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Contrasting demographic histories revealed in two invasive populations of the dry rot fungus Serpula lacrymans

Citation

Skrede, Inger et al. (2021), Contrasting demographic histories revealed in two invasive populations of the dry rot fungus Serpula lacrymans, Dryad, Dataset, https://doi.org/10.5061/dryad.ttdz08kxx

Abstract

Globalization and international trade have impacted organisms around the world leading to a considerable number of species establishing in new geographic areas. Many organisms have taken advantage of human-made environments, including buildings. One such species is the dry rot fungus Serpula lacrymans, which is the most aggressive wood-decay fungus in indoor environments in temperate regions. Using population genomic analyses of 36 full genome sequenced isolates, we demonstrated that European and Japanese isolates are highly divergent and the populations split 3,000 - 19,000 generations ago, probably predating human influence. Approximately 250 generations ago, the European population went through a tight bottleneck, likely corresponding to the fungus colonization of the built environment in Europe. The demographic history of these populations, probably lead to low adaptive potential. Only two loci under selection were identified using a Fst outlier approach, and selective sweep analyses identified three loci with extended haplotype homozygosity. The selective sweep analyses found signals in genes possibly related to decay of various substrates in Japan and in genes involved DNA replication and protein modification in Europe. Our results suggest that the dry rot fungus independently established in indoor environments in Europe and Japan and that invasive species can potentially establish large populations in new habitats based on a few colonizing individuals.

Methods

Full genome sequences from Illumina from 36 isolates of Serpula lacrymans were analyzed in parallel using two pipelines: (1) the first pipeline trimmed the data using TrimGalore version 0.3.3, aligned using Bowtie2 (Langmead & Salzberg), and SAMtools (Li et al. 2009) to include only reads that mapped concordantly and only once to remove PCR duplicates. Variants were called for each alignment using HaplotypeCaller, combined into a common variant file with GenotypeGVCFs and further quality filtered with VariantFiltration (QD<2.0||FS>60.0||MQ<40.0||MQRankSum< -12.5||ReadPosRankSum< -8.0) in Genome Analysis Tool Kit (GATK) (McKenna et al. 2010; Van der Auwera et al. 2013). (2) The second pipeline trimmed the sequences using Trimmomatic (Bolger et al. 2014), mapped the reads using BWAmem (Li 2013), filtered using SAMtools, called variants using BCFtools call and filtered with BCFtools view. For both pipelines, the sequence data were mapped to the monokaryotic S. lacrymans isolate S7.3, version 2 (Eastwood et al. 2011). Repetitive regions of the S. lacrymans v. 2 genome were annotated using the REPET package v.2.5 (Flutre et al. 2011), following the procedure outlined in (Sipos et al. 2017). Regions annotated as transposable element-derived were filtered from the SNP data set using BEDtools (Quinlan & Hall 2010). A combined data set using only SNPs called by both pipelines resulted in 419,196 high quality SNPs for the 36 isolates included in this analysis.

Usage Notes

The file is in vcf format, and gziped.