Genome annotation for Salminus brasiliensis specimen from the Upper Paraná Basin (LARGE Hap2), from LiftOn of RefSeq's VGP reference.

<p dir="ltr">Gene annotation was performed over LARGE’s principal Hap2 (GCA_059958755.1) with the aid of LiftOn(version 1.0.14), which invokes minimap2 (version 2.13) and minipro (version 0.18), departing from NCBI’s<i> </i>RefSeq general feature file (gff) and associated files, for VGP’s <i>S. brasiliensis </i>principal genome (Hap2 - GCF_030463535.1).<br>"A small fraction of lifted mRNAs (< 0.3%) showed protein_identity below 0.50, likely reflecting genuine sequence divergence between the Upper Paraná and Argentinian specimens; these features retain their identity scores as attributes in the GFF3, allowing users to apply identity thresholds appropriate to their analyses.

The distribution of protein_identity scores is consistent with the previously debated phylogeographic divergence reported within S. brasiliensis from lower La Plata River Basin in contrast to the Upper Paraná River Basin. The majority of loci (92.6% ≥ 0.99) showing high conservation and a minor fraction likely reflects lineage-specific sequence divergence rather than annotation error."<br></p>