4.1 Quality of this assembled genome improved
Compared to the published genome of F. chinensis (Yuan et al., 2021), the quality of our assembled genome improved significantly (Table S20). Primarily, the contig N50 increased from 59.00 Kb to 472.84 Kb, approximately eight times, and scaffold N50 increased from 28.92 Mb to 36.87 Mb. Secondly, the assembled complete ortholog proportion enhanced from 83.58% to 94.00% according to the BUSCO assessment, and the genome coverage enhanced from 82.46% to 96.15% according to the Illumina short read mapping test. In short, our assembled genome improved in both fragment length and completeness.
Initially, we assembled the contigs to 44 pseudochromosomes, but the heatmap revealed a low correlation between the contigs on the last pseudochromosome (Figure S5). Therefore, only 43 pseudochromosomes were assembled in the final version of the F. chinensis genome. We speculate that there are only 43 pairs of chromosomes in the somatic cell of F. chinensis , same as that in Marsupenaeus japonicus (Yuan et al., 2017).