2.5 Comparison analysis of chromosomes
Synteny relationships between the male and female O. bidensgenomes were analyzed using MUMmer4 with default settings (Marcais et al., 2018). The alignment results were filtered for more than 85% identity, and syntenic blocks of chromosomes were visualized using Circos (Krzywinski et al., 2009). The female O. bidens genome (https://ngdc.cncb.ac.cn/gwh/Assembly/22234) was annotated using a homology-based approach to search the D. rerio NCBI database using Gemoma (Keilwagen et al., 2019). The annotated protein-coding genes of male and female O. bidens genomes were used by Blastp (identity ≥ 95% and e-value ≤1E-5) to identify the male/female-specific gene sets. Structural variants of O. bidens genomes have been analyzed using Assemblytics (Nattestad and Schatz, 2016).
To uncover the unique chromosomal evolution mechanism of the O. bidens genome, synteny comparison of the hooks out carp and grass carp genomes (Wu et al., 2022) was performed using JCVI with c-scores of > 0.7, and tandem-nmax = 10 as filtering values (Tang et al., 2017).