Abstract
The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of the P. edulis chloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. The P. edulis chloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single copy region of 13,378 bp and a large single copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs, and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome of P. edulis differs from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151, 3,765 and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.
Highlights
Malpighiales is an order of flowering plants that belongs to the clade Eurosids I, known as Fabids (The Angiosperm Phylogeny Group, 2009)
The last step of the HGAP workflow is performed in order to significantly reduce the remaining InDel and base substitution errors in the draft assembly
Following extraction of reads containing only chloroplast genome sequence data and subsequent error correction, 2,340 PacBio RS reads from the clone insert Pe69Q4G9 were recovered, ranging from 500 to 22,458 bp, and containing a total of 94,052 bp assembled into a contig
Summary
Malpighiales is an order of flowering plants that belongs to the clade Eurosids I, known as Fabids (The Angiosperm Phylogeny Group, 2009) This large order includes 42 families, more than 700 genera, and contains approximately 16,000 species forming an extremely diverse group of plants in terms of their morphological and ecological aspects (The Angiosperm Phylogeny Group, 2009; Wurdack and Davis, 2009). The Passifloraceae family is a member of the Malpighiales (Judd et al, 2008) and consists of some 700 species of herbaceous or woody vines, shrubs and trees, classified in around 16 genera, and almost all its members belong to the large and variable genus Passiflora, popularly known as passion flowers or passion fruits (Feuillet, 2004). The main economic value lies in the production of passion fruit juice, an essential exotic ingredient in juice blends. Passiflora seed oil is well-suited for use as a regenerative ingredient in cosmetics products
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