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Exploiting a genomic library of Passiflora edulis: BACs screening and PacBio sequencing

Grant number: 16/00767-8
Support Opportunities:Scholarships abroad - Research Internship - Post-doctor
Effective date (Start): April 03, 2016
Effective date (End): July 02, 2016
Field of knowledge:Biological Sciences - Genetics - Plant Genetics
Principal Investigator:Maria Lúcia Carneiro Vieira
Grantee:Carla de Freitas Munhoz
Supervisor: Helene Berges
Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Research place: Institut National de la Recherche Agronomique, Toulouse (INRA), France  
Associated to the scholarship:13/11196-3 - Genomic library of Passiflora edulis f. flavicarpa: exploitation by sequencing of BAC-ends and sequencing of candidate (gene-rich) BACs, BP.PD

Abstract

The family Passifloraceae consists of about 700 species of herbaceous or woody vines, shrubs and trees, classified in around 16 genera, with almost all of its members belonging to the genus Passiflora, popularly known as passion fruits. In Brazil, the yellow passion fruit (Passilfora edulis) is a crop of considerable economic importance for both 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 passion fruit. Therefore, improving our understanding of passion fruit genome is very important and to some degree, a pre-requisite for the effective use of its genetic resources. Recently, our group has constructed a large-insert genomic library of P. edulis in collaboration with INRA at the French Plant Genomic Resources Center (CNRGV). Some aspects of this library have been already exploited and published and currently we propose to continue these studies through complete sequencing of some BAC candidates e.g. gene-rich. Consequently, we will be able to identify a large number of protein coding regions, candidate sequences for novel molecular markers and transposable elements as well as have a better idea of P. edulis genome organization. The Single Molecule Real-Time (SMRT) technology, implemented by Pacific Biosciences (PacBio), a third generation of sequencers, exhibits the most appropriate sequencing strategy to sequence large inserts. The service is available at the CNRGV and this technology has the advantage of producing long (>15 kb) and high quality reads, with high depth of sequencing and accuracy, greatly facilitating the sequence data assembly. Finally, the sequencing data generated in this project will allow us to investigate different genetic and genomic issues concerning the species. Furthermore, it will help us in the assembly and annotation of the complete genome of P. edulis. Besides, several ongoing research projects in different Brazilian institutions will benefit from our work.

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