Abstract
Some lineages of the Orchid genus Ophrys exhibit among the highest diversification rates reported so far. As a consequence of a such intense and rapid evolution, the systematics and the taxonomy of this genus remains unclear. A hybrid assembly approach based-on long- and short-read genomic data allowed us to outperform classical methods to successfully assemble whole plastid genomes for two new Ophrys species: O. aymoninii and O. lutea. Along with three other previously Ophrys plastid genome sequences, we then reconstructed the first whole plastome-based molecular phylogeny including representatives of the three mains recognized Ophrys lineages. Our results support the placement of the O. insectifera clade as sister group of ‘non-basal Ophrys’ rather than a basal position. Our findings corroborate recent results obtained from genomic data (RAD-seq and transcriptomes) but contrast with previous ones. These results therefore confirm that molecular phylogenetic hypotheses based on a limited number of loci (e.g. nrITS, matK, rbcL) may have provided a biased picture of phylogenetic relationships within Ophrys and possibly other plant taxa.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Joris A. M. Bertrand, Laboratoire Génome & Développement des Plantes (UMR 5096 UPVD/CNRS), Université de Perpignan Via Domitia, Bâtiment T, 58 avenue Paul Alduy, 66860 Perpignan Cedex 09, France. Email: joris.bertrand{at}univ-perp.fr
Joris Bertrand conducted fieldwork, analyzed the data and wrote the manuscript.
Anaïs Gibert contributed to fieldwork and manuscript writing.
Christel Llauro generated the long-read data set.
Olivier Panaud contributed to research funding and manuscript writing.