How should I store the data with duplicated keys in a document for MongoDB?

How should I store the data with duplicated keys in a document for MongoDB?

I am now encountering a problem when storing some data into MongoDB.To be
simple, its structure is illustrated below:
FEATURES Location/Qualifiers
source 1..4242774
/organism="Bacillus amyloliquefaciens subsp.
plantarum YAU
B9601-Y2"
/mol_type="genomic DNA"
/strain="YAU B9601-Y2"
/sub_species="plantarum"
/db_xref="taxon:1155777"
gene 412..1752
/gene="dnaA"
/locus_tag="BANAU_0001"
CDS 412..1752
/gene="dnaA"
/locus_tag="BANAU_0001"
/function="ATPase involved in DNA replication
initiation"
/codon_start=1
/transl_table=11
/product="Chromosomal replication initiator protein
dnaA"
/protein_id="CCG48023.1"
/db_xref="GI:380496985"
/db_xref="GOA:H8XCH4"
/db_xref="UniProtKB/TrEMBL:H8XCH4"
/translation="MENILDLWNQALAQIEKKLSKPSFETWMKSTKAHSLQGDTLTIT
APNEFARDWLESRYLHLIADTIYELTGEELSVKFVIPQNQDEEDFLPKPQVKKAAKEE
PSDFPQSMLNPKYTFDTFVIGSGNRFAHAASLAVAEAPAKAYNPLFIYGGVGLGKTHL
MHAIGHYVIDHNPSAKVVYLSSEKFTNEFINSIRDNKAVDFRNRYRNVDVLLIDDIQF
LAGKEQTQEEFFHTFNTLHEESKQIVISSDRPPKEIPTLEDRLRSRFEWGLITDITPP
DLETRIAILRKKAKAEGLDIPNEVMLYIANQIDSNIRELEGALIRVVAYSSLINKDIN
ADLAAEALKDIIPSSKPKVITIKEIQRIVGQQFNIKLEDFKAKKRTKSVAFPRQIAMY
LSREMTDSSLPKIGEEFGGRDHTTVIHAHEKISKLLIDDEQLQQQVKEIKELLK"
gene 1937..3073
/gene="dnaN"
/locus_tag="BANAU_0002"
CDS 1937..3073
/gene="dnaN"
From my illustration ,you can see that the key "gene" and "CDS" will be
repeated for many times and from the MongoDB , I know that duplicated keys
in a document is forbidden.So , my question is , how should I organize the
data structure in mongoDB?