4. Classification of repeated elements in 3 Amoebophrya genomes (AT5, A25, and A120) using REPET. The x-axis represents the cumulated number of bases of repeated elements in the genome. Figure S5. Conserved motif of the putative splice leader (SL) in A25 and A120. Figure S6. Alignments of gene encoding the putative spliced leader (SL) gene in A25 and A120. Figure S7. Gene orientation change rate in 3 Amoebophrya genomes. Figure S8. Number of orthologs genes shared by selected taxa. Figure S9. Boxplot of the dN/dS ratios of orthologous genes between A25 and A120, calculated using the model average method (MA). Figure S10. Synteny dot-plot obtained by comparison between Amoebophrya A25 and AT5 genomes. Figure S11. Synteny dot-plot obtained by comparison between Amoebophrya A120 and AT5 genomes. Figure S12. Intron length distribution. Figure S13. GC content distribution. Figure S14. Multiple alignments of U2 snRNAs. Figure S15. Multiple alignments of U4 snRNAs. Figure S16. Multiple alignments of U5 snRNAs. Figure S17. Multiple alignments of U6 snRNAs. Figure S18. Secondary structure of Amoebophrya snRNA. Figure S19. Example of introner elements (IEs) in Amoebophrya. Figure S20. Distribution the direct repeats with size ranging between 3 and 8 nucleotides in A25. Figure S21. Distribution of the direct repeats with size ranging between 3 and 8 nucleotides in A120. Figure S22. Composition of direct repeats in introners elements. The diversity in composition of the three (a, b, c) most abundant of direct repeats in introner elements in A25 (up) and A120 (down). Figure S23. Terminal inverted repeat locations around the splicing sites in A25 and A120. The position of inverted repeats according to the location of the splice sites in A25 and A120. Left, the inverted repeats of A120 are located at 1–5 the nucleotides upstream and downstream of the splice sites. Right, the inverted repeats of A25 are located at the 1–6 nucleotides in upstream and downstream of the splice sites. Figure S24. The flowchart for the in silico search of introner elements. Figure S25. Hierarchical clustering analysis (pairwise similarity and OrthoMCL) of all intron families and of the inverted repeats in A25 and A120. Figure S26. Percentage of genes with assigned functions in relation with introns composition. Figure S27. Difference in the proportion of IEs-containing-genes compared to their KEGG assignment in A25 and A120. Figure S28. Distribution of conserved introns. Table S1. RCC number, date and site of isolation of strains considered in this study. Table S2. Metrics of Nanopore runs for the two Amoebophrya strains. Table S3. Search for pathways involved in plastidial functions that are entirely independent of plastid-encoded gene content. Table S4. Number of the different types of introns identified in A25 and A120 genomes. Table S5. Search for RNA editing in A25 and A120 introns. Table S6. Putative Amoebophrya A25 and A120 snRNP homologs. Table S7. Classification into families of non-canonical introns in A25 and A120. Table S8. RNAseq read assembly statistics of Amoebophrya A25 and A120 corresponding samples from the different time of infection and to the free-living stage (dinospore only). Table S9. Total number of contigs belonging to samples from different stages of infection and the proportion of them that were aligned against the genomes of both Amoebophrya A25 and A120. ND corresponds to “not determined” when no measurement was done. Table S10. Metabolic pathway screened in A25 and A120 proteomes.

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 from annelids are indicated in color. Node statistical support values (>70 %) come from non-parametric bootstrapping using 100 replicates. (.pdf)

International audience; Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya. We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.

Understanding factors that generate, maintain, and constrain host-parasite associations is of major interest to biologists. Although little studied, many extremely virulent micro-eukaryotic parasites infecting microalgae have been reported in the marine plankton. This is the case for Amoebophrya, a diverse and highly widespread group of Syndiniales infecting and potentially controlling dinoflagellate populations. Here, we analyzed the time-scale gene expression of a complete infection cycle of two Amoebophrya strains infecting the same host (the dinoflagellate Scrippsiella acuminata), but diverging by their host range (one infecting a single host, the other infecting more than one species). Over two-thirds of genes showed two-fold differences in expression between at least two sampled stages of the Amoebophrya life cycle. Genes related to carbohydrate metabolism as well as signaling pathways involving proteases and transporters were overexpressed during the free-living stage of the parasitoid. Once inside the host, all genes related to transcription and translation pathways were actively expressed, suggesting the rapid and extensive protein translation needed following host-cell invasion. Finally, genes related to cellular division and components of the flagellum organization were overexpressed during the sporont stage. In order to gain a deeper understanding of the biological basis of the host-parasitoid interaction, we screened proteins involved in host-cell recognition, invasion, and protection against host-defense identified in model apicomplexan parasites. Very few of the genes encoding critical components of the parasitic lifestyle of apicomplexans could be unambiguously identified as highly expressed in Amoebophrya. Genes related to the oxidative stress response were identified as highly expressed in both parasitoid strains. Among them, the correlated expression of superoxide dismutase/ascorbate peroxidase in the specialist parasite was consistent with previous studies on Perkinsus marinus defense. However, this defense process could not be identified in the generalist Amoebophrya strain, suggesting the establishment of different strategies for parasite protection related to host specificity.