<div>Background: &ldquo;Lasona&rdquo; (Allium cepa var. aggregatum G. Don) is a multi-bulb cultivar commonly grown in the Northern Philippines as an annual crop. This, together with bulb onion, are the two main types of onions produced in the country, but the majority of onions exported from the Philippines are the latter. However, despite its importance to the human diet, no complete chloroplast genome sequence has been reported to date. Hence, the assembled plastome can be utilized as a resource for distinguishing the taxon and elucidating its evolutionary relationship with other Allium species, particularly within the aggregatum group. 
 
Methods: Using Illumina sequencing data, we assembled and annotated the complete chloroplast genome of A. cepa var. aggregatum accession from the germplasm collection of the Institute of Crop Science, University of the Philippines, Los Ba&ntilde;os, Laguna. Moreover, the morphology of the genotyped accession was characterized to ensure that the genome assembled is attributed to the correct taxon. The voucher specimen (ICROPS 1374) was deposited at the Philippine Herbarium of Cultivated Plants of the Institute of Crop Science. 
 
Result: The complete chloroplast (cp) genome had a sequence length of 153,587-bp long, with 36.8% overall GC content. A total of 126 functional genes were found, comprising 80 mRNA genes, 38 tRNA genes and 8 rRNA genes. We annotated 43 genes that code for photosynthesis, 29 genes for self-replication and 6 other genes for other functions. This is the first complete chloroplast genome of Allium cepa var. aggregatum. The phylogenetic analysis of the assembled genome, together with 21 other Allium accessions and 12 other Amaryllidaceae species, revealed that the A. cepa accessions formed a distinct clade despite infraspecific plastome variations. Comparison among earlier published plastomes of A. cepa showed that the assembled A. cepa var. aggregatum chloroplast genome was distinct in sequence length and composition. The observed differences could be utilized to further elucidate differences needed for varietal identification. 
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The Complete Chloroplast Genome of &ldquo;Lasona&rdquo; (Allium cepa var. Aggregatum G. Don), an Important Indigenous Vegetable in the Northern Philippines