Abstract
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.
Highlights
The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit
Bacterial artificial chromosome (BAC) library construction and characterization The Passiflora edulis BAC library consists of 82,944 individual BAC stored clones in 216 (384-wells) plates and is kept at the French Plant Genomic Resource Center (CNRGV)
Our data confirmed that partial digestion of high molecular weight DNA with the restriction enzyme HindIII (1–2 U/plug as optimal concentration) was critical to produce fragments with a good size range, leading to a good quality of the BAC library containing fragments with acceptable insert sizes, important for future whole genome study
Summary
The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The genus was divided into four subgenera, Astrophea (57 species), Decaloba (220) Deidamioides (13), and Passiflora (240) [3]. In the subgenus Astrophea (n = 12), shrubs or true trees tend to occur, distributed in lowland tropical South America. Species of Decaloba include herbaceous vines with small flowers and fruits occurring throughout the entire distribution of the genus and referred to as the ‘n = 6 group’. Lianas or herbaceous vines are typical in the Deidamioides subgenus (n = 12), species of which are found throughout Central and South America and Mexico. The Passiflora subgenus comprises herbaceous or woody lianas with exotic flowers and edible fruits, distributed throughout Central and South America and the Southern US.
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