Chloroplast genomes of Passiflora: structure, evolutionary inferences and gene transfer to the nucleus

• Grant number: 17/04216-9
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Effective date (Start): June 01, 2017
• Effective date (End): April 30, 2020
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Maria Lúcia Carneiro Vieira
• Grantee: Luiz Augusto Cauz dos Santos
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated scholarship(s): 19/09210-4 - Chloroplast genomes in the genus Passiflora: cp-DNA sequencing, annotation and comparative studies, BE.EP.DD 18/06939-0 - Comparative analysis of chloroplast genomes in the genus Passiflora: cp-DNA isolation and sequencing, BE.EP.DD

Abstract

The Passifloraceae family is composed of approximately 700 species, most of them belonging to the genus Passiflora. In Brazil, the yellow passion fruit (Passiflora edulis) has economic importance for the production of industrialized juice as well as to fresh fruit consumption. Our research team has been working to contribute for building up the body of knowledge on genetics of the cultivated species i.e. P. edulis and P. alata and, more recently, on genomics and transcriptomics of P. edulis. In collaboration with INRA/Toulouse, France, a large insert genomic BAC library was constructed (Ped-B-Flav). This library contains 82,944 clones with 6-fold depth of coverage of the whole genome. By exploiting the library sequences, it was possible to describe the chloroplast genome (cp DNA) of P. edulis, the first entirely sequenced within the Passifloraceae family. In the present work, we aim at to give continuity to the study on the organization of the Passiflora chloroplast genomes. We intend to sequence the cp DNA of eight species of Passiflora, two from each subgenus i.e. Astrophea, Decaloba, Deidamioides and Passiflora as well as to carry on a comparative study, and subsequently trace possibly evolutionary hypotheses. In parallel, on the basis of entire sequences of ~100 BAC, obtained via PacBio RS II platform, we intend to analyze the nuclear sequences of P. edulis for identifying nuclear genes that code for proteins that are imported into chloroplasts. Our results will certainly help narrow the knowledge gap in Passiflora genomics, but also make available to scientific community new information and tools, which will allow the development of new theoretical and applied studies to this genus. (AU)

Scientific publications

(4)

(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)

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, OCT 2020. (17/11815-6, 19/09210-4, 17/04216-9, 19/07838-6)

MUNHOZ, CARLA FREITAS; COSTA, ZIRLANE PORTUGAL; CAUZ-SANTOS, LUIZ AUGUSTO; EGOAVIL REATEGUI, ALINA CARMEN; RODDE, NATHALIE; CAUET, STEPHANE; DORNELAS, MARCELO CARNIER; LEROY, PHILIPPE; VARANI, ALESSANDRO DE MELLO; BERGES, HELENE; et al. A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species. SCIENTIFIC REPORTS, v. 8, AUG 29 2018. (17/04216-9, 14/25215-2, 13/11196-3)

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, JUL 2021. (18/21469-0, 17/11815-6, 19/07838-6, 17/04216-9, 18/25242-0)

CHAVARRIA-PEREZ, LOURDES MARIA; GIORDANI, WILLIAN; GRACAS DIAS, KAIO OLIMPIO; COSTA, ZIRLANE PORTUGAL; MASSENA RIBEIRO, CAROLINA ALBUQUERQUE; BENEDETTI, ANDERSON ROBERTO; CAUZ-SANTOS, LUIZ AUGUSTO; PEREIRA, GUILHERME SILVA; BACHEGA FEIJO ROSA, JOAO RICARDO; FRANCO GARCIA, ANTONIO AUGUSTO; et al. Improving yield and fruit quality traits in sweet passion fruit: Evidence for genotype by environment interaction and selection of promising genotypes. PLoS One, v. 15, n. 5, MAY 14 2020. (12/09100-5, 16/12977-7, 10/06702-9, 18/09069-7, 17/04216-9)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

SANTOS, Luiz Augusto Cauz dos. Chloroplast genome evolution in Passiflora. 2020. Doctoral Thesis - Universidade de São Paulo (USP). Escola Superior de Agricultura Luiz de Queiroz (ESALA/BC) Piracicaba.