Other than what other monks pointed out, I believe a big question mark you had was why the root element, in this case the 'gene', was not in the hash.

The answer is that the default style of XML::Simple is not to keep root element, if you want see the root, do this:

use XML::Simple;
use Data::Dumper;

use strict;
use warnings;

my $data = do {local $/;<DATA>};
my $xml  = new XML::Simple(keeproot => 1);# this is what you want
my $tree = $xml->XMLin($data);

print Dumper($tree);

__DATA__
<?xml version="1.0" ?>
<gene id = "3" label = "gene_of_interest" />
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