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 self-incompatibility and the MADS-box gene family, allowing us to infer expansions and contractions within specific subfamilies. Finally, we recovered the organellar DNA. Structural rearrangements and two mitoviruses, besides relics of other mobile elements, were found in the chloroplast and mt-DNA molecules, respectively. This study presents the first draft genome assembly of a wild Passiflora species, providing a valuable sequence resource for genomic and evolutionary studies on the genus, and support for breeding cropped passionfruit species.
Highlights
Passiflora (Passifloraceae, Malpighiales) is a neotropical genus encompassing hundreds of species with widespread distribution in the American continent, including the Amazonian and Andean regions
Note that we evaluated the possibility of using the available P. edulis genome sequence (Xia et al, 2021) to assist in assembling the P. organensis genome
Our analysis suggests a massive expansion of the long terminal repeat (LTR)-RT Tekay evolutionary lineage (Gypsy superfamily), representing up to 54 Mbp of the genome, accompanied by an expansion of long interspersed nuclear elements spanning ∼14 Mb
Summary
Passiflora (Passifloraceae, Malpighiales) is a neotropical genus encompassing hundreds of species with widespread distribution in the American continent, including the Amazonian and Andean regions. (Souza et al, 2004; Yotoko et al, 2011) that is not attributable to polyploidy. Passiflora species morphology is highly variable, with a 10-fold variation in genome size It is the species with the smallest genome species, P. organensis (subgenus Decaloba) seems to be evolving by diversification of different repeat types; the largest, P. quadrangularis (subgenus Passiflora), evolved by accumulating retrotransposons, especially Angela and Tekay elements, which comprise most of its genome (Sader et al, 2021)
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