T. indotineae reference genome annotation

Annotation of the T. indotineae reference genome (GenBank GCA_023065905.1; strain TIMM20114). Annotation completed as follows: The <i>T. indotineae</i> reference genome was annotated by identifying repeat content using Repeatmodeler v2.0.3 (25) (engine NCBI) with CD-HIT (26), ReCon v1.08 (27), RMBlast v2.11.0, Tandem Repeats Finder v4.09 (28), RepeatScout v1.06 (29) and RepeatMasker v4.1.2-p1 (30). The output of Repeatmodeller was then used as a library for RepeatMasker to identify all instances of repeats and soft mask the genome (parameter -xsmall). Gene annotation on the repeat masked assembly was achieved using the Braker2 (31) pipeline (parameters –fungus –softmasking), which uses Samtools v0.1.19-44428cd (23), Bamtools v2.4.0 (32), Diamond v2.0.4 (33), Genemark-ET v4.15 (34), and Augustus v3.2.1 (35). The pipeline identified 5,451 protein-coding genes, and BUSCO assessment resulted in 90.8% complete BUSCOs.