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.

BackgroundThe passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. However, very little is known about the genome of the species. Therefore, improving our understanding of passion fruit genomics is essential and to some degree a pre-requisite if its genetic resources are to be used more efficiently. In this study, we have constructed a large-insert BAC library and provided the first view on the structure and content of the passion fruit genome, using BAC-end sequence (BES) data as a major resource.ResultsThe library consisted of 82,944 clones and its levels of organellar DNA were very low. The library represents six haploid genome equivalents, and the average insert size was 108 kb. To check its utility for gene isolation, successful macroarray screening experiments were carried out with probes complementary to eight Passiflora gene sequences available in public databases. BACs harbouring those genes were used in fluorescent in situ hybridizations and unique signals were detected for four BACs in three chromosomes (n = 9). Then, we explored 10,000 BES and we identified reads likely to contain repetitive mobile elements (19.6% of all BES), simple sequence repeats and putative proteins, and to estimate the GC content (~42%) of the reads. Around 9.6% of all BES were found to have high levels of similarity to plant genes and ontological terms were assigned to more than half of the sequences analysed (940). The vast majority of the top-hits made by our sequences were to Populus trichocarpa (24.8% of the total occurrences), Theobroma cacao (21.6%), Ricinus communis (14.3%), Vitis vinifera (6.5%) and Prunus persica (3.8%).ConclusionsWe generated the first large-insert library for a member of Passifloraceae. This BAC library provides a new resource for genetic and genomic studies, as well as it represents a valuable tool for future whole genome study. Remarkably, a number of BAC-end pair sequences could be mapped to intervals of the sequenced Arabidopsis thaliana, V. vinifera and P. trichocarpa chromosomes, and putative collinear microsyntenic regions were identified.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-816) contains supplementary material, which is available to authorized users.

Yellow and sweet passion fruit are insect-pollinated species native to the tropics. Fruits are used commercially for human consumption worldwide. The yellow passion fruit is an outcrossing species with selfincompatible flowers. However, the reproductive system of the sweet passion fruit (Passiflora alata) has not been well elucidated. The objective of this work was to characterize aspects of the mating system in the sweet passion fruit using random amplified polymorphic DNA (RAPD) and microsatellite markers, particularly the rate of outcrossing in P. alata progenies. A multilocus outcrossing rate of t m = 0.994 was determined from RAPD and t m = 0.940 from microsatellites, supporting P. alata as an outcrossing species. The fixation indices of the maternal generation (F m ) were )0.200 and 0.071 with RAPD and microsatellite loci, respectively, indicating the absence of inbreeding in the maternal generation. The paternity correlation (r p ) varied from )0.008 with RAPD markers to 0.208 with microsatellite markers, suggesting a low probability of finding full sibs within the progenies. The results demonstrated that all progenies assessed in this study were derived from outcrossing.The genus Passiflora is comprised of over 400 species, 120 of which are native to Brazil. South America is considered the main centre of Passiflora genetic diversity and species are distributed from sea level to the Andes Mountains. Yellow passion fruit (Passiflora edulis Sims f. flavicarpa Deg.) and sweet passion fruit (P. alata Curtis) are grown commercially for their edible and aromatic fruits and used in juice concentrate blends consumed worldwide. In addition, the plant leaves, and to a lesser extent fruit pulp contains passiflorine, a substance with sedative and antispasmodic action used in the pharmaceutical industry (Rudnicki et al. 2007).Yellow passion fruit is an outcrossing species with perfect, self-incompatible (Bruckner et al. 1995, Rego et al. 2000 insect-pollinated flowers. However, the reproductive system of the sweet passion fruit has not been well elucidated, which is essential to establish strategies for selection and improvement, and to propose effective approaches for conservation (Endels et al. 2007). Braga et al. (2005) suggested that sweet passion fruit is an outcrossing species, with levels of self-sterility easily overcome artificially.Intrinsic factors such as flower colour and morphology, and environmental attributes including pollinator behaviour and flowering plant abundance can indicate the mating system of a plant species (Varassin et al. 2001, Parzies et al. 2008). In addition, the rate of outcrossing (t) is a key parameter of the mating system best estimated using genetic markers generated from plant progenies (Baye and Becker 2004). It measures the fraction of seeds in a given population generated by outcrossing; when t = 0, population is completely autogamous and when t = 1 population is panmitic. The complement is the fraction because of selfing, s = 1 ) t. There are two possibilities for computing the...

Passiflora edulis is the major species of passionflowers grown worldwide, mainly for juice production and fresh fruit, in climates ranging from cool subtropical (purple variety) to warm tropical (yellow variety). The bacterial leaf spot, caused by Xanthomonas axonopodis pv. passiflorae (Xap) can be a serious disease affecting passion fruit production in commercial orchards, particularly under moist field conditions. In this study we describe a first analysis of host gene expression in this pathosystem. We used suppression subtractive hybridization to construct two cDNA libraries enriched for transcripts induced and repressed by Xap, respectively, 24 h post inoculation with a highly virulent strain. High-quality sequences were obtained resulting in 998 unisequences that were used for annotation. In accordance with BLASTX results performed by Blast2GO tool, 86.7% of the unisequences showed similarity to other plant species' proteins related to different functional categories. Sixty-three transcripts were similar to Arabidopsis thaliana defence-related proteins identified in the PLAZA platform. In silico predicted protein-protein interactions were detected on the basis of the STRING database for 35 of the 63 defence-related proteins. At this early stage of interaction, a set of genes was selected from Blast2GO categorization results and analysed by quantitative PCR (qPCR). The expression profiles changed in response to the pathogen for 76% of these genes (48/63) and the differences in expression ratios ranged from 0.51-fold to 1.83-fold. In later stages of interactions (5 and 9 days post inoculation) when disease-associated symptoms were visible, qPCR analyses were performed for 14 genes selected from both libraries. The expression profiles of all genes were found to be changed by the pathogen. The gene that responded most strongly to the pathogen attack encodes a lipoxygenase 2. In inoculated plants, its expression was induced 500-fold and 300-fold, 5 and 9 dpi, respectively, compared to controls, suggesting an important role of this gene in passion fruit defence. Moreover, we showed that most of the genes involved in well-known pathogen recognition signalling pathways were repressed by Xap and this lends support to the idea that the jasmonic acid signalling pathway fails to be activated during the first hours of interaction.

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