title: Understanding the evolution of holoparasitic plants: the complete plastid genome of the holoparasite Cytinus hypocistis (Cytinaceae).
abstract: Background and Aims Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome. Methods We sequenced and assembled de novo the plastid genome of Cytinus hypocistis using a shotgun approach on genomic DNA. Phylogenomic analyses based on coding regions were performed on Malvidae. For each coding region present in Cytinus, we tested for relaxation or intensification of selective pressures in the Cytinus lineage compared with autotrophic Malvales. Key Results Cytinus hypocistis has an extremely divergent genome that is among the smallest sequenced to date (19·4 kb), with only 23 genes and no inverted repeat regions. Phylogenomic analysis confirmed the position of Cytinus within Malvales. All coding regions of Cytinus plastome presented very high substitution rates compared with non-parasitic Malvales. Conclusions Some regions were inferred to be under relaxed negative selection in Cytinus, suggesting that further plastome reduction is occurring due to relaxed purifying selection associated with the loss of photosynthetic activity. On the other hand, increased selection intensity and strong positive selection were detected for rpl22 in the Cytinus lineage, which might indicate an evolutionary role in the host-parasite arms race, a point that needs further research.
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.|Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
authors.forename: Cristina
authors.initials: C
authors.lastname: Roquet
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.|Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
authors.forename: Éric
authors.initials: É
authors.lastname: Coissac
authors.affiliation: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Cruaud
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.|Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
authors.forename: Martí
authors.initials: M
authors.lastname: Boleda
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.|Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Boyer
authors.affiliation: CEA-Institut de Génomique, Genoscope, Centre National de Séquençage, FR-91057 Evry Cedex, France.
authors.forename: Adriana
authors.initials: A
authors.lastname: Alberti
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.|Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Gielly
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.|Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Taberlet
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.|Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
authors.forename: Wilfried
authors.initials: W
authors.lastname: Thuiller
authors.affiliation: Conservatoire Botanique National Alpin, Domaine de Charance, FR-05000 Gap, France.
authors.forename: Jérémie
authors.initials: J
authors.lastname: Van Es
authors.affiliation: Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, BP 53, FR-38000 Grenoble, France.|Laboratoire d'Ecologie Alpine, CNRS, BP 53, FR-38000 Grenoble, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Lavergne
keywords: Chloroplast genome; Cytinaceae; Cytinus hypocistis; Malvales; mycoheterotroph; parasite; plastome evolution; selective pressure