Abstract
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.
Highlights
Among the most speciose family of flowering plants that orchids (Orchidaceae) form, some lineages of the genus Ophrys display among the highest diversification rates ever reported (Givnish et al 2015; Breitkopf et al 2015)
The systematics and the taxonomy is problematic in Ophrys for which different authors recognize a number of species ranging from 9 to 354
Several molecular phylogenetic studies show that the genus Ophrys is basically subdivided in three main sub-lineages: a first clade formed by the Ophrys insectifera group, a second clade consisting of the groups B to E (O. tenthredinifera (B), O. speculum (C), O. bombyliflora (D), called ‘archaic Euophrys’ by Tyteca and Baguette (2017), plus the so-called Pseudophrys group (E) and a third clade to which belong the groups F to J (O. apifera (F), O. sphegodes (G), O. fuciflora (H), O. scolopax (I) and O. umbilicata (J), called ‘recent Euophrys’)
Summary
Among the most speciose family of flowering plants that orchids (Orchidaceae) form, some lineages of the genus Ophrys display among the highest diversification rates ever reported (Givnish et al 2015; Breitkopf et al 2015). We aim to reconstruct a phylogenomic hypothesis to test whether whole plastid genomic data rather support the inner placement of the O. insectifera (A) group or alternatively, its basal position in the Ophrys genus. Aveyronensis J.J.Wood) (Bertrand et al, 2019), none of which are members of the O. insectifera (A) group To fill this knowledge gap, we generated genomic data for Ophrys aymoninii (Breistr.) Buttler We relied on a hybrid approach to assemble the whole plastid genomes of the two Ophrys taxa mentioned above This consists in a combination of long reads (here, Oxford Nanopore Technologies reads that can span repeated DNA regions known to be difficult to assemble) with the low error rate of short (paired-end) reads (here, Illumina reads). Gene annotation and basic downstream analyses were carried out as described in our former study (Bertrand et al 2019, see Appendix1)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
