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.

塔氏靛蓝霉（T. indotineae）参考基因组（GenBank登录号GCA_023065905.1；菌株TIMM20114）的注释信息。注释流程如下：该参考基因组的重复序列注释通过重复序列注释工具Repeatmodeler v2.0.3（引用25，运行引擎为NCBI），结合CD-HIT（引用26）、ReCon v1.08（引用27）、RMBlast v2.11.0、串联重复查找工具Tandem Repeats Finder v4.09（引用28）、RepeatScout v1.06（引用29）以及重复序列屏蔽工具RepeatMasker v4.1.2-p1（引用30）完成。随后将Repeatmodeler的输出结果作为重复序列库，供RepeatMasker识别所有重复序列实例并对基因组进行软屏蔽（参数设置为-xsmall）。针对经重复序列屏蔽后的基因组组装序列，使用基因注释流程Braker2（引用31）完成基因注释，参数为–fungus –softmasking；该流程依赖的工具包括Samtools v0.1.19-44428cd（引用23）、Bamtools v2.4.0（引用32）、Diamond v2.0.4（引用33）、基因预测工具Genemark-ET v4.15（引用34）以及基因预测软件Augustus v3.2.1（引用35）。该流程共注释得到5451个蛋白质编码基因，经通用单拷贝同源基因基准评估（BUSCO）后，完整BUSCO占比为90.8%。