Assembly of the T. ichikawai genome
A scaffold-level assembly of the T. ichikawai genome was generated under the stLFR2Supernova pipeline (Wang et al., 2019) with Supernova 2.1.1 (Weisenfeld et al., 2017). Parameters for the Supernova run were set to MAX_READS = 400000000 and MINSIZE = 200. The assembly was polished automatically with the Pilon software tool (Walker et al., 2014). The quality of the genome assembly was evaluated using the completeness estimated by BUSCO version 5.4.4 (Simão et al., 2015) with a database of ray-finned fishes (Actinopterygii odb10). Transposable elements (TEs) and other repeat sequences of the T. ichikawai genome were identified using RepeatModeler version 2.0.3 (Flynn et al., 2020) with Dfam 3.7 repeat database. Second, the TEs and repeats within the T. ichikawaigenome were soft-masked by RepeatMasker version 4.1.2-p1 (http://www.repeatmasker.org).