Genomic annotation of the yellow drum

Structural and functional gene annotation of the assembled genome was predicted using de novo, homolog-based, and PacBio full-length transcriptome-based strategies. The repetitive sequences detected above were masked before de novo prediction annotation. We used both Augustus (augustus-3.2.1) 26 and Genscan 27 to formulate de novo predictions, yielding 38,857 and 38,807 protein-coding genes, respectively. The protein sequences of closely related fish species, including <i>D. rerio</i>, <i>G. morhua</i>, <i>G. aculeatus</i>, <i>O. niloticus</i>, <i>O. latipes</i>, <i>T. rubripes</i>, <i>T. nigroviridis</i>, and <i>X. maculatus</i>, were downloaded from Ensembl 28 to facilitate homolog-based gene prediction. All of the protein sequences were mapped to the yellow drum genome using the Basic Local Alignment Search Tool All (BLASTALL). We predicted 23,119 genes based on the PacBio full-length transcriptomic data, which were then used in transcriptome-based annotation. We then integrated the results of the de novo predictions, homolog-based annotations, and transcriptome-based annotations using GLEAN 29, finally obtaining a dataset containing 27,069 protein-coding genes