I haven't taken the time to absorb your dense spec, but I think reading all your data into a hash-of-arrays might help. I also show how to find the uniq types.

my %data;
while (<DATA>) {
    chomp;
    my ($k, $v) = split /,\s+/;
    push @{ $data{$k} }, $v;
}

for my $contig (sort keys %data) {
    my %uniq = map { $_ => 1 } map { s/_.*//; $_ } @{ $data{$contig} }
+;
    print "$contig = ";
    print join ' ', sort keys %uniq;
    print "\n";
}

__DATA__
contig_8, maxima_contig_63500
contig_8, orange_scaffold_0026
contig_8, clementine_scaffold_6
contig_8, ponkan_scaffold_27456
contig_8, medica_contig_12945
contig_8, maxima_contig_235908
contig_8, ponkan_scaffold_144138
contig_9, maxima_contig_63500
contig_9, orange_scaffold_0026
contig_9, clementine_scaffold_6
contig_9, ponkan_scaffold_27456
contig_9, medica_contig_12945
contig_9, maxima_contig_235908
contig_9, ponkan_scaffold_144138
contig_9, ponkan_scaffold_144138
[download]

output:

contig_8 = clementine maxima medica orange ponkan
contig_9 = clementine maxima medica orange ponkan
[download]

• perldsc