The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales

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.

Passifloraplastome sequencing reveals widespread genomic rearrangements

“…). The total number of inversions in our study (8) differs from Jansen et al () for P. biflora (10) and Cauz‐Santos et al () for P. edulis (3). The difference may be the result of the much larger number of species included in this study.…”

“…All Passiflora plastomes examined lack an intact rpl22 gene. A truncated rpl22 pseudogene in Passiflora has been reported previously in P. biflora, P. quadrangularis, P. cirrhiflora (Jansen et al, ) and P. edulis (Cauz‐Santos et al, ). The discovery of independent transfers of rpl22 to the nucleus in two other rosid families, Fabaceae and Fagaceae, prompted the suggestion of a nuclear transfer in Passiflora (Jansen et al, ).…”

“…Previous studies with limited taxon sampling documented the loss of genes and introns from Passiflora plastomes (Downie et al, ; Hansen et al, ; Jansen et al, , ) and only one complete plastome has been published (Cauz‐Santos et al, ). Using a draft plastome sequence Jansen et al () estimated that 11 gene and intron losses and 10 inversions occurred in P. biflora (subg.…”

“…Using a draft plastome sequence Jansen et al () estimated that 11 gene and intron losses and 10 inversions occurred in P. biflora (subg. Decaloba ) and Cauz‐Santos et al () identified multiple gene and intron losses and three inversions in the complete plastome of P. edulis (subg. Passiflora ).…”

“…The accD gene was suggested to be missing from the plastome of P. biflora . Similarly Cauz-Santos et al (2017) documented tandem repeat elements within the accD of P. edulis and suggested it was not functional. We found similar tandem repeats within accD (Table S8) splitting the conserved domain into two or more fragments.…”