ena-STUDY-UNIVERSITY OF PERPIGNAN/CNRS-03-08-2021-08:21:37:502-861
Conservation genomics of the Pyrenean Larkspur (Ranunculaceae: Delphinium montanum)
We aimed at generating genomic data for a Pyrenean endemic plant species (Ranunculaceae: Delphinium montanum) which is considered as under serious threat. Out of its conservation status, this species represents a technical and methodological challenge as it is polyploid (autotetraploid) and has a relatively important genome size (1C-value estimated at 10.32 pg). Species endemic to restricted geographical ranges represent a particular conservation issue, be it for their heritage interest. In a context of global change, this is particularly the case for plants which belong to high-mountain ecosystems and, because of their ecological requirements, are doomed to survive or disappear on their 'sky islands'. The Pyrenean Larkspur (Delphinium montanum, Ranunculaceae) is endemic to the Eastern part of the Pyrenees (France and Spain). It is now only observable at a dozen of localities and some populations show signs of decline, such as a recurrent lack of flowering. Implementing population genomic approach (e.g. RAD-seq like) is particularly useful to understand genomic patterns of diversity and differentiation in order to provide recommendations in term of conservation. However, it remains challenging for species such as D. montanum that are autotetraploid with a large genome size (1C-value > 10 pg) as most methods currently available were developed for diploid species. In this project, we genotyped 106 individuals from 9 localities using a RAD-seq like protocol (i.e. 'nGBS': 2x 250 pb, expected 1.5 Million reads/sample). For one particular individual, we also generated 260 Gb of short-reads whole-genome shotgun data (i.e. 2 x 150 pb), 15 Gb of data of leaf transcriptome (2x150 bp), sequenced two flowcells of short-reads (Oxford Nanopore Technology MinIon) with the aim to assemble a first draft genome for this species.
We aimed at generating genomic data for a Pyrenean endemic plant species (Ranunculaceae: Delphinium montanum) which is considered as under serious threat. Out of its conservation status, this species represents a technical and methodological challenge as it is polyploid (autotetraploid) and has a relatively important genome size (1C-value estimated at 10.32 pg). Species endemic to restricted geographical ranges represent a particular conservation issue, be it for their heritage interest. In a context of global change, this is particularly the case for plants which belong to high-mountain ecosystems and, because of their ecological requirements, are doomed to survive or disappear on their 'sky islands'. The Pyrenean Larkspur (Delphinium montanum, Ranunculaceae) is endemic to the Eastern part of the Pyrenees (France and Spain). It is now only observable at a dozen of localities and some populations show signs of decline, such as a recurrent lack of flowering. Implementing population genomic approach (e.g. RAD-seq like) is particularly useful to understand genomic patterns of diversity and differentiation in order to provide recommendations in term of conservation. However, it remains challenging for species such as D. montanum that are autotetraploid with a large genome size (1C-value > 10 pg) as most methods currently available were developed for diploid species. In this project, we genotyped 106 individuals from 9 localities using a RAD-seq like protocol (i.e. 'nGBS': 2x 250 pb, expected 1.5 Million reads/sample). For one particular individual, we also generated 260 Gb of short-reads whole-genome shotgun data (i.e. 2 x 150 pb), 15 Gb of data of leaf transcriptome (2x150 bp), sequenced two flowcells of short-reads (Oxford Nanopore Technology MinIon) with the aim to assemble a first draft genome for this species.