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Unraveling the genome of Passiflora organensis: a reference for Passifloraceae and evolutionary studies

Grant number: 19/07838-6
Support Opportunities:Scholarships in Brazil - Post-Doctoral
Effective date (Start): September 01, 2019
Effective date (End): April 30, 2023
Field of knowledge:Biological Sciences - Genetics - Plant Genetics
Principal Investigator:Maria Lúcia Carneiro Vieira
Grantee:Zirlane Portugal da Costa
Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
Associated scholarship(s):22/01884-9 - Analysis of the repetitive portion of Passifloraceae genomes, BE.EP.PD

Abstract

The Passiflora is the richest genus of the Passifloraceae family, with many species occurring in Brazil, placing the country in an outstanding position regarding the genetic resources. Passiflora plants are cultivated for many purposes, and mostly for human consumption and juice production. The main cultivated species in Brazil are Passiflora edulis (the yellow passion fruit) and P. alata (the sweet passion fruit). Due to the quality of the fruits and juice industrialization, the yellow passion fruit is grown in 95% of the orchards. Nevertheless, little is known about the genetics and genomics of the species. Our research group is pioneer in investigating those aspects and has generated particular information about. With the aim of studying the P. edulis genome, a genomic library inserted in BACs was constructed, covering 6× the genome of the species. Initially, 10,000 sequences (up to 1,000 bp) were obtained, totaling 6.2 Mb, whose characterization provided the first view about this genome. Subsequently, about 112 inserts (100,000 bp each) were selected for complete sequencing, obtaining 10.4 Mb of data, totaling ~1% of the genome. This region is rich in genes, and 1,833 genes were predicted. However, there is no reference genome for Passifloraceae. A reference genome would contribute to several genetic, molecular and evolutionary analyses. However, obtaining of a plant genome, particularly a large genome, such as the one of P. edulis (1,230 Mb), is not such a trivial task, and the cost is still a limiting factor. Thus, this project aims to obtain the complete genome of Passiflora organensis, a native species of Brazil, which has the smallest genome of the genus (250 Mb), providing a reference genome for Passifloraceae. P. organensis belongs to the Decaloba subgenus (2n= 12) different from P. edulis that belongs to Passiflora subgenus (2n= 18). To this end, the long read sequencing methodology, Pacbio platform, will be used, ensuring a high quality assembly. Sequences will be characterized through the prediction and functional annotation of genes, and characterization and chromosome distribution of transposable elements. This project has a partnership with CNRGV-INRA (France), where it is intended to carry out an internship in the 1st year to perform the bioinformatics' analyzes, and then to initiate the comparative studies with P. edulis sequences. The results will constitute a sequence database for Passifloraceae, which will be available for the scientific community.

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
COSTA, ZIRLANE PORTUGAL; VARANI, ALESSANDRO MELLO; CAUZ-SANTOS, LUIZ AUGUSTO; SADER, MARIELA ANALIA; GIOPATTO, HELENA AUGUSTO; ZIRPOLI, BRUNA; CALLOT, CAROLINE; CAUET, STEPHANE; MARANDE, WILLIAN; SOUZA CARDOSO, JESSICA LUANA; et al. genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensi. PLANT GENOME, v. 14, n. 3, . (18/21469-0, 17/11815-6, 19/07838-6, 17/04216-9, 18/25242-0)
SADER, MARIELA; VAIO, MAGDALENA; CAUZ-SANTOS, LUIZ AUGUSTO; DORNELAS, MARCELO CARNIER; VIEIRA, MARIA LUCIA CARNEIRO; MELO, NATONIEL; PEDROSA-HARAND, ANDREA. Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. PLANTA, v. 253, n. 4, . (19/07838-6)
CAUZ-SANTOS, LUIZ AUGUSTO; DA COSTA, ZIRLANE PORTUGAL; CALLOT, CAROLINE; CAUET, STEPHANE; ZUCCHI, MARIA IMACULADA; BERGES, HELENE; VAN DEN BERG, CASSIO; CARNEIRO VIEIRA, MARIA LUCIA. A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes. GENOME BIOLOGY AND EVOLUTION, v. 12, n. 10, p. 1841-1857, . (17/11815-6, 19/09210-4, 17/04216-9, 19/07838-6)

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