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Fig. 2 | Mobile DNA

Fig. 2

From: Horizontal transfer of a retrotransposon between parasitic nematodes and the common shrew

Fig. 2

Test for contamination/horizontal transfer with long reads and paired-end reads. 1. Selection of reads that code for a specific RTE. (a) Long reads are selected if they code for the RTE, (b) paired-end reads are selected if one of the mates maps to a RTE region in the reference assembly, (c) paired-end reads are selected if one of the mates codes for the RTE. RTE sequences were previously identified with RepeatMasker in the individual reads and/or the reference assembly. 2. The selected long reads or non RTE-coding read pair mates are compared against two databases. One database (cyan: “self”) contains genomes of the taxon of the tested species, without the genome of the species itself. A second database (blue: “non-self”) contains genomes of the taxon of the species from which the RTE originates. 3. Depending on the comparisons of the reads to the databases, a decision is being made whether the reads containing the RTE belong to the tested species (hit “self” database) and are based on horizontal transfer (cyan), or if the complete long reads/read pairs belong to another taxon (hit “non-self” database) and are based on contamination (blue). Green rectangle: RTE sequence

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