title: Begin at the beginning: A BAC-end view of the passion fruit (Passiflora) genome.
abstract: BACKGROUND
  The 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.
  
  
  RESULTS
  The 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%).
  
  
  CONCLUSIONS
  We 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.
authors.forename: Anselmo Azevedo
authors.initials: AA
authors.lastname: Santos
authors.forename: Helen Alves
authors.initials: HA
authors.lastname: Penha
authors.forename: Arnaud
authors.initials: A
authors.lastname: Bellec
authors.forename: Carla de Freitas
authors.initials: Cde F
authors.lastname: Munhoz
authors.forename: Andrea
authors.initials: A
authors.lastname: Pedrosa-Harand
authors.forename: Hélène
authors.initials: H
authors.lastname: Bergès
authors.affiliation: Departamento de Genética, Universidade de São Paulo, Escola Superior de Agricultura "Luiz de Queiroz", P,O, Box 83, 13400-970 Piracicaba, Brazil. mlcvieir@usp.br.
authors.forename: Maria Lucia Carneiro
authors.initials: ML
authors.lastname: Vieira
mesh_terms: D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D004251:DNA Transposable Elements / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics / Q000379:methods*; D018895:Microsatellite Repeats / Q000235:genetics; D016366:Open Reading Frames / Q000235:genetics; D029598:Passiflora / Q000235:genetics*; D018626:Retroelements / Q000235:genetics
chemical_list: D004251:DNA Transposable Elements; D018626:Retroelements