Instead of this:

my $xml = XMLin($data);
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I'd recommend this:

my $genes = XMLin($data, 
  keyattr    => { gene => 'id' },
  forcearray => [ 'gene' ],
);
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My reasoning:

• the return value from XMLin() is a Perl data structure not XML, so $xml is not a very descriptive name
• you are 'folding' the list of gene elements into a hash keyed on the 'id' - it's more readable/maintainable to spell out your requirements rather than relying on the defaults
• any element listed in 'keyattr' should usually also be listed in 'forcearray'

The XML::Simple strict mode node expands on this theme.

Also, you could give XMLin() the DATA globref directly:

XMLin(\*DATA, ...);
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