A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis

Abstract

The genus Passiflora comprises a large group of plants popularly known as passionfruit, much appreciated for their exotic flowers and edible fruits. The species (∼500) are morphologically variable (e.g., growth habit, size, and color of flowers) and are adapted to distinct tropical ecosystems. In this study, we generated the genome of the wild diploid species Passiflora organensis Gardner by adopting a hybrid assembly approach. Passiflora organensis has a small genome of 259 Mbp and a heterozygosity rate of 81%, consistent with its reproductive system. Most of the genome sequences could be integrated into its chromosomes with cytogenomic markers (satellite DNA) as references. The repeated sequences accounted for 58.55% of the total DNA analyzed, and the Tekay lineage was the prevalent retrotransposon. In total, 25,327 coding genes were predicted. Passiflora organensis retains 5,609 singletons and 15,671 gene families. We focused on the genes potentially involved in the locus determining

Annotation of the Turnera subulata (Passifloraceae) Draft Genome Reveals the S-Locus Evolved after the Divergence of Turneroideae from Passifloroideae in a Stepwise Manner

“…Our analysis revealed that 53.63% of the T. subulata genome is composed of repetitive elements ( Figure 2 ); this is somewhat less than Passiflora . The P. organensis genome is composed of 58.55% repetitive elements [ 25 ], P. cincinnata (60.49%) and P. quadrangularis (73.42%) [ 26 ]. We also analyzed the repetitive element composition of the S -locus haplotypes using EDTA [ 27 ] ( Supplementary Figure S1 ).…”

“…Class I repetitive elements were the most abundant (56.44%) in T. subulata , with COPIA elements making up 99.52 Mb or 17.73% of the genome. Similarly, 58.55% of repetitive elements fell into Class I in P. organensis ; however, the majority fell into the subfamily GYPSY [ 25 ]. In both Primula veris and Linum tenue, Class I sequences were the most abundant, the majority of which were labeled as unclassified [ 4 , 11 ].…”

“…With the recent release of two Passiflora genomes [ 25 , 61 ], we were able to identify the location of the S -genes’ and their paralogs’ closest Passiflora orthologs. TsBAHD and its two closest homologs all shared a homolog in both species of Passiflora and TsYUC6 and its closest homolog shared a homolog in both species of Passiflora .…”

“…To identify potential duplication events prior to the divergence of Turnera and Passiflora , CoGE:Blast [ 104 ] was used to identify the location of the S -genes’ closest homologs in the recently published Passiflora edulis [ 60 ] and P. organensis [ 25 ] genomes.…”

“…OrthoVenn2 was used to identify orthologous clusters shared between P. edulis [ 60 ], P. organensis [ 25 ], Populus trichocarpa, Manihot esculenta, and Ricinus communis. Both Passiflora datasets were downloaded from CoGE:Blast; R. communis [ 21 ] was downloaded from Phytozome.…”