Fig. 5

LTR retrotransposons are disproportionately active at the protein level compared to other TEs. a Schematic illustrating representative TEs previously identified in mosquitoes (not to scale). Filled boxes indicate protein-coding regions, open boxes and grey shading indicate non-translated regions and conserved non-coding domains (grey). Note that not all SINEs are tRNA-like. Bracketed ORFs are not always found in that TE subclass. Typical terminal amino acids are indicated for non-LTR retrotransposons, SINEs and helitrons. Env-like, envelope-like protein (incomplete); gag, group antigen; LTR, long-terminal repeat retrotransposons; MITE, miniature inverted repeat transposable element; non-LTR, non-LTR retrotransposon; PLE, Penelope-like element; pol, polymerase; SINE, short interspersed element; TIR, terminal inverted repeat. b Absolute abundance of proteins derived from known mosquito protein-coding TEs in the total PIT proteome (i) and for all PIT hits associated with two or more peptides (ii). c Relative enrichment of proteins from detected TEs using >30% (i), >40% (ii) and >50% (iii) amino acid identity as a threshold for TE discovery (>45% sequence coverage throughout). Enrichment is shown relative to the proportion of the Ae. aegypti reference genome that is comprised of sequences derived from each respective TE subclass (genome (%)) [8], relative to the total copy number of elements from each TE subclass within the Ae. aegypti reference genome (genome (copy #)) [8], and relative to the total number of entries for each TE subclass in the TEfam database used to identify TEs in our dataset. Enrichment is shown relative to LTR retrotransposons. d as for (c), except that only PIT hits identified through more than two peptides are shown