Dataset Information

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

ABSTRACT: 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 1,900 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.

SUBMITTER: Munhoz CF

PROVIDER: S-EPMC6115403 | biostudies-literature | 2018 Aug

REPOSITORIES: biostudies-literature

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

Munhoz Carla Freitas CF Costa Zirlane Portugal ZP Cauz-Santos Luiz Augusto LA Reátegui Alina Carmen Egoávil ACE Rodde Nathalie N Cauet Stéphane S Dornelas Marcelo Carnier MC Leroy Philippe P Varani Alessandro de Mello AM Bergès Hélène H Vieira Maria Lucia Carneiro MLC

Scientific reports 20180829 1

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 1,900 ...[more]

PMID: 30158558

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Project description:Purple passion fruit, Passiflora edulis Sims f. edulis, is an important semi-perennial, fruit bearing vine originating in South America that produces a commercial tropical juice pulp for international and national consumption. Within the round purple passion fruit are a large number of membranous seed sacs each containing individual seeds. Little is known about the seed anatomy of the commercial passion fruit, differences between wild collected and commercial types, and its effect on seedling germination. Therefore, our main objective for this study was to analyze the seed anatomy variability of different germplasm as well as the effect on viability and germination of the seeds of this species. Germplasm was evaluated from three sources: (1) commercial cultivars grown in current production areas, (2) genebank accession from the national seed bank, and (3) landraces collected across different high and mid-elevation sites of the Andean region. A total of 12 morphometric descriptors related to seed anatomy were evaluated on the 56 genotypes, of which three were most informative: Angle to the vertex which is related to the shape of the seed, the thickness of the tegument and the horizontal length; separating the seed according to its source of origin. Germination was found to be positively correlated with the number (r = 0.789) and depth (r = 0.854) of seed pitting. Seeds of the commercial cultivars had more seed pits and higher germination compared to seeds of landraces or genebank accessions showing a possible effect of domestication on the crop. Interestingly, passion fruits often germinate during the rainy season as escaped or wild seedlings especially in the disturbed landscapes of coffee plantations, so some dormancy is needed but faster germination is needed for intensive cultivation. Harnessing passion fruit diversity would be useful as the semi-domesticated landraces have valuable adaptation characteristics to combine with rapid germination selected in the commercial cultivars. The variability of seed pitting with cultivars more pitted than landraces possibly resulting in faster germination may indicate that purple passion fruit is still undergoing a process of selection and domestication for this trait.

Dataset Information

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

Publications

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

Similar Datasets

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