Fig. 4

Visualisation of Class I LINEs. A Multiple sequence alignment (MSA) of a LINE retrotransposon showing typical shorter copies of the TE that manifest in truncations at the 5′ end. The consensus fasta sequence of Schistosoma mansoni “Perere-5” autonomous LINE retrotransposon (GenBank accession BN000796.1) was downloaded and used as query to search the S. mansoni genome for highly similar sequences (Protocol 8). The MSA was generated with MUSCLE [25] and re-ordered manually for display purposes. The resulting alignment is seen at the top, with dashed boxes marking the start (5′ end) and end (3′ end) of the alignment and the respective magnified views. Arrows indicate the first (5′ end panel) and last (3′ end panel) nucleotides of the alignment that correspond to the start and end of the TE alignment of the full-length consensus sequence. Some of the sequences that are part of this alignment are truncated at the 5′ end and are shown as shorter sequences in the alignments (arrowhead). In this particular example, a number of full-length sequences retrieved from the genome (as evidenced by high homology and sharp transition to non-homologous flanking sequences at the 5′ end of the alignments) enables generation of a full-length consensus sequence. B Target Site Duplications (TSDs) are found flaking TE insertions. A LINE retrotransposon is used to illustrate how TSDs can be seen in a MSA. Unlike the consistent TSD length of LTR and DNA transposon families, LINEs, as in the example, have variable length TSDs (dashed boxes). In this example, the 3′ end of the alignment is jagged due to the presence of a microsatellite GTAA (arrowhead indicates a sequence with two full copies). The bottom panel (in black and white) shows hypothetical TSDs that illustrate the variability observed in biological settings