Whole plastid genome-based phylogenomics supports an inner placement of the O. insectifera group rather than a basal position in the rapidly diversifying Ophrys genus (Orchidaceae)

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 taxonomy of this genus remain 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 species of Ophrys: 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.

KEYWORDS:

• Bee orchids
• chloroplast (cp) genome
• hybrid genome assembly
• systematics
• third generation sequencing

Acknowledgments

We thank Marie-Christine Carpentier, Moaine El Baidouri, Panpan Zhang and the Mechanisms of AdaptatioN and GenOmics (MANGO) team for the support they provided with bioinformatic analyses.

Disclosure statement

The authors declare no conflict of interest.

Author contributions

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.

Supplementary material

Supplemental data for this article can be accessed here.

Additional information

Funding

This study is set within the framework of the “Laboratoires d’Excellences (LABEX)” TULIP [ANR-10-LABX-41] and was supported by a “Bonus Qualité Recherche” grant from the Université de Perpignan Via Domitia.