#!/usr/bin/perl

use strict; # https://perlmonks.org/?node_id=11113581
use warnings;

my $filename = 'file.fasta';
open my $handle, '<', $filename or die "$! opening $filename";
my @array;
while( <$handle> )
  {
  /^>/ and push @array, '';
  $array[-1] .= $_;
  }
use Data::Dumper; print Dumper \@array;