Deciphering the genome of Passiflora: sequencing of BAC-ends and candidate BACs

• Grant number: 14/25215-2
• Support Opportunities: Regular Research Grants
• Start date: August 01, 2015
• End date: October 31, 2017
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Maria Lúcia Carneiro Vieira
• Grantee: Maria Lúcia Carneiro Vieira
• Host Institution: Escola Superior de Agricultura Luiz de Queiroz (ESALQ). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Associated researchers: Claudia Barros Monteiro Vitorello

Abstract

Passiflora edulis, the passion fruit, is a tropical fruit species of economic importance, which is greatly appreciated for in natura consumption and reported to inspire cosmetic and pharmaceutical companies to create plant-derived compounds. Our research group has been building knowledge about the commercial species of Passiflora, namely for characterizing segregating populations, generating linkage maps and mapping quantitative loci associated with yield and fruit quality. However, very little is known about the composition and structure of Passiflora's genome. Recently, in collaboration with H. Bergès, at the Centre National de Ressources Génomiques Végétales, INRA, France, we have constructed a representative large-insert BAC library (Ped-B-Flav), which contains ~83.000 clones and provides 6× coverage of the genome of P. edulis. Then, we started to sequence the BAC-ends, producing 9.700 high-quality sequences. We were able to identify repetitive elements, coding sequences and microsyntenic regions between Passiflora edulis and the sequenced phylogenetic closest relatives Populus trichocarpa and Vitis vinifera. With the goal of continuing to build knowledge about the Passiflora genome we propose the sequencing of a new set of BAC-ends, to perform the comparative genomic mapping, as well as to sequence 200 pre-selected BACs entirely (100 kb each). We can expect the knowledge gained from this project will be useful for generating a set of sequences of the Passiflora genome. (AU)

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)

DA COSTA, ZIRLANE PORTUGAL; CAUZ-SANTOS, LUIZ AUGUSTO; RAGAGNIN, GEOVANI TOLFO; VAN SLUYS, MARIE-ANNE; DORNELAS, MARCELO CARNIER; BERGES, HELENE; VARANI, ALESSANDRO DE MELLO; CARNEIRO VIEIRA, MARIA LUCIA. Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis. MOLECULAR BIOLOGY REPORTS, v. 46, n. 6, p. 6117-6133, DEC 2019. (14/25215-2)

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)

CAUZ-SANTOS, LUIZ A.; MUNHOZ, CARLA F.; RODDE, NATHALIE; CAUET, STEPHANE; SANTOS, ANSELMO A.; PENHA, HELEN A.; DORNELAS, MARCELO C.; VARANI, ALESSANDRO M.; OLIVEIRA, GIANCARLO C. X.; BERGES, HELENE; et al. The Chloroplast Genome of Passiflora edulis (Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales. FRONTIERS IN PLANT SCIENCE, v. 8, MAR 10 2017. (14/25215-2)