#!/usr/bin/perl-w
use strict;
use warnings;

my %hash=();
my $key = '';
while(<>){
    chomp;
    if($_ =~ /^>gi.*\[(.+)\]\s>gi.*/){
        $key = $1;
    }else{
        $hash{$key} .= $_;
    }
}

foreach(keys %hash){
    print join("\n",$_,$hash{$_}),"\n";
}
[download]

This does what you need