4. Discussion
Despite their ecological and economic importance, few crab genomes have been reported. C. japonica is of major interest, because it is the most important near-shore economic crab. Moreover, C. japonicahas long tolerance to desiccation. In the present study, we assembled the first chromosome-level C. japonica genome with a genome size of 1431.02 Mb and a contig N50 of 29.67 Mb, which is larger than the genome size of P. trituberculatus (1.00 Gb) (Tang et al., 2020) of family Portunidae but smaller than that of S. paramamosain(1.55 Gb) (Zhao et al., 2021). The genome size after short Illumina read correction and long PacBio read correction was also confirmed by survey sequence results (1,398 Mb). Notably, the number (n = 51) of chromosomes assembled based on Hi-C reads differs from the karyotype analysis result (n = 57) (Yan et al., 2009). Some C. japonica chromosomes have extremely small morphology and are rich in repeat elements, and most chromosomes in the mitosis metaphase are spot-shaped and difficult to distinguish; therefore, identifying all C. japonica chromosomes through Hi-C interaction is very difficult (Lou et al., 2004). In fact, we did find some unmanageable repeat sequences through Hi-C interaction. A large number of sequencing reads (short Illumina reads and long PacBio reads) can be successfully mapped to the assembled genome sequence, which means that these reads have high consistency. Meanwhile, 86.40% complete BUSCOs were found in the C. japonica genome; thus, the genome that we assembled is more complete. A total of 824.02 Mb of repeat elements were identified and account for 57.65% of the C. japonica genome. We speculate that the high proportion of repeat elements is one of the critical reasons for the large genome size ofC. japonica . In fact, previous association analysis between the number of whole-genome repetitive sequences and genome size in 44 plants and 68 vertebrates confirmed that the proportion of repetitive sequences is positively correlated with genome size (Gao et al., 2018). Additionally, we obtained accurate genome-annotated information through many methods. In conclusion, we presented a basic resource for exploringC. japonica biological processes at the genomic level.