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Additional file 1: Table S1. Octopus vulgaris samples utilized for sequencing. Table S2. Counts of the assembled Octopus vulgaris and O. bimaculoides transcriptomes. Table S3. Counts of the repeats composition for the assembled Octopus vulgaris transcriptome. Table S4. LINEs used for phylogenetic analysis. Fig. S1. Completeness of Octopus transcriptomes. Fig. S2. Stringent classification of lncRNAs. Fig. S3. Most represented GO Molecular Function and Cellular Component classes. Fig. S4. Percentages of transcripts associated to transposable elements. Fig. S5. Southern blot analysis of the Octopus vulgaris LINE element. Fig. S6. In situ hybridization for LINE in the brain (SEM, SUB and OL) and arm of adult Octopus vulgaris, and relative controls.

Additional file 6. Expression profiles of the 4 most expressed LINE. A) and C) LINE2A and LINE2C1 have similar expression profiles and are mostly expressed in EMS cell (4-cell stage) and in MSx2 cell (16-cell stage). B) LINE2B is expressed in 8-cell E, in AB cells and in MSx1 cell of the 16-cell stage. D) LINE2F is expressed ~ 5-fold with respect to LINE 2A, 2B and 2C1 and its expression seems to be related to 16-cell stage Ea and Ep cells.

Additional file 1. TE occupancy in C. elegans, Drosophila, mouse and human reference genomes. Genomic occupancy of the 5 TE classes (DNA – light red, RC - ochre, LINE – light green, LTR - cyan and SINE - purple) in C. elegans, D. melanogaster, M. musculus and H. sapiens genomes. More than 70% of C. elegans TE are DNA transposons, ~ 60% of Drosophila TE are annotated as LTR and intriguingly Drosophila genome completely lacks SINE, ~ 40% of mouse TE are annotated as SINE and ~ 45% of human TE are LINE. TE annotation files for the 5 species have been retrieved from UCSC database (https://genome.ucsc.edu).

Additional file 5. CER1 and LTRCER1 expression profiles in the C. elegans early embryo. A) CER1 and B) LTRCER1 expression profiles. CER1 and LTRCER1 are the most expressed LTR elements. The two LTR are expressed in the 1-, 2-, 4- and 8-cell stages while their expression in the 16-cell stage is very low. Their expression profiles recapitulate the global expression pattern of LTR elements.

Additional file 7. Expression profiles of the 4 most expressed DNA transposons. A) CEMUDR1 has an LTR-like expression profile: it is expressed in the 1-, 2-, 4- and 8-cell stages and not in the 16-cell stage. B) Chapaev-1 has a constant expression profile that recapitulates the general DNA transposon class profile of expression. C) and D) PALTA3 and PALTTTAAA3 have a non-LTR-like profile of expression: these TE are mostly expressed in 16-cell stage AB cells.

Additional file 4. TE expression profiles in the C. elegans early embryo. For each TE belonging to DNA, LTR, LINE and SINE classes (rows) are reported the log10(RPM) expression values of each replicate of the 31 cells analyzed (columns). Black color means no expression, green low and red high expression. The horizontal color band above the picture corresponds to different stages (1-, 2-, 4-, 8- and 16-cell stages – left to right), while the vertical color band on the left side of the picture indicates the TE classes (DNA, LTR, LINE, SINE – top to bottom).

Additional file 7. Expression profiles of the 4 most expressed DNA transposons. A) CEMUDR1 has an LTR-like expression profile: it is expressed in the 1-, 2-, 4- and 8-cell stages and not in the 16-cell stage. B) Chapaev-1 has a constant expression profile that recapitulates the general DNA transposon class profile of expression. C) and D) PALTA3 and PALTTTAAA3 have a non-LTR-like profile of expression: these TE are mostly expressed in 16-cell stage AB cells.

Far from being devoid of life, Antarctic waters are home to Cryonotothenioidea, which represent one of the fascinating cases of evolutionary adaptation to extreme environmental conditions in vertebrates. Thanks to a series of unique morphological and physiological peculiarities, which include the paradigmatic case of loss of hemoglobin in the family Channichthyidae, these fish survive and thrive at sub-zero temperatures. While some of the distinctive features of such adaptations have been known for decades, our knowledge of their genetic and molecular bases is still limited. We generated a reference de novo assembly of the icefish Chionodraco hamatus transcriptome and used this resource for a large-scale comparative analysis among five red-blooded Cryonotothenioidea, the sub-Antarctic notothenioid Eleginops maclovinus and seven temperate teleost species. Our investigation targeted the gills, a tissue of primary importance for gaseous exchange, osmoregulation, ammonia excretion, and its role in fish immunity. One hundred and twenty genes were identified as significantly up-regulated in Antarctic species and surprisingly shared by red- and white-blooded notothenioids, unveiling several previously unreported molecular players that might have contributed to the evolutionary success of Cryonotothenioidea in Antarctica. In particular, we detected cobalamin deficiency signatures and discussed the possible biological implications of this condition concerning hematological alterations and the heavy parasitic loads typically observed in all Cryonotothenioidea.