Biology subjects

Rasplus, J.-Y.

Publications and source records attributed to Rasplus, J.-Y..

4 recordsLinked to original sources

bioRxiv2018

Optimised DNA extraction and library preparation for minute arthropods: application to target enrichment in chalcid wasps used for biocontrol.

Enriching subsets of the genome prior to sequencing allows focusing effort on regions that are relevant to answer specific questions. As experimental design can be adapted to sequence many samples simultaneously, using such approach also contributes to reduce cost. In the field of ecology and evolution, target enrichment is increasingly used for genotyping of plant and animal species or to better understand the evolutionary history of important lineages through the inference of statistically robust phylogenies. Limitations to routine target enrichment by research laboratories are both the complexity of current protocols and low input DNA quantity. Thus, working with tiny organisms such as micro-arthropods can be challenging. Here, we propose easy to set up optimisations for DNA extraction and library preparation prior to target enrichment. Prepared libraries were used to capture 1432 Ultra-Conserved Elements (UCEs) from microhymenoptera (Chalcidoidea), which are among the tiniest insects on Earth and the most commercialized worldwide for biological control purposes. Results show no correlation between input DNA quantities (1.8-250ng, 0.4 ng with an extra whole genome amplification step) and the number of sequenced UCEs. Phylogenetic inferences highlight the potential of UCEs to solve relationships within the families of chalcid wasps, which has not been achieved so far. The protocol (library preparation + target enrichment), allows processing 96 specimens in five working days, by a single person, without requiring the use of expensive robotic molecular biology platforms, which could help to generalize the use of target enrichment for minute specimens.

evolutionary biology↗

bioRxiv2018

Revisiting the phylogeny of Ficus (Moraceae): When Next Generation Sequencing corroborates Past Generation Botanists

Despite their ecological and evolutionary importance, fig trees still lack a resolved phylogeny. We used multiple analytical approaches and 600 conserved RAD-seq loci collected across 40 representative species to infer phylogenetic relationships among the major clades of Ficus. Our results converged on a fully resolved phylogeny that contradicts previous hypotheses by not placing section Pharmacosycea sister to all other fig trees. Instead, we find that subgenus Sycomorus is sister to two clades, one comprising all other gynodioecious sections, and the other containing all monoecious sections. Our results corroborate earlier botanists hypotheses and provide a baseline for future classification. We infer the evolution of key traits (growth form, breeding system and pollination mode) and find that, contrary to previous hypotheses, the ancestor of extant fig trees was likely a gynodioecious and actively pollinated tree. Our results open new opportunities to explore diversification patterns in fig trees and better understand their mutualistic interaction with wasps.

evolutionary biology↗

bioRxiv2018

Climate change and the potential distribution of Xylella fastidiosa in Europe

The bacterium Xylella fastidiosa (Xf) is a plant endophyte native to the Americas that causes worldwide concern. Xf has been recently detected in several regions outside its natural range including Europe. In that context, accurate estimates of its response to climate change are required to design cost-efficient and environment-friendly control strategies. In the present study, we collected data documenting the native and invaded ranges of the three main subspecies of Xf: fastidiosa, pauca and multiplex, as well as two strains of Xf subsp. multiplex recently detected in southern France (ST6 and ST7). We fitted bioclimatic species distribution models (SDMs) to forecast their potential geographic range and impact in Europe under current and future climate conditions. According to model predictions, the geographical range of Xf as presently reported in Europe is small compared to the large extent of suitable areas. The European regions most threatened by Xf encompass the Mediterranean coastal areas of Spain, Greece, Italy and France, the Atlantic coastal areas of France, Portugal and Spain as well as the south-western regions of Spain and lowlands in southern Italy. Potential distribution of the different subspecies / strains are contrasted but all are predicted to increase by 2050, which could threaten several of the most economically important wine-, olive- and fruit-producing regions of Europe, warranting the design of control strategies. Bioclimatic models also predict that the subspecies multiplex might represent a threat to most of Europe under current and future climate conditions. These results may serve as a basis for future design of a spatially informed European-scale integrated management strategy, including early detection surveys in plants and insect vectors, quarantine measures as well as agricultural practices.

ecology↗

bioRxiv2018

Using insects to detect, monitor and predict the distribution of Xylella fastidiosa: a case study in Corsica

We sampled ca 2500 specimens of Philaenus spumarius throughout Corsica without a priori on the presence of symptoms on plants. We screened 448 specimens for the presence of Xylella fastidiosa (Xf) using qPCR and a custom nested PCR. qPCR appeared versatile and under-estimated the prevalence of Xf. Nested PCR showed that Xf was present in all populations. Molecular results were validated by prediction on the distribution of Xf made from tests conducted on plants, which shows the pertinence of using vectors in risk assessment studies. Xf was detected in tenerals and adults. Thus, P. spumarius could acquire Xf from its host plant, mostly Cistus monspeliensis in Corsica, which may act as reservoir for the next season. This contrasts with other observations and suggests that management strategies may have to be adapted on a case-by-case basis. At least two genetic entities and several variants of Xf not yet identified on plants were present in the insects, which suggests ancient introductions of Xf and a probable underestimation of the current diversity of the strains present in Corsica. Interestingly 6% of the specimens carried two subspecies. Studies are wanted to better characterize the strains present in Corsica and know how the disease was introduced, spread and why no sign of a potential epidemic was detected earlier. This study shows that, when sensitive enough methods are implemented, insects can be used to predict and better assess the exact distribution of Xf. Insects are indeed easy to collect, Xf multiply only in their foregut and does not become circulative, which facilitates its detection.\n\nKey messageO_LIInsect vectors can be used to detect, monitor and predict the distribution of Xylella fastidiosa\nC_LIO_LIThe widely used qPCR approach is not sensitive enough to detect low bacterial load\nC_LIO_LIDifferent strains/subspecies of Xf are widely distributed in Corsica which suggests old introduction(s)\nC_LIO_LIStrategies to manage Xf may need to be set up on a case-by-case basis\nC_LIO_LIThere is an urgent need to take stock of the situation in Europe to avoid unnecessary economic pressure on certain geographical areas and agricultural sectors.\nC_LI

ecology↗