Biology subjects

Santoni, S.

Publications and source records attributed to Santoni, S..

3 recordsLinked to original sources

bioRxiv2018

Pervasive hybridizations in the history of wheat relatives

Bread wheat and durum wheat derive from an intricate evolutionary history of three genomes, namely A, B and D, present in both extent diploid and polyploid species. Despite its importance for wheat research, no consensus on the phylogeny of the wheat clade has emerged so far, possibly because of hybridizations and gene flows that make phylogeny reconstruction challenging. Recently, it has been proposed that the D genome originated from an ancient hybridization event between the A and B genomes1. However, the study only relied on four diploid wheat relatives when 13 species are accessible. Using transcriptome data from all diploid species and a new methodological approach, we provide the first comprehensive phylogenomic analysis of this group. Our analysis reveals that most species belong to the D-genome lineage and descend from the previously detected hybridization event, but with a more complex scenario and with a different parent than previously thought. If we confirmed that one parent was the A genome, we found that the second was not the B genome but the ancestor of Aegilops mutica (T genome), an overlooked wild species. We also unravel evidence of other massive gene flow events that could explain long-standing controversies in the classification of wheat relatives. We anticipate that these results will strongly affect future wheat research by providing a robust evolutionary framework and refocusing interest on understudied species. The new method we proposed should also be pivotal for further methodological developments to reconstruct species relationship with multiple hybridizations.

evolutionary biology↗

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↗

bioRxiv2016

Evolutionary forces affecting synonymous variations in plant genomes

Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic datasets based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.

evolutionary biology↗