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my $gene_to_find = 'NP_012';
my $matching_taxon;
...
} else {
   print("Gene $gene_to_find not found in any taxon.\n");
}

my $gene_to_find = 'NP_012';
my @matching_taxons;
...
} else {
   print("Gene $gene_to_find not found in any taxon.\n");
}