choroba was right that my original question was not clear. Thank you both for helping me on this, I really appreciate your help indeed. here is the code based on what I learned from here:

 my $hash1=shift;
 open (my $fh1, "<",$hash1) or die "$!";
    my %h1=();
    while (<$fh1>) {
        chomp;
        my ($k1,$v1)=split /\t/;
        $h1{$k1}=$v1;
}

my $hash2=shift;
 open (my $fh2, "<",$hash2) or die "$!";
    my %h2=();
    while (<$fh2>) {
        chomp;
        my ($k2,$v2)=split /\t/;
        $h2{$k2}=$v2;
}

my %combined_hash = map { $_ => join ',', map split(/,/, $h2{$_}),
                                       split /,/, $h1{$_}
                 } keys %h1;

while (my ($k, $v) = each %combined_hash) {
    print "$k\t$v\n";
}
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