Characterization and phylogenetic analysis of LINE elements in Entamoeba sp. A) Multiple sequence alignment of the 5' and 3' ends of Ei_LINE and insertion sites. The 5' and 3' termini are highlighted in bold. Target site duplications (TSD) are underlined. Ei_LINEs from contigs AANW02000355, AANW02001294, AANW02001046 and AANW02001402 are truncated and lack either the 5' or 3' end of the element. Genomic coordinates for Ei_LINEs excluding ISD are: AANW02000718 (41,801–46,844), AANW02000022 (38,839–43,869), AANW02000355 (5,491–6,819), AANW02001294 (486–1,665), AANW02001046 (2,758-1,949) and AANW02001402 (3,418-2,447). GenBank accessions of E. invadens contigs are indicated on the left. B) Phylogenetic analysis of the reverse transcriptase sequences from all identified Entamoeba LINEs compared to reverse transcriptases derived from different families of retroelements and retroviruses. Thin black lines, branches with bootstrap values below 500; bold grey lines, branches containing bootstrap values between 500 and 750; bold black lines, branches supported by bootstrap values above 750. Nodes containing Entamoeba LINEs are highlighted in blue.