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Preprints, Working Papers, ...

SNP4OrphanSpecies: A bio-informatic pipeline to isolate robust molecular markers for phylogeny, phylogeographical and population genetic studies of genetically orphan species

Abstract : Since several decades, an increase of disease or pest emergence due to introduction or environmental changes has been recorded, causing serious threats to ecosystems. Many of these events are associated to species having poor or no genomic resources (ie. genetically orphan species). This lack of resource is a serious limitation to understand the origin of emergent populations and to predict future consequences on ecosystems. Analysing population genetic diversity is an efficient method to rapidly obtain this information, but required to have available polymorphic genetic markers. We developed a generic bio-informatic pipeline to rapidly isolate these markers in the goal to be applied in numerous different invasive taxa, with a special focus on fungal pathogen and insect pests. This pipeline is based on a quick de-novo assembly genome obtained from a shotgun whole genome sequencing, using paired-end Illumina technology, and the isolation of single copy genes conserved in the related species of the emergent organisms. Previous studies have shown that intronic regions of these conserved genes generally contain several single nucleotide polymorphisms at the species level. The pipeline was tested on several invasive or expanding pathogen and pest species in Europe (Armillaria ostoyae, Bursaphelenchus xylophilus, Diplodia sapinea, Erysiphe alphitoides, Thaumetopoea pityocampa). For each tested species, we successfully isolated several pools of one hundred short gene regions which can be amplified in multiplex. The bio-informatic pipeline is easy to install and to use (i.e. using the concept of container embedding all the computer programs needed for the processing). It also uses little computer resources (i.e. few hundreds of Go, depending of the genome size of the targeted species). We hope that this robust and rapid method of genetic marker isolation will be useful for numerous laboratories involved in the understanding of biological invasions, but with little available resources in bio-informatic.
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Preprints, Working Papers, ...
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https://hal.archives-ouvertes.fr/hal-03425003
Contributor : Cyril Dutech Connect in order to contact the contributor
Submitted on : Wednesday, November 10, 2021 - 4:49:04 PM
Last modification on : Tuesday, April 5, 2022 - 3:44:41 AM
Long-term archiving on: : Friday, February 11, 2022 - 7:31:22 PM

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Benjamin Penaud, Benoît Laurent, Marine Milhes, Camille Noûs, François Erhemann, et al.. SNP4OrphanSpecies: A bio-informatic pipeline to isolate robust molecular markers for phylogeny, phylogeographical and population genetic studies of genetically orphan species. 2021. ⟨hal-03425003⟩

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