2.3. Repeats Identification and Synteny Analysis

The de novo repeat identification was performed using RepeatModeler v.2.0.1 and RepeatMasker v.4.1.0 [55] with the option ‘-species’ set to Euglenozoa. The repeats families were annotated using BLASTX and BLASTN with the e-value set to 0.01.

Synteny analysis was completed using SyMAP v.5.0.5 [56] with the following settings: minimum size of sequence to load, 500 bp; minimum number of anchors required to define a synteny block, 7; synteny blocks merged in case of overlaps; and, only the larger block kept if two synteny blocks overlapped on a chromosome. For synteny inferences, the pseudo-chromosomes that were produced by Companion were used with the sequences of L. major Friedlin as a reference. The cross-mapping of pseudo-chromosomes was visualized using Chromosomer v.0.1.4 [57].