A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species

Carla Freitas Munhoz, Zirlane Portugal Costa, Luiz Augusto Cauz-Santos, Alina Carmen Egoávil Reátegui, Nathalie Rodde, Stéphane Cauet, Marcelo Carnier Dornelas, Philippe Leroy, Alessandro de Mello Varani, Hélène Bergès, Maria Lucia Carneiro Vieira
2018 Scientific Reports  
Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about
more » ... genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes. The Passifloraceae family belongs to the Malpighiales order and is a member of the Rosids clade, according to classical and molecular phylogenetic analysis. The family consists of 700 species, classified in 16 genera. The majority of species belong to the genus Passiflora (~530 species), popularly known as passion fruits 1 . This genus is widely distributed in tropical and subtropical regions of the Neotropics. Approximately 150 species are native to Brazil, which is acknowledged to be an important centre of diversity 2 . Among the American tropical species of Passiflora, 60 fruit-bearing species are marketed for human consumption. Moreover, several species and hybrids have been produced for ornamental purposes (see www.passiflora.it;) 3 , and pharmacologists have found that passion fruit vines contain bioactive compounds that are used in traditional folk medicines as anxiolytics and antispasmodics 4 . Passiflora edulis is the major species of passionflowers grown for fresh fruit consumption and juice production in climates ranging from cool subtropical (purple variety) to warm tropical (yellow variety). Species grown particularly in Brazil include P. edulis (sour passion fruit) and P. alata (sweet passion fruit). Because of the quality of its fruit and yield for processing into commercial
doi:10.1038/s41598-018-31330-8 pmid:30158558 fatcat:upnsgnmmhjcfnl6druil3u3wwi