RAD sequencing data from: A first inference of the phylogeography of the worldwide invader Xylosandrus compactus
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13 octobre 2021
- doi: 10.15454/ETBWEP
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Teddy Urvois et al., « RAD sequencing data from: A first inference of the phylogeography of the worldwide invader Xylosandrus compactus », Recherche Data Gouv, ID : 10.15454/ETBWEP
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We used the RADIS pipeline (Cruaud et al. 2016) to i) demultiplex individuals using process_radtags (Catchen et al. 2013), ii) homogenise read length and remove a few low-quality bases at the 3’-ends by trimming reads to 139 bp and iii) remove PCR duplicates using clone_filter (Catchen et al. 2013). We analysed the data using STACKS (Catchen et al. 2013; Rochette et al. 2019), and decided to focus exclusively on the results obtained with M = 6 and n = 4. Using the BWA-MEM algorithm (Li and Durbin 2009), we mapped the loci obtained on Ambrosiella xylebori's genome (Vanderpool et al. 2018) (accession number: ASM277803v1) to create a blacklist. Xylosandruscompactus.vcf contains Xylosandrus compactus' loci. It was obtained by using the blacklist to filter the fungus’ reads in STACKS’ populations module, and removing loci with a mean depth lower than 8 or shared by less than 70% of the specimens (r = 0.7). Ambrosiellaxylebori.vcf contains Ambrosiella xylebori's loci. It was obtained by using the loci mapping on Ambrosiella xylebori's genome as a whitelist in STACKS' populations module, , and removing loci with a mean depth lower than 4 or shared by less than 70% of the specimens (r = 0.3). popmap.txt corresponds to the popmap file. metadata-RADseq-Xylosandrus-compactus.csv contains all information on specimens used in the RAD sequencing experiment.