The Chloroplast Genome ofPassiflora edulis(Passifloraceae) Assembled from Long Sequence Reads: Structural Organization and Phylogenomic Studies in Malpighiales.
The family Passifloraceae consists of some 700 species classified in around 16 genera. Almost all its members belong to the genusPassiflora. In Brazil, the yellow passion fruit (Passiflora edulis) is of considerable economic importance, both for juice production and consumption as fresh fruit. The availability of chloroplast genomes (cp genomes) and their sequence comparisons has led to a better understanding of the evolutionary relationships within plant taxa. In this study, we obtained the complete nucleotide sequence of theP. edulischloroplast genome, the first entirely sequenced in the Passifloraceae family. We determined its structure and organization, and also performed phylogenomic studies on the order Malpighiales and the Fabids clade. TheP. edulischloroplast genome is characterized by the presence of two copies of an inverted repeat sequence (IRA and IRB) of 26,154 bp, each separating a small single copy region of 13,378 bp and a large single copy (LSC) region of 85,720 bp. The annotation resulted in the identification of 105 unique genes, including 30 tRNAs, 4 rRNAs, and 71 protein coding genes. Also, 36 repetitive elements and 85 SSRs (microsatellites) were identified. The structure of the complete cp genome ofP. edulisdiffers from that of other species because of rearrangement events detected by means of a comparison based on 22 members of the Malpighiales. The rearrangements were three inversions of 46,151, 3,765 and 1,631 bp, located in the LSC region. Phylogenomic analysis resulted in strongly supported trees, but this could also be a consequence of the limited taxonomic sampling used. Our results have provided a better understanding of the evolutionary relationships in the Malpighiales and the Fabids, confirming the potential of complete chloroplast genome sequences in inferring evolutionary relationships and the utility of long sequence reads for generating very accurate biological information.
Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba Brazil.
Luiz A
LA
Cauz-Santos
Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba Brazil.
Carla F
CF
Munhoz
Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-Tolosan France.
Nathalie
N
Rodde
Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-Tolosan France.
Stephane
S
Cauet
Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, PiracicabaBrazil; FuturaGene Brasil Tecnologia Ltda., São PauloBrazil.
Anselmo A
AA
Santos
Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, PiracicabaBrazil; Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, JaboticabalBrazil.
Helen A
HA
Penha
Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas Brazil.
Marcelo C
MC
Dornelas
Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal Brazil.
Alessandro M
AM
Varani
Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba Brazil.
Giancarlo C X
GC
Oliveira
Institut National de la Recherche Agronomique, French Plant Genomic Resource Center, Castanet-Tolosan France.
Hélène
H
Bergès
Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba Brazil.
Maria Lucia C
ML
Vieira
Fabids; Malpighiales; Passiflora; chloroplast genome; phylogenomics; single molecule real-time (SMRT) sequencing