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Comparative analysis of chloroplast genomes in the genus Passiflora: cp-DNA isolation and sequencing

Grant number: 18/06939-0
Support Opportunities:Scholarships abroad - Research Internship - Doctorate (Direct)
Effective date (Start): June 10, 2018
Effective date (End): September 09, 2018
Field of knowledge:Biological Sciences - Genetics - Plant Genetics
Principal Investigator:Maria Lúcia Carneiro Vieira
Grantee:Luiz Augusto Cauz dos Santos
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:17/04216-9 - Chloroplast genomes of Passiflora: structure, evolutionary inferences and gene transfer to the nucleus, BP.DD

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. The Passiflora genus has been studied using morphological and molecular descriptors, and despite the recent taxonomical classification into four subgenera, there are unsolved phylogenetic relationships in this group, mainly on the existence of the subgenus Deidamioides. The lack of DNA data and is one of the reasons for the difficult to make phylogenetic inferences in this genus. With the objective to understand the genome of passionflowers, our group has constructed a large-insert genomic library of P. edulis in collaboration with INRA at the French Plant Genomic Resources Center (CNRGV), and the exploitation of this library generated the chloroplast (cp) genome sequence of P. edulis, the first chloroplast genome sequenced in the Passifloraceae family. Interestingly, we detected inversions in the structure of P. edulis cp-genome that allows us hypothesizing on the evolution of passionflowers, since these inversions could be particular to this genus. Taking this into account the analysis of the cp-DNA structure combined with phylogenomics of the species from all Passiflora subgenera could certainly help us to understand about the evolutionary history of this genus. Therefore, we propose to analyze the cp-genome of Passiflora species by chloroplast isolation and cp-DNA sequencing using the Single Molecule Real-Time (SMRT) technology, implemented by Pacific Biosciences (PacBio). However, access to information on cp-genomes is every critical. The most critical step is the chloroplast DNA isolation without nuclear DNA contamination that usually adheres to the outer chloroplast membrane. This is the main contribution that we expect to solve through the collaboration with CNRGV. Finally, the sequencing data generated in this project will allow us to investigate different aspects of the Passiflora chloroplast genome structure and evolution, and make available to scientific community information and tools to new studies applied to this genus. (AU)

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