Genomic Insights into the Population Structure and Adaptive Variation of Mullus barbatus in the Mediterranean Sea

Genome annotation of Mullus barbatus from Massa et al. - Genomic Insights into the Population Structure and Adaptive Variation of Mullus barbatus in the Mediterranean Sea (under review). Methods: To identify the geneset, we mapped the produced RNAseq reads against the genome reference using HISAT2 (v.2.2). The resulting bam files were merged and sorted using samtools (v1.7). Then to predict the gene models we used BRAKER3 (v3.0), providing as evidence the RNA alignments and similarity with known proteins as well. To produce the protein similarity hint file, we downloaded known proteins from UniProt and aligned them against the M. barbatus reference genome using miniprot (v0.13). The predicted geneset was reduced to one isoform per gene with AGAT (v1.4) and was then evaluated using BUSCO (v5.3.1). To functionally annotate the predicted geneset, we conducted a BLASTp search against UniProt Database and ran InterProScan (v5). Results: RNA sequencing produced 524.34 million reads that were mapped against the genome with an average of 85% mapping rate. Gene prediction yielded 35,727 genes including 43,217 transcripts. From those 39,625 had a hit against UniProt and 33,003 had a protein domain assigned through InterProScan search. Finally, BUSCO completeness assessment showed that 92.7% of the searched genes are present in the predicted geneset, 91.5% in single copy and 1.2% as duplicated. Additionally, 3.1% of genes were fragmented, and 4.2% were missing.