$VAR1 = {
          'gene' => {
                      '1' => {
                               'gene_seq' => {
                                               'startpos' => '5999',
                                               'id' => '1'
                                             },
                               'label' => 'gene_of_interest'
                             },
                      '2' => {
                               'gene_seq' => {
                                               'startpos' => '96819',
                                               'id' => '2'
                                             },
                               'label' => 'Another_gene_of_interest'
                             }
                    }
        };

##</code><code>##

$xml->{gene}

##</code><code>##

$xml->{gene}->{1}
or 
$xml->{gene}->{2}

##</code><code>##

$xml->{gene}->{1}->{gene_seq}
$xml->{gene}->{1}->{label}
$xml->{gene}->{2}->{gene_seq}
$xml->{gene}->{2}->{label}

##</code><code>##

$xml->{gene}->{1}->{gene_seq}->{startpos}
$xml->{gene}->{1}->{gene_seq}->{id}
$xml->{gene}->{2}->{gene_seq}->{startpos}
$xml->{gene}->{2}->{gene_seq}->{id}

##</code><code>##

my $xml  = XMLin($data, keyattr => [ ]);

##</code><code>##

my $xml  = XMLin($data, keyattr => { gene => 'id', gene_seq => 'id' } );

##</code><code>##

my $xml  = XMLin($data, 
  keyattr    => { gene => 'id', gene_seq => 'id' }, 
  forcearray => [ 'gene', 'gene_seq' ]
);