Fig. 2

Transposable elements (TEs) and their role in genetic variation in An. stephensi. a Proportion of TEs (counted in bp) that were uncovered by the new reference assembly of An. stephensi. Many LTR and non-LTR TEs are identified for the first time. b Similar to many other LTR and non-LTR retrotranspososons, LTR elements AST266LTR and AST281LTR and non-LTR element NLTR-32 do not have any closely related counterpart in An. gambiae. As shown here, only small parts of these TE sequences were known. c Insertion of a polymorphic LTR fragment immediately upstream of the highly conserved gene Enolase. The insertion creates a gap between the promoters and the transcription start sites in half of the alleles and may disrupt transcription of the gene. d A polymorphic DNA element AST524 located in the 3′ UTR of gcl creates a null gcl allele. e Comparison of TE compositions in the autosomal, X, and Y chromosomal sequences. Not only are most of the Y sequences repeats (Additional file 1: Figure S6), but the majority of Y TEs are LTR elements. f LTR retrotransposon AST301 is present in intact copies only in Y contigs. Its counterparts in the autosomes and X chromosome are fragmented and more diverged than the AST301 sequences found on the Y sequences